Multiple-trait QTL mapping and genomic prediction for wool traits in sheep

Bolormaa, Sunduimijid; Swan, Andrew A.; Brown, Daniel J.; Hatcher, Sue; Moghaddar, Nasir; van der Werf, Julius H.; Goddard, Michael E.; Daetwyler, Hans D.

doi:10.1186/s12711-017-0337-y

Genetics Selection Evolution

Table 7 Examples of pleiotropic effects of SNPs selected from the multi-trait analyses on the individual traits (signed values with |t| > 1 are shown)

From: Multiple-trait QTL mapping and genomic prediction for wool traits in sheep

CHR:POS^a	GFW	YLD	SL	SS	FD	FDC	CU	WR	BC	CC	DAG	SST	WE	CHA	FR	DU	COL	CLZ	CLYZ	CLY	CLX	SK	Gene code
1:244,308,221			2.0	1.3	−5.5	1.1	−1.3			−1.4					−1.3		−2.8		1.3				TRPC1
3:37,206,022		−1.5	−4.1	−1.1	−5.5	2.7	1.2		−1.1	1.0		−2.9			1.6		1.1		−1.1				LCLAT1
3:39,080,949		2.1	3.2		−5.5		−3.7			1.0		2.7					1.2	−1.9		−2.0	−1.8		ANTXR1
3:58,612,068	−1.3	3.1	3.0		5.0	−3.2		−3.1	−1.6					−1.7	−2.6		1.3	−2.2		−2.4	−2.5	−1.5	KRCC1
3:59,019,274⁽⁶⁾			9.5	2.4	4.1	−3.7	1.1	−7.0	−4.3	−3.9	−1.4				−4.4	2.3			1.1			−4.9	FOXI3
3:60,384,564	3.5		−5.0			2.7	−2.5	5.6	1.8	1.2					3.3	−2.8	1.9		1.2			3.9	TTL
3:133,925,825	−1.4	1.6			−1.6	−1.3		−2.5	−1.0	−1.4		−2.9		−4.6	−1.5		−1.4					−1.7	KRT86
3:137,105,001	3.5		1.4					1.4				2.0	−1.3	1.4								1.2	WNT1
3:202,672,118	−2.0	−2.5			6.1	−2.6	3.0		−2.4	−3.2		1.9		2.3		1.3		−2.3	1.1	−2.2	−2.3
4:62,652,234		−1.4	−1.8		−2.4	1.4	2.7	1.8				−1.7		−2.4				5.1	−3.0	4.5	4.5		BMPER
5:48,528,440⁽³⁾	2.8	2.2	3.3		2.0	1.3	−3.2	−1.3			−1.6		2.0				2.7	2.9	−1.1	2.7	2.8		FTL
6:37,256,712⁽⁴⁾	4.4		−2.3	−1.5		3.6	−1.8					1.6		3.5	3.2		1.0	−1.1					NCAPG/LCORL
6:86,591,198	−1.1	1.3	1.2		−1.5	1.8		−2.4		2.7			2.0	3.5	3.0			−1.3		−1.3	−1.4	−1.4	GC
6:94,602,390			−3.7		−3.7		1.2		1.5			−2.2					−3.0		−1.1				FGF5
6:114,171,155	1.2				2.8			−1.5	−1.2		1.1		−1.4				−1.6	−5.3	2.5	−4.8	−4.8		TRMT44
7:57,834,812	3.4	1.5	1.8	−1.3	−2.2		−1.1	−1.5	−1.2	−1.3			1.4	1.2		1.0	1.7	−1.0		−2.1	−1.5		FGF7
8:31,242,591⁽⁵⁾	−2.4	−3.1	−1.3	−1.3	−5.5		4.7	−1.3		−1.6	1.1	−1.7			−1.1		−1.5	1.3	−2.3
11:26,333,173	5.0	−1.6	1.0	−2.0	−1.9	2.7	−2.6		−1.1								1.5						ALOX15
11:49,956,916	4.5	2.1	2.1				−5.5	1.2	−1.0	1.3	2.3			−1.3									FASN
13:22,846,602				−2.2	−1.3				1.3	5.3	1.9	−1.0					−2.5						PIP4K2A
13:62,872,216⁽⁶⁾		−2.5	−3.8	1.8	−4.1	−5.5	1.7			1.1		−3.3	−2.7	−5.3				2.2		2.1	2.0		RALY
14:55,112,107⁽²⁾	−1.5	1.1	−1.1	1.1	−5.5	−4.6	2.3		−2.6			−3.3	−1.2	−1.6					−1.5				BCL2L12
15:13,764,013⁽²⁾		1.0	1.1	−3.3			−5.0			1.0			1.8				1.8	−2.0		−1.7	−1.6		MAML2
15:72,565,587			−1.5		−6.6	−1.3	−1.2		−1.0	−1.5		−2.8	−1.5	−2.7	1.3	−2.0	−1.3	2.7	−1.7	2.3	2.3		ALX4
19:658,455⁽³⁾	5.3	−11.3	3.3		2.3	−2.2	−2.1			−1.1	1.1	−3.9	−1.3	−3.6	−2.0	−2.0	−2.8	−1.2	1.7			−2.3	LANCL2
21:5,529,725	2.0	1.0			1.3	2.2	−4.9			1.6		−2.2	1.8					−1.2		−1.2	−1.2	−3.4	NOX4
22:34,770,924	1.4	1.2		−2.1	−4.3			−2.6		−1.6	1.4	1.2	1.3	1.4		2.4	2.1			−1.1	−1.0		ATRNL1
23:44,250,113⁽⁵⁾	−2.2		1.2	2.2	2.4	−5.3		−1.9	−2.4	−4.3	−3.1		1.6					−2.2		−2.2	−2.3
24:35,659,971					−1.7		1.0	2.9		1.3	1.1						−1.5	4.1		5.1	5.1	1.1	ACHE
25:35,306,299⁽¹¹⁾	−3.8	−4.0	−3.1	−8.7	−3.8	6.4	4.4		1.2	3.4	−1.8			2.9		1.3		2.1	−2.9				MAT1A
26:22,464,394			2.4		5.5					−1.1	1.1	3.7	1.3					−2.1	2.2	−1.6	2.0		DLC1

Traits at yearling age: FDC = FDCV; CU = CURV; WR = BRWR; BC = BCOV; CC = CCOV; SST = SSTRC, WE = WEATH, CHA = CHAR; FR = FLROT; DU = DUST; COL = GCOL; CLZ = COLZ; CLYZ = COLYZ; CLY = COLY; CLX = COLX; SK = SKINQ
^aOvine chromosome and position of SNPs, and the superscript numbers in brackets are the number of SNPs that have a similar pattern of pleiotropic effects within a distance of 1 to 1.5 Mb

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