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 4 Summary of QTL detected by GEMMA for YW 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
6_39^a	0.305	20.81	103	LCORL	Intron	[18, 21, 30, 37,38,39, 55, 56]; Cattle, sheep; stature, SimAngus mid-test metabolic weight association, muscle and organ growth, feed intake and gain association, growth and carcass traits, skeletal growth and muscle mass
14_25^a	0.399	13.82	3	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_38^a	0.222	11.00	20	HERC6, PPM1K	Intergenic	[49, 58, 59]; Cattle; milk, fat, and protein yield, metabolic processes, feed efficiency association
6_42^a	0.344	11.00	11	KCNIP4	Intron	[39, 41, 42]; Chicken, cattle, human; growth and muscle mass trait association, potassium channel activity
6_37^a	0.330	10.12	8	SNCA, GPRIN3	Intergenic	[61,62,63,64]; Human, goat, equine; neurological regulation, milk and meat associations, tendon tissue association
5_60^a	0.042	9.62	2	LOC527216, LOC788998	Intergenic	NA
6_41^a	0.247	8.44	6	SLIT2	Intron	[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
6_36^a	0.227	8.23	20	CCSER1	Intron	[14, 60]; Cattle, human; body and carcass weight association, regulator of mitosis
14_26^a	0.357	6.94	12	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
7_93^a	0.286	6.23	14	LOC101905238, ARRDC3	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_40^a	0.109	6.21	11	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_27^a	0.348	6.04	6	NSMAF	Intron	[30, 68]; Cattle, human; Angus residual feed intake association, immune system response
2_05	0.497	5.15	3	IWS1	Intron	[69]; Human; chromatin modification, histone chaperone, maintenance of virus latency

^a Indicates QTL was detected in EMMAX analysis

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ISSN: 1471-2164

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