Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

BMC Genomics

Table 7 Genome-wide significant SNPs for mammary system traits

Trait	SNP name	Chr.	Position (bp)	Nearest gene	Distance (bp)	Heritability/-log₁₀(P)^b	Threshold
Rear udder	ARS-BFGL-NGS-111920	14	44029634	LOC100337279	within	0.01330	0.00891
Rear udder	Hapmap50827-BTA-94026	24	2166631	LOC100336384	39,890	0.01130	0.00891
Udder texture	ARS-BFGL-NGS-104839	3	88712390	LOC100295233	within	0.00873	0.00872
	BTA-41935-no-rs	17	72284836	DRG1	within	0.01670	0.00872
	BTB-01236227	20	15824409	HTR1A	264,560	0.00941	0.00872
Median suspensory	BTB-00089278	2	26942975	LRP2	within	0.01080	0.00874
	BTB-01007411	4	37145925	SEMA3E	960	0.00995	0.00874
	ARS-BFGL-NGS-35982	5	5693439	NAP1L1	81,318	0.00941	0.00874
	ARS-BFGL-NGS-29118	13	8497369	MACROD2	within	0.01490	0.00874
	ARS-BFGL-NGS-52278^a	12	89182471	RAB20	within	7.85^b	6.02^c
Fore attachment	ARS-BFGL-NGS-114960	29	36024434	NTM	448,744	0.01050	0.00965
Fore teat Placement	ARS-BFGL-NGS-113245	19	59068269	SLC39A11	within	0.01290	0.00892
Teat length	BTB-01255458	10	99270875	PDIA6	80,295	0.01030	0.00911
Rear attach height	ARS-BFGL-NGS-20052	2	107616903	CDK5R2	3,609	0.00988	0.00904
Rear attach height	Hapmap43038-BTA-76203	6	50316616	LOC100298058	12,846	0.00997	0.00904
Rear attach Width	BTB-01478363	20	17370437	BAG1	210,690	0.00938	0.00924
Rear teat Placement	ARS-BFGL-NGS-31730	11	44265651	SH3RF3	within	0.00927	0.00864
	BTB-01230622	15	62600934	DCDC5	61,622	0.01200	0.00864

Note: Heritability and threshold were obtained using the LASSO method; -log₁₀(P) was calculated using SMMA. ^aSNP detected by SMMA only; ^b-log₁₀(P) obtained from SMMA; ^cthreshold of SMMA. Nearest gene are symbols of gene full name in the NCBI database (http://www.ncbi.nlm.nih.gov/).

ISSN: 1471-2164