Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

Table 3 Candidate genes for wool traits and live weight in Merino sheep

Trait	Gene	Chr	Start	End	Window rank	Specifically expressed tissue (P-value^a)	Specifically associated domain (P-value^b)
MFD	BNC1	18	22,758,417	22,784,473	TOP3	Skin (1.6E− 09)	Dermatology (2.0E− 15)
CVFD	ENDOV	11	51,243,368	51,257,814	TOP10	Skin (0.03)	CNS (1.0E− 5)
CN	CDC6	11	40,114,668	40,125,179	TOP1	Embryonic (< 2.2E− 16)	Immune (2.1E− 09)
CN	RARA	11	40,151,341	40,172,203	TOP1	Skin (0.04)	Immune (2.5E− 14)
CN	IGFBP4	11	40,250,021	40,260,382	TOP1	Liver (6E− 13)	Immune (8.4E− 12)
CN & MSL	GHR	16	31,832,933	32,000,445	TOP3 & TOP9	Liver (< 2.2E− 16)	Metabolic (3.1E− 17)
MSL & GFW	PPP1R3D	13	55,922,753	55,923,652	TOP7 & TOP5	Muscle (< 2.2E− 16)	Immune (0.002)
LW	CHRNB1	11	26,753,567	26,761,779	TOP2	Muscle (< 2.2E− 16)	Skeletal (8.8E− 39)
LW	ADSL	3	215,669,356	215,684,701	TOP3	Muscle (< 3.5E− 14)	Metabolic (9.2E− 14)
LW	SPHK1	11	54,357,681	54,359,873	TOP4	Immune (< 2.2E− 16)	Immune (3.4E− 20)

Chr, chromosome; MFD, mean fibre diameter; CVFD, coefficient of variation of the fibre diameter; CN, crimp number; MSL, mean staple length; GFW, greasy fleece weight; LW, live weight; CNS, central nervous system; GI tract, gastrointestinal tract
^aThe P-values were computed by comparing the expression (TPM) of the given gene in the target tissues with that in the remaining tissues
^bThe results were obtained from a phenome-wide association study (PheWAS), and the P-values were obtained from the top significant traits within the target domains

ISSN: 1297-9686