Single nucleotide polymorphisms in candidate genes associated with milk yield in Argentinean Holstein and Holstein x Jersey cows

Raschia, María Agustina; Nani, Juan Pablo; Maizon, Daniel Omar; Beribe, María José; Amadio, Ariel Fernando; Poli, Mario Andrés

doi:10.1186/s40781-018-0189-1

Journal of Animal Science and Technology

Table 1 SNPs included in the SNPlex genotyping panel

From: Single nucleotide polymorphisms in candidate genes associated with milk yield in Argentinean Holstein and Holstein x Jersey cows

Candidate gene	Marker	Location (BTA:bp)	Call rate	MAF	HWE p-value
ARL4A	rs43375517	4:20296999	98.1	0.39	0.14
ETV1	rs42213673	4:22111819	98.8	0.35	0.28
SNX13	rs41595314	4:26425057	98.6	0.07	8.10^− 3
LEP	rs29004488	4:93262056	97.4	0.33	0.02
OLR1	rs109019599	5:100254823	89.3	0.25	2.10⁻³
ABCG2	rs43702337	6:38027010	99.7	0.00	1.00
OPN	rs132812135	6:38120968	94.5	0.35	0.55
	rs110930453	6:38122665	93.1	0.42	0.87
	OPN3907^a	6:38128806
PPARGC1A	rs109579682	6:44875251	98.4	0.23	0.03
	rs133669403	6:44875315	97.5	0.08	0.09
	rs17870811	6:44875421	99.5	0.06	0.46
CSN1S1	CSN1_AB	6:87146017	87.9	0.00	1.00
	rs433385179	6:87148464	99.9	0.00	1.00
	rs43703010	6:87157262	96.8	0.15	0.64
CSN2	rs43703013	6:87181453	96.8	0.04	0.02
CSN2	rs43703011	6:87181619	97.6	0.27	0.01
CSN3	rs43706475	6:87390479	99.3	0.00	1.00
	rs43703015	6:87390576	99.4	0.19	0.33
	rs43703017	6:87390632	98.2	0.04	0.33
LGB	rs41255680	11:103301242
	rs41255685	11:103301690	75.3	0.08	< 1.10⁻⁶
	rs43691049	11:103303343
	rs109625649	11:103304757	83.5	0.10	0.56
DGAT1	rs109234250	14:1802265	62.8	0.10	0.61
DGAT1	rs109326954	14:1802266	62.8	0.10	0.61
STAT5A	rs109487069	19:43047829
GH	rs109191047	19:48768766	97.5	0.19	0.19
GH	rs137651874	19:48769040	98.1	0.48	0.10
FASN	rs208645216	19:51400139
FASN	rs41919985	19:51402032	78.7	0.15	2.10⁻³
GHR	rs385640152	20:31909478	98.8	0.09	0.84
PRLR	rs135164815	20:39115344	99.2	0.15	0.91
UTMP	rs132991801	21:59667572	96.0	0.42	0.03
LTF	rs41256920	22:53521978	99.2	0.23	0.39
LTF	rs43706485	22:53522038	95.5	0.19	0.93
PRL	rs211032652	23:35106206	99.5	0.08	0.57
PRL	rs110494133	23:35110974	97.4	0.21	3.10⁻⁶
SCD1	rs41255693	26:21144708	98.9	0.19	0.17

^aOPN3907 is a T deletion, not a SNP
Call rate, MAF and HWE p-value for the SNPs that did not present failure in the genotyping reactions are indicated. Markers bolded in black passed the quality control checks. Location of the SNPs is based on assembly UMD3.1

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ISSN: 2055-0391

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