Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

Table 4 Single nucleotide polymorphisms (SNPs) with log R ratio (LRR) values associated with carcass weight, carcass fat, and carcass conformation in Charolais (CH), Holstein-Friesians (HF), and Limousins (LM)

Chromosome	Position	Breed	Associated trait	Marginal R^{2 a}	Flanking genes
2	6.92 Mb	CH	Fat	0.0175	MSTN
2	8.01 Mb	CH	Fat	0.0136	MSTN
6	55.11 Mb	CH	Fat	0.0131	ARAP2
8	4.31 Mb	CH	Fat	0.0142	GALNLT6
13	27.45 Mb	CH	Fat	0.0240	OPTN, MCM10
2	90.47 Mb	HF	Weight	0.0287	FZD7, CDK15
21	18.53 Mb	HF	Weight	0.0194	NTRK3
26	27.13 Mb	HF	Weight	0.0287	SORCS1
1	24.98 Mb	HF	Conformation	0.0169	ROBO2, 5S rRNA, U2
7	5.59 Mb	HF	Conformation	0.0179	PGLS, NIBAN3
11	24.55 Mb	HF	Conformation	0.0233	ELM4
11	74.95 Mb	HF	Conformation	0.0176	FAM228A, FAM228B
13	68.22 Mb	HF	Conformation	0.0176	FAM83D
13	77.51 Mb	HF	Conformation	0.0157	KCNB1
18	4.24 Mb	HF	Conformation	0.0169	MON1B
19	17.08 Mb	HF	Conformation	0.0185	ASIC2
25	21.09 Mb	HF	Conformation	0.0155	COG7
26	42.62 Mb	HF	Conformation	0.0158	SPADH1, U6
13	55.30 Mb	HF	Fat	0.0175	CDH4
19	52.38 Mb	HF	Fat	0.0168	SLC26A11
22	58.14 Mb	HF	Fat	0.0146	WNT7A, 5S rRNA
6	44.26 Mb	LM	Weight	0.0177	5S rRNA, U6, DHX15
6	47.74 Mb	LM	Weight	0.0174	5S rRNA
11	30.81 Mb	LM	Weight	0.0167	PPP1R21
2	33.44 Mb	LM	Fat	0.0242	7SK RNA
5	20.16 Mb	LM	Fat	0.0124	5S rRNA
5	84.42 Mb	LM	Fat	0.0142	LMNTD1
7	64.07 Mb	LM	Fat	0.0131	7SK RNA
10	90.67 Mb	LM	Fat	0.0172	NRXN3, 5S rRNA
20	30.72 Mb	LM	Fat	0.0127	U6
20	33.02 Mb	LM	Fat	0.0143	PLCXD3
20	40.93 Mb	LM	Fat	0.0221	NPR3
21	37.67 Mb	LM	Fat	0.0123	U6
27	3.61 Mb	LM	Fat	0.0226	CSMD1, U6

^aThe marginal R² is the proportion of the variance that was attributable to the fixed effect in a linear mixed model, which for this model is the SNP LRR

ISSN: 1471-2164