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Table 3 Statistics summary for core haplotypes with P <0.01 after the relative extended haplotype homozygosity (REHH) test

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

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