A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content

  • Hui Zhang1, 2,

    Affiliated with

    • Shou-Zhi Wang1, 2,

      Affiliated with

      • Zhi-Peng Wang1, 2,

        Affiliated with

        • Yang Da3,

          Affiliated with

          • Ning Wang1, 2,

            Affiliated with

            • Xiao-Xiang Hu4,

              Affiliated with

              • Yuan-Dan Zhang5,

                Affiliated with

                • Yu-Xiang Wang1, 2,

                  Affiliated with

                  • Li Leng1, 2,

                    Affiliated with

                    • Zhi-Quan Tang1, 2 and

                      Affiliated with

                      • Hui Li1, 2Email author

                        Affiliated with

                        BMC Genomics201213:704

                        DOI: 10.1186/1471-2164-13-704

                        Received: 3 September 2012

                        Accepted: 10 December 2012

                        Published: 15 December 2012

                        Abstract

                        Background

                        Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF.

                        Results

                        A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens.

                        Conclusions

                        We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

                        Keywords

                        Abdominal fat Selection signature Extended haplotype homozygosity (EHH)

                        Background

                        The linkage disequilibrium (LD) is important in livestock genetics for its key role in genomic selection [1] and detecting the causal mutations of economically important traits [26]. Based on the LD information, there are two main methods to detect genes underlying phenotypic variation, including one from phenotype to genome and another one from genome to phenotype. The first method is performed by targeting particular candidate genes or by quantitative trait loci (QTL) mapping and positional cloning of QTL. In the second method, patterns of LD in populations that are incompatible with the hypothesis of genetic neutrality are identified, and these patterns are selection signatures [7]. The aim of the second method is to identify artificial selections by statistically evaluating the genomic data [7].

                        Allele frequencies underlying selection are expected to change. A neutral mutation will take many generations until the mutated allele reaches a high or low population frequency. In this case, the LD between the mutation and its neighboring loci will be degraded because of the recombination in every generation [8]. The frequency of a novel mutation will increase or decrease more rapidly than the neutral mutation because it is underlying artificial selection, so that the surrounding conserved haplotype was long [9, 10]. This is the background of the extended haplotype homozygosity (EHH) statistic method used to detect selection signatures [11]. There are also many other methods to detect selective sweeps from DNA sequence data, including the Tajima’s D[12] and Fay and Wu’s H-test [13] for selected mutations, measuring large allele-frequency differences among populations by FST[14], and the integrated Haplotype Score (iHS) [15], which is an extension of the EHH statistic [11]. Among these methods, the EHH test is particularly useful [7, 11]. The EHH test is used to detect artificial selections according to the characteristics of haplotypes within a single population, and do not require the genotype of the ancestor [7]. Furthermore, the EHH test is less sensitive to ascertainment bias than other approaches, so it was designed to work with SNP rather than sequencing data [7, 16].

                        The broilers used in this study were selected for eleven generations and genomic regions controlling AF deposition are expected to exhibit signatures of selective sweep. The aim of this study was to identify the selection signatures underlying the artificial selection for AF in chicken and to investigate the genes important for AF deposition.

                        Methods

                        Ethics statement

                        All animal work was conducted according to the guidelines for the care and use of experimental animals established by the Ministry of Science and Technology of the People’s Republic of China (Approval number: 2006–398) and approved by the Laboratory Animal Management Committee of Northeast Agricultural University.

                        DNA samples and data preparation

                        Broilers used in this study were from two Northeast Agricultural University broiler lines divergently selected for AF content (NEAUHLF). The two lines have been selected since 1996 using AF percentage (%AFW or AFP) and plasma very low-density lipoprotein (VLDL) concentration as selection criteria [17]. The two lines were selected for 11 generations and the AFP changes over the 11 generations are shown in Figure 1. A total of 475 individuals from generation 11 of NEAUHLF were used in this study.
                        http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_Fig1_HTML.jpg
                        Figure 1

                        The separation of AFP over 11 generations between lean and fat lines.

                        Genotyping was carried out using the Illumina chicken 60K SNP chip containing a total of 57636 SNPs. Markers were filtered to exclude loci with unknown positions, monomorphic loci and loci with a minor allele frequency <0.05.

                        The haplotype and LD analysis

                        The fastPHASE [18] (http://​depts.​washington.​edu/​fphase/​download/​) was used to reconstruct the haplotypes for every chromosome using the default parameters. The reconstructed haplotypes were inserted into HAPLOVIEW v4.1 [19] to estimate LD statistics based on pairwise r2 and to construct the blocking pattern in the candidate regions of interest to enable selection signature analysis.

                        The EHH test

                        The “core region” was defined as the region in the genome characterized by the strong LD among SNPs involving a set of “core haplotypes” [7]. The Sweep v.1.1 (http://​www.​soft82.​com/​get/​download/​windows/​sweep/​) was used to identify the core regions [11]. The algorithm defined a pair of SNPs to be in strong LD if the upper 95% confidence bound of D’ is between 0.70 and 0.98 [20]. The program was set to select core regions with at least two SNPs. EHH was defined as the probability that two randomly chosen haplotypes carrying the candidate core haplotype were homozygous for the entire interval spanning the core region to a given locus [11]. The EHH test [11] was based on one of the core haplotype vs. other haplotypes in the same position. The “Relative Extended Haplotype Homozygosity” (REHH) statistic corrects EHH for the variability in recombination rates [7]. It was computed by EHHt / http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_IEq1_HTML.gif ; with http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_IEq2_HTML.gif defined as the decay of EHH on all other core haplotypes combined. The REHH value was used in the current study to determine the selection signatures. To determine the significance of REHH values, the haplotypes were ordered into 20 bins according to their frequencies [7]. The REHH values of each haplotype in a candidate region were compared with all equally frequent haplotypes and the P-values were obtained [11]. The significant selection signatures were defined as P<0.01.

                        Results

                        Markers and core haplotypes

                        A total of 43034 SNPs on 28 autosomes in chickens were included in the selection signature analysis (Table 1). These markers covered 950.68 Mb of the genome, with an average of 22.09 kb between adjacent markers.
                        Table 1

                        Summary of genome-wide marker and core region (CR) distribution in the lean and fat lines

                        Chr

                        SNP (n)1

                        Chr length (Mbp)

                        Mean distance (kb)

                        No. CR (n)

                        Mean CR length (kb)

                        Coverage CR length2 (kb)

                        Max CR length (kb)

                        CR length/Chr length3

                        CR SNPs4 (n)

                        Max CR SNPs (n)

                        CR SNPs/SNP5

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        Lean line

                        Fat line

                        1

                        7135

                        200.95

                        28.16

                        881

                        920

                        125.59

                        114.92

                        110644.43

                        105728.03

                        2288.64

                        2191.34

                        0.55

                        0.53

                        3906

                        3716

                        19

                        19

                        0.55

                        0.52

                        2

                        5290

                        154.46

                        29.20

                        639

                        695

                        149.62

                        108.91

                        95606.56

                        75690.16

                        2048.43

                        2042.96

                        0.62

                        0.49

                        3260

                        2628

                        19

                        19

                        0.62

                        0.50

                        3

                        4081

                        113.65

                        27.85

                        517

                        533

                        121.58

                        108.97

                        62855.68

                        58081.43

                        863.98

                        735.27

                        0.55

                        0.51

                        2301

                        2107

                        19

                        19

                        0.56

                        0.52

                        4

                        3313

                        94.16

                        28.42

                        411

                        428

                        137.96

                        108.07

                        56701.29

                        46255.07

                        2087.33

                        611.37

                        0.60

                        0.49

                        1992

                        1676

                        19

                        19

                        0.60

                        0.51

                        5

                        2170

                        62.23

                        28.68

                        260

                        266

                        138.85

                        105.39

                        36101.29

                        28034.75

                        823.62

                        816.35

                        0.58

                        0.45

                        1282

                        1032

                        19

                        19

                        0.59

                        0.48

                        6

                        1714

                        35.84

                        20.91

                        217

                        225

                        94.92

                        72.79

                        20598.01

                        16377.61

                        535.90

                        523.04

                        0.57

                        0.46

                        983

                        826

                        19

                        19

                        0.57

                        0.48

                        7

                        1769

                        38.17

                        21.58

                        197

                        232

                        111.15

                        86.03

                        21897.27

                        19958.16

                        621.29

                        2163.72

                        0.57

                        0.52

                        1048

                        899

                        19

                        19

                        0.59

                        0.51

                        8

                        1394

                        30.62

                        21.97

                        159

                        175

                        111.56

                        96.82

                        17738.07

                        16944.10

                        1914.74

                        1949.21

                        0.58

                        0.55

                        791

                        763

                        19

                        19

                        0.57

                        0.55

                        9

                        1168

                        24.02

                        20.57

                        159

                        153

                        78.35

                        75.92

                        12457.00

                        11615.65

                        413.33

                        403.29

                        0.52

                        0.48

                        613

                        557

                        19

                        17

                        0.52

                        0.48

                        10

                        1297

                        22.42

                        17.29

                        172

                        176

                        70.99

                        63.35

                        12210.13

                        11148.99

                        387.48

                        347.35

                        0.54

                        0.50

                        735

                        699

                        19

                        19

                        0.57

                        0.54

                        11

                        1196

                        21.87

                        18.29

                        128

                        156

                        124.72

                        83.15

                        15964.06

                        12971.74

                        886.96

                        1093.97

                        0.73

                        0.59

                        871

                        706

                        19

                        19

                        0.73

                        0.59

                        12

                        1324

                        20.45

                        15.44

                        169

                        184

                        71.34

                        51.16

                        12057.10

                        9412.86

                        352.96

                        369.92

                        0.59

                        0.46

                        809

                        633

                        19

                        19

                        0.61

                        0.48

                        13

                        1128

                        18.32

                        16.24

                        144

                        141

                        75.86

                        75.09

                        10924.53

                        10584.67

                        373.56

                        373.56

                        0.60

                        0.58

                        695

                        656

                        19

                        19

                        0.62

                        0.58

                        14

                        984

                        15.76

                        16.02

                        127

                        123

                        75.17

                        68.77

                        9546.48

                        8459.25

                        402.70

                        402.70

                        0.61

                        0.54

                        598

                        544

                        19

                        19

                        0.61

                        0.55

                        15

                        1010

                        12.93

                        12.80

                        123

                        133

                        58.20

                        50.28

                        7158.60

                        6687.12

                        407.05

                        407.05

                        0.55

                        0.52

                        567

                        541

                        19

                        19

                        0.56

                        0.54

                        16

                        12

                        0.17

                        13.87

                        3

                        1

                        41.85

                        67.25

                        125.54

                        67.25

                        64.36

                        67.25

                        0.74

                        0.40

                        9

                        3

                        4

                        3

                        0.75

                        0.25

                        17

                        844

                        10.61

                        12.57

                        112

                        108

                        59.07

                        43.89

                        6616.05

                        4740.59

                        242.32

                        236.98

                        0.62

                        0.45

                        523

                        394

                        19

                        19

                        0.62

                        0.47

                        18

                        845

                        10.89

                        12.88

                        112

                        121

                        48.74

                        45.96

                        5459.42

                        5561.31

                        317.30

                        317.30

                        0.50

                        0.51

                        431

                        431

                        12

                        19

                        0.51

                        0.51

                        19

                        804

                        9.89

                        12.31

                        117

                        110

                        36.01

                        48.41

                        4212.67

                        5325.00

                        406.27

                        371.08

                        0.43

                        0.54

                        353

                        421

                        14

                        19

                        0.44

                        0.52

                        20

                        1460

                        13.92

                        9.53

                        184

                        181

                        45.89

                        46.33

                        8442.96

                        8386.18

                        273.60

                        270.67

                        0.61

                        0.60

                        904

                        888

                        19

                        19

                        0.62

                        0.61

                        21

                        726

                        6.88

                        9.47

                        81

                        90

                        47.74

                        35.17

                        3867.13

                        3165.72

                        211.67

                        196.05

                        0.56

                        0.46

                        432

                        354

                        19

                        18

                        0.60

                        0.49

                        22

                        295

                        3.89

                        13.19

                        36

                        30

                        71.16

                        79.29

                        2561.59

                        2378.83

                        267.88

                        289.01

                        0.66

                        0.61

                        193

                        182

                        19

                        19

                        0.65

                        0.62

                        23

                        577

                        6.02

                        10.44

                        81

                        80

                        37.13

                        31.74

                        3007.73

                        2539.51

                        239.20

                        239.20

                        0.50

                        0.42

                        307

                        272

                        19

                        19

                        0.53

                        0.47

                        24

                        676

                        6.23

                        9.22

                        87

                        91

                        40.77

                        32.96

                        3546.91

                        2999.26

                        133.00

                        212.48

                        0.57

                        0.48

                        387

                        339

                        13

                        19

                        0.57

                        0.50

                        25

                        170

                        2.02

                        11.86

                        23

                        18

                        34.97

                        32.38

                        804.26

                        582.82

                        82.74

                        72.39

                        0.40

                        0.29

                        99

                        68

                        12

                        10

                        0.58

                        0.40

                        26

                        617

                        5.03

                        8.16

                        81

                        85

                        34.55

                        59.60

                        2798.60

                        2515.94

                        246.20

                        278.91

                        0.56

                        0.50

                        345

                        312

                        19

                        19

                        0.56

                        0.51

                        27

                        472

                        4.84

                        10.25

                        60

                        59

                        46.66

                        40.46

                        2799.62

                        2387.38

                        384.65

                        482.24

                        0.58

                        0.49

                        299

                        215

                        19

                        19

                        0.63

                        0.46

                        28

                        563

                        4.46

                        7.92

                        77

                        79

                        36.64

                        27.66

                        2820.93

                        2185.41

                        520.13

                        172.85

                        0.63

                        0.49

                        336

                        318

                        19

                        19

                        0.60

                        0.56

                        Total

                        43034

                        950.68

                        22.09

                        5357

                        5593

                        102.58

                        85.96

                        549523.91

                        480784.79

                        2288.64

                        2191.34

                        0.58

                        0.51

                        25069

                        22180

                        19

                        19

                        0.58

                        0.52

                        1The number of SNPs.

                        2Total length covered by core regions.

                        3The proportion of total core region lengths on chromosome length.

                        4Number of SNPs in core regions.

                        5The proportion of total number of SNPs in core regions on number of SNPs used.

                        For the SNPs analyzed in this study, the average minor allele frequency was 0.29 ± 0.13. A summary of genome-wide markers and core haplotype distribution in the data set is shown in Table 1. A total of 5357 and 5593 core regions spanning 549523.91 kb and 480784.79 kb of the genome, respectively, in the lean and fat lines were detected (Table 1). Mean core region length was estimated as 102.58±37.24 kb and 85.96±26.65 kb, with a maximum of 2288.64 kb and 2191.34 kb in the lean and fat lines, respectively (Table 1). Chromosome 1 was the largest chromosome in chickens, and it had the largest haplotypic structures in the genome, which covered 110644.43 kb and 105728.03 kb in the lean and fat lines, respectively. For each chromosome, the proportion of length covered by core regions vs. total length, as well as the number of SNPs forming core regions vs. the total number of SNPs, are shown in Table 1. The distribution of the size of core regions is shown in Figure 2. Overall, 25069 and 22180 SNPs in the lean and fat lines, respectively, participated in forming core regions, with a range of 2 to 19 SNPs per core.
                        http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_Fig2_HTML.jpg
                        Figure 2

                        Distribution of SNP numbers in the core regions (A) and the length of core regions (B) in lean and fat lines.

                        Whole genome selection signatures

                        For all 5357 and 5593 core regions in the lean and fat lines, respectively, a total of 44822 and 46775 EHH tests, with an average of 8.37 and 8.36 tests per core region, were calculated. To find outlying core haplotypes, we calculated REHH at 1 Mb distances both on the upstream and downstream sides. Figure 3 shows the distribution of REHH values vs. haplotype frequencies in the lean and fat lines, respectively. Corresponding P-values are indicated by different colored symbols. The –log10 of the P-values associated with REHH against the chromosomal position was plotted to visualize the chromosomal distribution of outlying core haplotypes with frequency <25% (Figure 4). The results indicated that these selection signals were not uniformly distributed across all chromosomes, with a substantial overrepresentation on chromosomes 1, 2, 3 and 4.
                        http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_Fig3_HTML.jpg
                        Figure 3

                        Distribution of REHH vs. core haplotype frequencies in the lean and fat lines. Core haplotypes with P-values lower than 0.05 and 0.01 are presented in blue and red, respectively.

                        http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_Fig4_HTML.jpg
                        Figure 4

                        Genome-wide map of P -values for core haplotypes with frequency >0.25 in lean and fat lines, respectively. Dashed lines display the threshold level of 0.01.

                        The genome-wide statistics of the selection signature test, including the number of tests and outlying core haplotypes for each chromosome, are presented in Table 2. Of 16677 and 18346 tests on core haplotypes with frequency ≥0.25, there were 51 and 57 tests with P<0.01 in the lean and fat lines, respectively. There were 153 and 251 tests with P<0.05 in the lean and fat lines, respectively.
                        Table 2

                        The number of tests on core haplotypes (CH) (both sides) with frequency≥0.25 and P -values of REHH test

                        Chr

                        Lean line

                        Fat line

                        Test on CH

                        P-value <0.05

                        P-value <0.01

                        Test on CH

                        P-value <0.05

                        P-value <0.01

                        1

                        2806

                        113

                        4

                        3063

                        138

                        12

                        2

                        2009

                        105

                        8

                        2271

                        104

                        3

                        3

                        1654

                        79

                        10

                        1705

                        74

                        8

                        4

                        1273

                        58

                        6

                        1371

                        66

                        5

                        5

                        844

                        34

                        3

                        883

                        36

                        4

                        6

                        699

                        25

                        2

                        757

                        31

                        2

                        7

                        638

                        29

                        2

                        770

                        31

                        5

                        8

                        464

                        16

                        1

                        574

                        33

                        2

                        9

                        516

                        20

                        1

                        564

                        19

                        1

                        10

                        540

                        23

                        2

                        582

                        27

                        1

                        11

                        397

                        15

                        1

                        534

                        20

                        2

                        12

                        503

                        14

                        0

                        619

                        20

                        1

                        13

                        447

                        19

                        3

                        474

                        22

                        1

                        14

                        379

                        14

                        0

                        418

                        16

                        1

                        15

                        329

                        12

                        1

                        420

                        18

                        2

                        17

                        350

                        16

                        0

                        348

                        14

                        2

                        18

                        354

                        12

                        2

                        432

                        13

                        2

                        19

                        334

                        12

                        1

                        338

                        13

                        0

                        20

                        561

                        28

                        3

                        566

                        19

                        0

                        21

                        255

                        6

                        0

                        304

                        11

                        0

                        22

                        105

                        5

                        1

                        85

                        2

                        0

                        23

                        258

                        11

                        0

                        245

                        12

                        1

                        24

                        287

                        9

                        0

                        308

                        12

                        2

                        25

                        46

                        1

                        0

                        36

                        1

                        0

                        26

                        231

                        11

                        0

                        253

                        4

                        0

                        27

                        181

                        8

                        0

                        184

                        7

                        0

                        28

                        217

                        5

                        0

                        242

                        14

                        0

                        Total

                        16,677

                        700

                        51

                        18,346

                        777

                        57

                        The conformity of the distribution of Tukey’s outliers was examined, with outlying core haplotypes defined at the threshold level of 0.01. Figure 5 displays box plots of the distribution of –log10 (P-values) within each bin of core haplotype frequency. The results indicated that the extreme outliers appear in the small haplotype frequencies bins.
                        http://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-704/MediaObjects/12864_2012_4655_Fig5_HTML.jpg
                        Figure 5

                        Box plot of the distribution of P -values in core haplotype frequency bins in the lean (left) and fat (right) lines. The dashed and continuous lines indicated the threshold P-values of 0.01 and 0.001, respectively.

                        Mapping selection signatures to genes

                        A summary of statistics for 51 and 57 positively selected core regions with P<0.01 of the REHH tests in the lean and fat lines, respectively, is presented in Table 3. Corresponding genes were identified by aligning the core positions with the chicken genome sequence (Table 3). The full genes names were from Ensembl online (http://​www.​ensembl.​org/​index.​html). A total of 66 and 46 genes in the core regions were detected in the lean and fat lines, respectively, including RB1 (retinoblastoma 1), BBS7 (Bardet-Biedl syndrome 7), MAOA (monoamine oxidase A), MAOB (monoamine oxidase B), EHBP1 (EH domain binding protein 1), LRP2BP (LRP2 binding protein), LRP1B (low-density lipoprotein receptor-related protein 1B), MYO7A (myosin VIIA), MYO9A (myosin IXA) and PRPSAP1 (phosphoribosyl pyrophosphate synthetase-associated protein 1). The haplotype analysis of these genes revealed that the haplotype frequencies were significantly different (P<0.01) between the two lines (Table 4).
                        Table 3

                        Statistics summary for core haplotypes with P <0.01 after the relative extended haplotype homozygosity (REHH) test

                        Lean line

                        Chr

                        Core position

                        Hap Freq

                        EHH

                        REHH1

                        REHH P-value1

                        Genes

                        1

                        39360501-39455853

                        0.46

                        0.98

                        3.99

                        0.0027

                        /

                        1

                        49926970-49964278

                        0.30

                        0.97

                        4.18

                        0.0021

                        C12orf69, WBP11, H2A4, H2B1, H4, H32, H2B8

                        1

                        173098805-173190831

                        0.37

                        0.99

                        4.25

                        0.0027

                        RB1, LPAR6, O57531, RCBTB2

                        1

                        198071099-198113519

                        0.55

                        0.80

                        3.03

                        0.0031

                        GDPD4, MYO7A

                        2

                        3631683-3739002

                        0.32

                        0.70

                        4.88

                        0.0004

                        Q5ZK34

                        2

                        19934135-20028093

                        0.30

                        0.97

                        3.88

                        0.0035

                        RSU1

                        2

                        26912546-26974875

                        0.28

                        1.00

                        3.65

                        0.0050

                        /

                        2

                        99818321-100051643

                        0.41

                        1.00

                        3.00

                        0.0047

                        GNAL, NRGN

                        2

                        131104507-131150076

                        0.48

                        0.98

                        3.24

                        0.0029

                        Q6V0P0, INTS8, F1P3N8

                        2

                        143016981-143059231

                        0.36

                        0.97

                        3.46

                        0.0034

                        /

                        2

                        145836411-145908271

                        0.30

                        1.00

                        3.72

                        0.0045

                        /

                        2

                        150489129-150540434

                        0.34

                        1.00

                        3.51

                        0.0044

                        /

                        3

                        3794973-3861882

                        0.30

                        0.79

                        4.72

                        0.0005

                        C20orf26, CRNKL1

                        3

                        3794973-3861882

                        0.30

                        0.82

                        3.85

                        0.0020

                        C20orf26, CRNKL1

                        3

                        10257926-10454969

                        0.55

                        0.49

                        2.49

                        0.0019

                        F1NRN6

                        3

                        14895290-14957057

                        0.44

                        0.72

                        3.16

                        0.0048

                        PLCB4

                        3

                        26957549-26996618

                        0.46

                        0.80

                        3.69

                        0.0009

                        /

                        3

                        26957549-26996618

                        0.46

                        0.83

                        3.47

                        0.0013

                        /

                        3

                        27303800-27335510

                        0.52

                        0.92

                        3.78

                        0.0009

                        SRBD1

                        3

                        27382993-27430067

                        0.54

                        0.84

                        3.77

                        0.0009

                        SRBD1

                        3

                        35555718-35610466

                        0.47

                        0.66

                        3.02

                        0.0031

                        E1C4G2

                        3

                        68936320-69076223

                        0.27

                        0.98

                        3.79

                        0.0041

                        RPF2, GTF3C6, Q5F484, CDK19

                        4

                        3522359-3551494

                        0.59

                        0.54

                        3.10

                        0.0023

                        MBNL3

                        4

                        9568761-9604871

                        0.55

                        1.00

                        2.95

                        0.0040

                        /

                        4

                        17765695-17819334

                        0.41

                        1.00

                        3.56

                        0.0037

                        F1NEF4, HMGB3

                        4

                        46149116-46190279

                        0.36

                        0.99

                        3.35

                        0.0044

                        EREG, Q645M5

                        4

                        55424480-55472209

                        0.66

                        0.9

                        2.60

                        0.0005

                        TRPC3, BBS7

                        4

                        83051637-83117974

                        0.39

                        0.87

                        3.72

                        0.0022

                        /

                        5

                        9740941-9828144

                        0.49

                        1.00

                        3.42

                        0.0014

                        IF4G2, CTR9, MRVI1

                        5

                        23825115-23872187

                        0.41

                        0.78

                        3.19

                        0.0030

                        O93582

                        5

                        42592517-42679460

                        0.30

                        1.00

                        3.70

                        0.0044

                        /

                        6

                        6546601-6626145

                        0.39

                        1.00

                        4.42

                        0.0011

                        /

                        6

                        35354459-35390346

                        0.38

                        0.99

                        3.72

                        0.0030

                        PTPRE

                        7

                        28869664-28906344

                        0.31

                        1.00

                        4.88

                        0.0015

                        MYLK

                        7

                        35674098-35715122

                        0.67

                        0.48

                        2.09

                        0.0027

                         

                        8

                        6107407-6172105

                        0.36

                        0.63

                        3.72

                        0.0020

                        IER5, KIAA1614, XPR1

                        9

                        16264832-16366749

                        0.45

                        0.97

                        4.04

                        0.0024

                        PSMD1, ARMC9, B3GNT7

                        10

                        5831963-5856349

                        0.59

                        0.97

                        1.83

                        0.0034

                        /

                        10

                        19717086-19745274

                        0.48

                        1.00

                        2.90

                        0.0011

                        CHSY1

                        11

                        17094961-17160195

                        0.30

                        0.63

                        3.35

                        0.0001

                        BCDO1, GAN

                        13

                        2628777-2664596

                        0.35

                        1.00

                        3.94

                        0.0048

                        Q5ZHQ9

                        13

                        2726706-2746894

                        0.39

                        0.79

                        4.06

                        0.0041

                        /

                        13

                        16758621-16783127

                        0.26

                        0.69

                        3.26

                        0.0050

                        FSTL4

                        15

                        7345639-7377799

                        0.26

                        0.54

                        2.38

                        0.0004

                        SEZ6L, ASPHD2, HPS4

                        18

                        9949736-10015444

                        0.39

                        1.00

                        2.34

                        0.0031

                        SPAG9

                        18

                        10117401-10135964

                        0.39

                        1.00

                        2.64

                        0.0013

                        F1NM51

                        19

                        8727596-8786448

                        0.60

                        0.55

                        1.77

                        0.0038

                        MSI1

                        20

                        9090808-9113453

                        0.29

                        0.95

                        6.18

                        0.0036

                        MYT1

                        20

                        9246245-9278998

                        0.32

                        0.80

                        5.39

                        0.0040

                        E1C8M0

                        20

                        9879361-9899719

                        0.27

                        0.96

                        6.40

                        0.0030

                        CSK21

                        22

                        2952274-3002268

                        0.29

                        0.29

                        3.93

                        0.0039

                        /

                        Fat line

                        1

                        51248496-51279543

                        0.33

                        0.81

                        4.45

                        0.0018

                        TCF20

                        1

                        58120009-58215364

                        0.55

                        0.99

                        3.15

                        0.0016

                        Q8UVD4

                        1

                        60171076-60254771

                        0.46

                        1.00

                        4.12

                        0.0049

                        /

                        1

                        67763862-67830818

                        0.26

                        0.96

                        4.06

                        0.0026

                        /

                        1

                        68213617-68257241

                        0.61

                        0.94

                        4.21

                        0.0016

                        SOX5

                        1

                        69634186-69686357

                        0.66

                        0.99

                        2.89

                        0.0003

                        /

                        1

                        101535615-101635667

                        0.29

                        1.00

                        5.24

                        0.0005

                        SAMSN1

                        1

                        114789487-114875623

                        0.29

                        0.99

                        3.66

                        0.0048

                        MAOB, MAOA

                        1

                        125909995-126011984

                        0.35

                        1.00

                        3.77

                        0.0036

                        E1BTB5

                        1

                        154665510-154752965

                        0.72

                        0.89

                        2.09

                        0.0034

                        /

                        1

                        181800227-181883545

                        0.33

                        0.99

                        4.00

                        0.0033

                        A1XGV6

                        1

                        181800227-181883545

                        0.33

                        1.00

                        3.81

                        0.0043

                        A1XGV6

                        2

                        76768841-76854523

                        0.31

                        1.00

                        4.30

                        0.0041

                        /

                        2

                        151203953-151251059

                        0.62

                        0.82

                        2.32

                        0.0033

                        TRAPPC9

                        2

                        153117092-153143883

                        0.71

                        0.77

                        1.68

                        0.0038

                        /

                        3

                        9177907-9222825

                        0.38

                        0.95

                        4.00

                        0.0024

                        EHBP1

                        3

                        9177907-9222825

                        0.38

                        0.90

                        3.66

                        0.0039

                        EHBP1

                        3

                        16143474-16194865

                        0.30

                        0.98

                        4.98

                        0.0016

                        /

                        3

                        24945839-24986772

                        0.61

                        0.70

                        2.15

                        0.0014

                        /

                        3

                        44265116-44311493

                        0.40

                        0.99

                        3.50

                        0.0050

                        UNC93A

                        3

                        69863850-69906698

                        0.34

                        1.00

                        4.29

                        0.0038

                        /

                        3

                        85874137-85931473

                        0.41

                        1.00

                        3.97

                        0.0031

                        LMBRD1

                        3

                        97227680-97337906

                        0.28

                        0.99

                        3.81

                        0.0042

                        /

                        4

                        11582141-11642538

                        0.27

                        0.96

                        4.53

                        0.0029

                        /

                        4

                        40653593-40713404

                        0.32

                        0.93

                        4.40

                        0.0010

                        C4orf20, LRP2BP, SNX25

                        4

                        55950677-55991394

                        0.28

                        0.99

                        4.55

                        0.0028

                        /

                        4

                        55950677-55991394

                        0.28

                        1.00

                        4.36

                        0.0036

                        /

                        4

                        86719441-86754976

                        0.57

                        0.75

                        2.88

                        0.0048

                        /

                        5

                        556571-628531

                        0.25

                        0.67

                        4.37

                        0.0026

                        F1NYX6, PLCB2, BUB1B, PAK6

                        5

                        40239840-40261525

                        0.29

                        0.97

                        4.48

                        0.0038

                        VSX2, F1N9P5

                        5

                        47240577-47282933

                        0.40

                        0.95

                        2.91

                        0.0029

                        RIN3, LGMN

                        5

                        59811459-59880511

                        0.39

                        0.66

                        3.36

                        0.0041

                        /

                        6

                        26756202-26793956

                        0.34

                        0.98

                        3.94

                        0.0049

                        /

                        6

                        29341938-29401207

                        0.32

                        0.97

                        5.50

                        0.0007

                        ABLIM1

                        7

                        30090927-30155133

                        0.30

                        0.88

                        3.77

                        0.0033

                        F1NF72

                        7

                        31374271-31418061

                        0.42

                        1.00

                        2.88

                        0.0049

                        LYPD1, NCKAP5

                        7

                        33795201-33904515

                        0.47

                        1.00

                        2.20

                        0.0025

                        LRP1B

                        7

                        36818722-36875768

                        0.26

                        0.99

                        3.95

                        0.0024

                        Q9DEH4

                        7

                        37031922-37124566

                        0.56

                        1.00

                        2.92

                        0.0047

                        STAM2, FMNL2

                        8

                        5597-492518

                        0.56

                        0.99

                        1.94

                        0.0036

                        F1NF53

                        8

                        2178258-2252969

                        0.47

                        0.92

                        4.20

                        0.0004

                        NEK7

                        9

                        2952291-3007034

                        0.41

                        0.71

                        3.85

                        0.0044

                        /

                        10

                        763998-831991

                        0.50

                        0.78

                        5.04

                        0.0004

                        MYO9A, F1P0M4

                        11

                        9804894-9826761

                        0.47

                        0.52

                        3.11

                        0.0014

                        /

                        11

                        16253047-16303345

                        0.58

                        0.35

                        1.80

                        0.0040

                        /

                        12

                        1157199-1170169

                        0.37

                        0.63

                        4.57

                        0.0030

                        /

                        13

                        1533552-1640154

                        0.40

                        1.00

                        3.41

                        0.0049

                        SRA1, APBB3, F1NH59

                        14

                        8048059-8173629

                        0.42

                        0.86

                        3.09

                        0.0015

                        /

                        15

                        8495796-8543001

                        0.29

                        1.00

                        4.86

                        0.0003

                        TBX6, CRKL, KLHL22

                        15

                        8495796-8543001

                        0.29

                        0.99

                        4.43

                        0.0006

                        TBX6, CRKL, KLHL22

                        17

                        3250605-3271593

                        0.27

                        0.97

                        3.91

                        0.0033

                        /

                        17

                        4062173-4087131

                        0.26

                        0.94

                        3.77

                        0.0040

                        C4PCF3

                        18

                        4433126-4445816

                        0.26

                        0.79

                        5.99

                        0.0037

                        PRPSAP1

                        18

                        8365846-8400245

                        0.47

                        0.80

                        3.53

                        0.0038

                        /

                        23

                        935267-970086

                        0.31

                        0.91

                        5.40

                        0.0040

                        EDN2

                        24

                        5613517-5633477

                        0.28

                        0.86

                        4.38

                        0.0024

                        ZW10, F1NC10

                        24

                        6145308-6158962

                        0.31

                        0.80

                        5.30

                        0.0047

                        /

                        1REHH and P-values are presented for upstream and downstream sides from each core haplotype, respectively.

                        Table 4

                        Haplotype frequencies in the lean and fat lines of the core regions including 10 important genes

                        Gene and core regions

                        Haplotype Number

                        Haploptypes

                        Haplotype frequency

                        P-value1

                        Lean line

                        Fat line

                        MAOB, MAOA

                        1

                        CAAGG

                        0.645

                        0.615

                        <0.001

                        Chr1: 114789487-114875623

                        2

                        AAAGA

                        0.197

                        0

                        3

                        CGGAG

                        0.158

                        0.269

                        4

                        CGAGA

                        0

                        0.077

                        5

                        AAAGG

                        0

                        0.038

                        RB1

                        1

                        GGAA

                        0.421

                        0.410

                        <0.001

                        Chr1: 173098805-173190831

                        2

                        GAGG

                        0.368

                        0.103

                        3

                        GAAA

                        0.211

                        0.192

                        4

                        AAGG

                        0

                        0.244

                        5

                        AGGA

                        0

                        0.038

                        6

                        GAGA

                        0

                        0.013

                        MYO7A

                        1

                        AGG

                        0.618

                        0.090

                        <0.001

                        Chr1: 198071099-198113519

                        2

                        GAA

                        0.316

                        0.207

                        3

                        GGA

                        0.066

                        0.652

                        4

                        GAG

                        0

                        0.037

                        5

                        GGG

                        0

                        0.014

                        EHBP1

                        1

                        GGG

                        0.855

                        0.090

                        <0.001

                        Chr3: 9177907-9222825

                        2

                        GAG

                        0.132

                        0.359

                        3

                        AGG

                        0.013

                        0.128

                        4

                        GGA

                        0

                        0.423

                        LRP2BP

                        1

                        GGGG

                        0.443

                        0.487

                        <0.001

                        Chr4: 40653593-40713404

                        2

                        AAAA

                        0.338

                        0.211

                        3

                        GGAA

                        0.176

                        0

                        4

                        AAGG

                        0.044

                        0.303

                        BBS7

                        1

                        AGGC

                        0.605

                        0.282

                        <0.001

                        Chr4: 55424480-55472209

                        2

                        GAAA

                        0.368

                        0.301

                        3

                        AAAA

                        0.026

                        0

                        4

                        AGAC

                        0

                        0.198

                        5

                        AGAA

                        0

                        0.161

                        6

                        GAAC

                        0

                        0.058

                        LRP1B

                        1

                        AGAGAC

                        0.361

                        0.013

                        <0.001

                        Chr7: 33795201-33904515

                        2

                        GGAGGA

                        0.197

                         

                        3

                        AGAAGA

                        0.105

                        0.154

                        4

                        GGGGGA

                        0.066

                        0.449

                        5

                        AGAAGC

                        0.057

                        0.346

                        6

                        GAGGGA

                        0.055

                        0.038

                        7

                        GAGAGA

                        0.050

                        0

                        8

                        GGAAGA

                        0.049

                        0

                        9

                        GAGGAA

                        0.026

                        0

                        10

                        GGAGAA

                        0.018

                        0

                        11

                        AGAAAC

                        0.016

                        0

                        MYO9A

                        1

                        GGGAA

                        0.355

                        0.051

                        <0.001

                        Chr10: 763998-831991

                        2

                        AAGAA

                        0.276

                        0.358

                        3

                        AAGAG

                        0.237

                        0

                        4

                        GGGGA

                        0.118

                        0.013

                        5

                        AGGAA

                        0.013

                        0.065

                        6

                        AGAAA

                        0

                        0.500

                        7

                        AAAAA

                        0

                        0.013

                        PRPSAP1

                        1

                        AGA

                        0.816

                        0.615

                        <0.001

                        Chr18: 4433126-4445816

                            
                         

                        2

                        GGG

                        0.118

                        0.026

                         

                        3

                        AAG

                        0.066

                        0.090

                         

                        4

                        AGG

                        0

                        0.269

                        1 P-values of Fisher’s Exact Test for difference analysis of haplotype frequencies between lean and fat lines.

                        Mapping selection signatures to QTLs

                        The chicken QTL database available online (http://​www.​animalgenome.​org/​cgi-bin/​QTLdb/​GG/​index) was explored to identify any overlapping of the core regions with significant REHH P-values (P<0.01) and published QTLs in chickens. The approximate positions of the overlapping QTLs for each core region are listed in Table 5. There were many overlaps between the core regions with significant REHH P-values (P<0.01) and published QTLs for AF content in chickens.
                        Table 5

                        Reported QTL near the core regions with P <0.01 in the lean and fat lines

                        Lean line

                        Chr

                        Core region (bp)

                        Trait

                        QTL position (bp)

                        F-ratio

                        P-value

                        Reference

                        1

                        39360501-39455853

                        AFP

                        1937738-52700434

                        1.474

                        Suggestive

                        [21]

                        1

                        49926970-49964278

                        AFP

                        25998723-65961966

                        1.732

                        Suggestive

                        [21]

                        AFW

                        25998723-65961966

                        1.882

                        Suggestive

                        [21]

                        AFW

                        48175152- 51977642

                        8.14

                        Significant

                        [22]

                        1

                        173098805-173190831

                        AFW

                        158352237- 182910620

                        3.18

                        Significant

                        [23]

                        AFP

                        171224834- 174526878

                        20.34

                        Significant

                        [23]

                        2

                        3631683-3739002

                        AFW

                        3097660- 4097660

                        3.38

                        Suggestive

                        [24]

                        3

                        3794973-3861882

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        3

                        10257926-10454969

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFW

                        6841859-13986734

                        8.16

                        Significant

                        [22]

                        AFP

                        6841859- 57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859- 44850897

                        7.4

                        Significant

                        [25]

                        3

                        14895290-14957057

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFW

                        6841859-13986734

                        8.16

                        Significant

                        [22]

                        AFP

                        6841859- 57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859- 44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        13986734-25508863

                        \

                        Suggestive

                        [26]

                        3

                        26957549-26996618

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859- 57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859- 44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        24160710-51592221

                        \

                        Suggestive

                        [27]

                        AFW

                        25508863- 35512024

                        \

                        Suggestive

                        [26]

                        3

                        27303800-27335510

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859- 57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859- 44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        24160710-51592221

                        \

                        Suggestive

                        [27]

                        AFW

                        25508863- 35512024

                        \

                        Suggestive

                        [26]

                        3

                        27382993-27430067

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859- 57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859- 44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        24160710-51592221

                        \

                        Suggestive

                        [27]

                        AFW

                        25508863- 35512024

                        \

                        Suggestive

                        [26]

                        3

                        35555718-35610466

                        AFP

                        800029-110574691

                        1.364

                        Suggestive

                        [21]

                        AFW

                        35512024-40755790

                        18.5

                        Significant

                        [28]

                        AFP

                        35512024-40755790

                        13.1

                        Significant

                        [28]

                        4

                        17765695-17819334

                        AFW

                        17425871-18425871

                        \

                        Significant

                        [29]

                        4

                        46149116-46190279

                        AFW

                        42005559- 51609571

                        2.26

                        Suggestive

                        [30]

                        4

                        55424480-55472209

                        AFP

                        51266614- 88408499

                        16.0

                        Significant

                        [25]

                        4

                        83051637-83117974

                        AFP

                        51266614- 88408499

                        16.0

                        Significant

                        [25]

                        AFW

                        80258156-88408499

                        6.9

                        Significant

                        [25]

                        AFW

                        81539616- 84618310

                        2.04

                        Suggestive

                        [30]

                        5

                        23825115-23872187

                        AFW

                        18412554-42717839

                        21.8

                        Significant

                        [25]

                        AFP

                        18723157- 43339045

                        19.4

                        Significant

                        [25]

                        AFW

                        19782191- 30162990

                        \

                        Suggestive

                        [26]

                        AFW

                        19782191- 30162990

                        7.04

                        Significant

                        [31]

                        5

                        42592517-42679460

                        AFW

                        18412554-42717839

                        21.8

                        Significant

                        [25]

                        AFP

                        18723157- 43339045

                        19.4

                        Significant

                        [25]

                        AFW

                        37226264-53779276

                        6.74

                        Significant

                        [31]

                        6

                        35354459-35390346

                        AFP

                        29647151- 37399694

                        6.9

                        Significant

                        [25]

                        7

                        28869664-28906344

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        AFW

                        28166221- 29166221

                        9.78

                        Significant

                        [32]

                        AFW

                        28166221- 29166221

                        \

                        Significant

                        [33]

                        7

                        35674098-35715122

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        9

                        16264832-16366749

                        AFW

                        13658592-23770679

                        5.03

                        Suggestive

                        [22]

                        AFW

                        15457880-16457880

                        7.0

                        Suggestive

                        [34]

                        10

                        19717086-19745274

                        AFP

                        16519830- 20778533

                        9.9

                        Significant

                        [28]

                        13

                        16758621-16783127

                        AFW

                        16327806- 18173123

                        2.10

                        Suggestive

                        [30]

                        15

                        7345639-7377799

                        AFW

                        1917251- 10769106

                        10.2

                        Significant

                        [25]

                        AFP

                        2388961-10769106

                        12.8

                        Significant

                        [25]

                        AFW

                        2798507-10769106

                        8.13

                        Significant

                        [22]

                        AFW

                        2798507-10769106

                        5.67

                        Suggestive

                        [22]

                        AFW

                        3717446-7928397

                        2.21

                        Suggestive

                        [30]

                        AFP

                        3717446-7928397

                        2.22

                        Suggestive

                        [30]

                        Fat line

                        1

                        51248496-51279543

                        AFP

                        1937738-52700434

                        1.474

                        Suggestive

                        [21]

                        AFW

                        48175152- 51977642

                        8.14

                        Significant

                        [22]

                        AFP

                        25998723- 65961966

                        1.732

                        Suggestive

                        [21]

                        AFW

                        25998723- 65961966

                        1.882

                        Suggestive

                        [21]

                        1

                        58120009-58215364

                        AFP

                        25998723- 65961966

                        1.732

                        Suggestive

                        [21]

                        AFW

                        25998723- 65961966

                        1.882

                        Suggestive

                        [21]

                        AFW

                        55261695-67128747

                        12.18

                        Significant

                        [35]

                        1

                        60171076-60254771

                        AFP

                        25998723- 65961966

                        1.732

                        Suggestive

                        [21]

                        AFW

                        25998723- 65961966

                        1.882

                        Suggestive

                        [21]

                        AFW

                        55261695-67128747

                        12.18

                        Significant

                        [35]

                        1

                        67763862-67830818

                        AFW

                        67327367-68327367

                        \

                        Significant

                        [33]

                        1

                        68213617-68257241

                        AFW

                        67327367-68327367

                        \

                        Significant

                        [33]

                        1

                        101535615-101635667

                        AFW

                        89938943-167462479

                        9.4

                        Significant

                        [36]

                        AFW

                        94157976- 102460326

                        6.11

                        Suggestive

                        [35]

                        1

                        114789487-114875623

                        AFW

                        113344161- 132660888

                        7.90

                        Suggestive

                        [35]

                        AFW

                        114143603- 115143603

                        7.1

                        Significant

                        [36]

                        1

                        125909995-126011984

                        AFW

                        113344161- 132660888

                        7.90

                        Suggestive

                        [35]

                        1

                        181800227-181883545

                        AFW

                        158352237-182910620

                        3.18

                        Significant

                        [23]

                        3

                        9177907-9222825

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        AFW

                        6841859- 13986734

                        8.16

                        Significant

                        [22]

                        AFW

                        6841859- 13986734

                        5.8

                        Suggestive

                        [22]

                        AFP

                        6841859-57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859-44850897

                        7.4

                        Significant

                        [25]

                        3

                        16143474-16194865

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859-57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859-44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        13986734-25508863

                        \

                        Suggestive

                        [26]

                        3

                        24945839-24986772

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859-57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859-44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        13986734-25508863

                        \

                        Suggestive

                        [26]

                        AFW

                        24160710-51592221

                        \

                        Suggestive

                        [27]

                        3

                        44265116-44311493

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        AFP

                        6841859-57396057

                        7.9

                        Significant

                        [25]

                        AFW

                        6841859-44850897

                        7.4

                        Significant

                        [25]

                        AFW

                        24160710-51592221

                        \

                        Suggestive

                        [27]

                        AFW

                        40755790-45203763

                        7.5

                        Significant

                        [28]

                        AFP

                        40755790-45203763

                        10.8

                        Significant

                        [28]

                        3

                        69863850-69906698

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        3

                        85874137-85931473

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        3

                        97227680-97337906

                        AFP

                        800029- 110574691

                        1.364

                        Suggestive

                        [21]

                        4

                        40653593-40713404

                        AFP

                        40473174-41473174

                        \

                        Significant

                        [32]

                        4

                        55950677-55991394

                        AFP

                        51266614- 88408499

                        16.0

                        Significant

                        [25]

                        4

                        86719441-86754976

                        AFP

                        51266614- 88408499

                        16.0

                        Significant

                        [25]

                        AFW

                        80258156-88408499

                        6.9

                        Significant

                        [25]

                        5

                        40239840-40261525

                        AFW

                        18412554- 42717839

                        21.8

                        Significant

                        [25]

                        AFP

                        18723157- 43339045

                        19.4

                        Significant

                        [25]

                        AFW

                        37226264- 53779276

                        6.74

                        Significant

                        [31]

                        AFW

                        40158255- 41158255

                        \

                        Significant

                        [37]

                        AFW

                        40158255- 41158255

                        \

                        Significant

                        [38]

                        AFP

                        40158255- 41158255

                        \

                        Significant

                        [38]

                        5

                        47240577-47282933

                        AFW

                        37226264- 53779276

                        6.74

                        Significant

                        [31]

                        5

                        59811459-59880511

                        AFW

                        51748760-60234891

                        \

                        Significant

                        [26]

                        AFW

                        53867807-62098509

                        11.87

                        Significant

                        [31]

                        AFW

                        53867807-62098509

                        6.82

                        Significant

                        [31]

                        7

                        30090927-30155133

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        7

                        31374271-31418061

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        7

                        33795201-33904515

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        AFW

                        32440861-34526547

                        2.08

                        Suggestive

                        [30]

                        7

                        36818722-36875768

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        7

                        37031922-37124566

                        AFW

                        25306930- 38010856

                        \

                        Suggestive

                        [27]

                        9

                        2952291-3007034

                        AFW

                        2798942-3798942

                        \

                        Significant

                        [32]

                        AFP

                        2972071-3972071

                        \

                        Significant

                        [32]

                        11

                        9804894-9826761

                        AFW

                        6272742- 12810705

                        2.15

                        Suggestive

                        [30]

                        12

                        1157199-1170169

                        AFP

                        734209- 12275026

                        5.22

                        Significant

                        [28]

                        AFP

                        734209- 12275026

                        4.51

                        Significant

                        [28]

                        AFP

                        813709-1813709

                        \

                        Significant

                        [32]

                        15

                        8495796-8543001

                        AFW

                        1917251- 10769106

                        10.2

                        Significant

                        [25]

                        AFP

                        2388961- 10769106

                        12.8

                        Significant

                        [25]

                        AFW

                        2798507- 10769106

                        8.13

                        Significant

                        [22]

                        AFW

                        2798507- 10769106

                        5.67

                        Suggestive

                        [22]

                        23

                        935267-970086

                        AFW

                        74802-1074802

                        \

                        Significant

                        [39]

                        Discussion

                        Selective sweep is used to detect genomic regions with reduced variation in allele frequency in any population experiencing divergent selection for specific traits. Here, we determined the feasibility of the selective sweep approach for finding genes important for AF deposition in chickens. The long-range haplotype test was employed, which detects selection signature by measuring the characteristics of haplotypes within the lean and fat lines divergently selected for AF content. There were 5357 and 5593 core regions in the lean and fat lines, respectively. When comparing the average marker spacing with mean core length and number of SNPs forming cores, we revealed that core regions are more likely to appear in regions with higher marker density.

                        The selection signatures on the whole genome were calculated, and a subset of putative core regions with significant REHH P-values (P<0.01) was identified. The genes in these core regions were detected and 10 genes, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were important for fatness. Among these 10 important genes, seven genes, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP and LRP1B, were all in the QTL regions reported previously for AF in chickens (Table 5). Although the other three genes, including MYO7A, MYO9A and PRPSAP1, were not in the QTL regions, these genes were also important for the AF deposition.

                        The known functions of these 10 genes were analyzed and the results indicated that they were likely to be linked with fatness. The RB1 gene regulates the C/EBP-DNA-binding activity during 3T3-L1 adipogenesis and plays a key role in adipocyte differentiation [40, 41].

                        The BBS7 gene is a member of the Bardet-Biedl syndrome (BBS) family. BBS is a pleiotropic genetic disorder characterized by obesity, photoreceptor degeneration, polydactyly, hypogenitalism, renal abnormalities, and developmental delay [42]. BBS is recognized to be a genetically heterogeneous autosomal recessive disorder mapped to eight loci [42]. Positional cloning and candidate genes identified six BBS genes, including BBS1, BBS2, BBS4, BBS6, BBS7, and BBS8[42]. These BBS genes may be important for obesity.

                        The MAOA and MAOB are two enzymes important for dopamine production. The dopamine levels influence the risk of obesity and MAOA and MOAB may be implicated in human obesity [43].

                        The EHBP1 gene is required for insulin-stimulated GLUT4 movements [44]. Insulin stimulates glucose transport in adipose tissues by recruiting intracellular membrane vesicles containing the glucose transporter GLUT4 to the plasma membrane [44]. The mechanisms involved in the biogenesis of these vesicles and their translocation to the cell surface were studied and the results indicated that EHD1 and EHBP1 are required for perinuclear localization of GLUT4, and the loss of EHBP1 disrupts insulin-regulated GLUT4 recycling in cultured adipocytes [44]. This indicates that the EHBP1 gene may be important in adipocyte differentiation.

                        The LRP2BP and LRP1B genes are two members of the low-density lipoprotein receptor family that participates in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins [45].

                        The MYO7A and MYO9A are two myosin genes. A spontaneous mutant mouse line, Myo7ash1-6J, was used to study the function of the MYO7A gene, and the result indicated that the mutant male homozygous mice displayed decreased body weight and body fat [46]. The MYO9A gene was in the BBS4 region of chromosome 15q22-q23 [47], which might be important for obesity.

                        The PRPSAP1 gene is named as phosphoribosyl pyrophosphate synthetase-associated protein 1. The results of differentially expressed genes associated with insulin resistance indicate that PRPSAP1 gene is associated with percentage of body fat [48].

                        The associations of these 10 genes with obesity or lipid metabolism were mainly in humans and mice. Because of the high conservation of these genes between humans, mice and chickens, the 10 genes might also be important for AF deposition in chickens.

                        Conclusions

                        Our results provide a genome-wide map of selection signatures in two chicken lines divergently selected for AF content. There were 51 and 57 core regions showing significant P-values (P<0.01) of selection signatures in the lean and fat lines, respectively. In these core regions there were a number of important genes, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1. These genes are important for AF deposition in chickens.

                        Abbreviations

                        AF: 

                        Abdominal fat

                        AFP: 

                        Abdominal fat percentage

                        AFW: 

                        Abdominal fat weight

                        BBS: 

                        Bardet-Biedl syndrome

                        CH: 

                        Core haplotypes

                        CR: 

                        Core region

                        EHH: 

                        Extended haplotype homozygosity

                        IHS: 

                        Integrated Haplotype Score

                        LD: 

                        Linkage disequilibrium

                        NEAU: 

                        Northeast Agricultural University

                        NEAUHLF: 

                        Northeast Agricultural University broiler lines divergently selected for abdominal fat content

                        NRC: 

                        National Research Council

                        QTL: 

                        Quantitative trait loci

                        REHH: 

                        Relative Extended Haplotype Homozygosity

                        SNP: 

                        Single nucleotide polymorphism

                        VLDL: 

                        Very low-density lipoprotein.

                        Declarations

                        Acknowledgements

                        The authors would like to acknowledge the members of the Poultry Breeding Group of the College of Animal Science and Technology in Northeast Agricultural University for managing the birds and collecting data. This research was supported by the China Agriculture Research System (No. CARS-42), National 863 Project of China (No. 2011AA100301), National 973 Project of China (No. 2009CB941604) and Program for Innovation Research Team in University of Heilongjiang Province (No. 2010td02).

                        Authors’ Affiliations

                        (1)
                        Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture
                        (2)
                        College of Animal Science and Technology, Northeast Agricultural University
                        (3)
                        Department of Animal Science, University of Minnesota
                        (4)
                        College of Biological Science, China Agricultural University
                        (5)
                        Animal Genetics and Breeding Unit, University of New England

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                        Copyright

                        © Zhang et al.; licensee BioMed Central Ltd. 2012

                        This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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