A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits

Table 3 List of putative causal variants with the signed significant t-values (|t| ≥ 2.0) across wool traits at yearling and adult ages

OAR pos. (bp) for most significant SNP	Annotation class for the most significant variant	M-GWAS Pval	ygfw	agfw	ycfw	acfw	ysl	asl	yfd	afd	ydcv	adcv	ycuv	acuv	yss	ass	ebwr	ebcov	Flanking genes^a
Chr3:58,729,692	Intronic	3.21E−43		4.6		3.9	− 10.9	− 5.5	− 6.7	− 3.9	3.3	5.1		− 3.2	− 2.3	− 4.2	6.9	3.5	THNSL2⁰
Chr25:35,305,108	Intronic	4.85E−40	5.1	2.9	6.7	3.3	4.6	4.6	4.4	2.8	− 9.6	− 6.8	− 4.5	− 3	10.4	8.8			MAT1A⁰
Chr19:840,732	Missense	4.44E−30	4.9	4.1				2			− 2.5		− 2.1	− 2.6					EGFR⁰
Chr13:62,835,771	Intergenic	3.30E−14		4	2	3.8	4	3.1	4.7	3.4	6.2	4.7		− 2.2	− 2.5		− 2.5		RALY¹⁶ EIF2S2⁷¹
Chr6:37,676,407	intergenic	4.87E-12	3.9	6.2	3.6	5.2	− 2.6			− 3.1	3.5	2.1							LCORL²²⁴
Chr15:72,567,959	intronic	5.92E-09					2.9		6.6	3.8							− 3.7		ALX4⁰
Chr3:86,858,557	Intronic	1.29E−07		2	2.3						5.1	3.7					− 2.7		EIF2AK2⁰
Chr9:82,254,047	Intronic	8.29E−07						3.8			3.9		− 2.8	− 2.1	− 2.7		− 2.9		ESRP1⁰
Chr23:43,896,965	Upstream	3.07E−06							− 3.3	− 2.9	5.4	3.4			− 3.3	− 2.5	3.6		MC2R^2.2
Chr23:43,896,965	Upstream	3.07E−06							− 3.3	− 2.9	5.4	3.4			− 3.3	− 2.5	3.6		MC5R²⁷
Chr9:29,973,331	Intergenic	4.59E−06	3.2		5.2		3.4	2.8						− 2.1			− 2.4		ZHX2³²⁷
Chr9:29,973,331	Intergenic	4.59E−06	3.2		5.2		3.4	2.8						− 2.1			− 2.4		HAS2⁹⁷⁰
Chr3:58,952,741	Intergenic	3.41E−06					2.8		4.2	3.4	−2.4		2			3.9	− 4.6	− 2.1	FOXI3³⁴
Chr3:58,952,741	Intergenic	3.41E−06					2.8		4.2	3.4	−2.4		2			3.9	− 4.6	− 2.1	THNSL2²¹³
Chr1:259,689,936	Intronic	1.97E−06				2.2	2	3.1		3.1			− 5.8	− 3.9		2.7	− 2.1		^bMX2⁰

^aNumber in superscript shows the distance to each gene in kb
^bMX2 lies very close to LOC101102526, which is a keratin-associated protein 10–12-like gene

ISSN: 1297-9686