Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

Smith, Johanna L.; Wilson, Miranda L.; Nilson, Sara M.; Rowan, Troy N.; Oldeschulte, David L.; Schnabel, Robert D.; Decker, Jared E.; Seabury, Christopher M.

doi:10.1186/s12864-019-6231-y

BMC Genomics

Table 2 Summary of QTL detected by GEMMA for BW in U.S. Gelbvieh beef cattle

From: Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

Chr_Mb	MAF	-log₁₀ P-value	Supporting SNPs	Positional Candidate Genes	Lead SNP Location	Scientific Precedence [reference]; organism; trait
14_25^a	0.398	29.56	41	PLAG1	3’UTR	[2, 14, 18, 21, 30, 32,33,34]; Cattle; SimAngus mid-test metabolic weight association, carcass weight, stature, body weight and milk
6_39^a	0.293	23.71	140	NCAPG	Exon^b	[18, 21, 30, 35,36,37,38,39]; Cattle, chicken; stature, calving ease and growth traits association, SimAngus mid-test metabolic weight association, fetal growth, carcass trait association, average daily gain and daily feed intake, muscle mass
14_26^a	0.396	14.63	33	IMPAD1, FAM110B	Intergenic	[30, 32, 34, 40]; Cattle; SimAngus mid-test metabolic weight association, carcass weight association, stature and body weight association, bone and cartilage system
6_42^a	0.186	9.66	9	KCNIP4	Intron	[39, 41, 42]; Chicken, cattle, human; growth and muscle mass trait association, potassium channel activity
14_24^a	0.244	8.93	35	XKR4	Intron	[2, 30, 43, 44]; Cattle; birth weight association, SimAngus mid-test metabolic weight association, growth trait association, feed intake and growth traits
20_05^a	0.193	8.65	21	LOC104975192, STC2	Intergenic	[30, 45]; Cattle, mouse; mid-test metabolic weight in Hereford and SimAngus, developing and adult tissue maintenance, body size, related to post-natal growth
7_93^a	0.283	8.00	30	ARRDC3, LOC104972872	Intergenic	[14, 22, 30, 46]; Cattle; body and carcass weight association, calving ease, average daily gain in Hereford, growth and muscularity, birth weight, weaning weight, yearling weight, and ribeye area in Angus
6_38^a	0.053	7.90	23	IBSP, LOC104972726	Intergenic	[13, 47,48,49]; Cattle, mouse, human; yearling weight association, bone formation and remodeling, cellular proliferation, milk fat and protein association
6_41^a	0.407	7.25	5	LOC782905, SLIT2	Intergenic	[39, 49,50,51,52,53]; Cattle, chicken, human; milk fat and protein association, organ and muscle weight, development of central nervous system, tumor suppressor activity
14_23^a	0.467	6.19	3	ST18	Intron	[54]; Human; regulation of apoptosis and inflammatory response
6_34^a	0.039	5.98	8	LOC104972717, LOC526089	Intergenic	NA
6_40^a	0.304	5.25	2	LCORL, LOC782905	Intergenic	[18, 21, 37,38,39, 50, 55, 56]; Cattle, sheep; stature, muscle and organ growth, feed intake and gain association, growth and carcass traits, skeletal growth and muscle mass

^a Indicates QTL was detected in EMMAX analysis
^b Indicates a predicted nonsynonymous mutation Ile➔Met, exon 9

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ISSN: 1471-2164

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