TABLE 4.

Suggested and associated SNPs with ewe composite traits at weaning in Baluchi sheep.

Chr	SNP	Position	Genes in 300 kb interval	Analysis method	Adjusted P-value	Trait(s)	MAF
3	rs428404187	131255497	NDUFA12, NR2C1, FGD6, VEZT, MIR331, METAP2	pGWAS and eGWAS	4.72 × 10–6 8.60 × 10–5	PWW, TLWW,and LMWW	0.03
5	rs398620273	32383306	HSD17B4, DMXL1, DTWD2	pGWAS	2.72 × 10–5	PWW, TLWW, and LMWW	0.28
2	rs412011189	1426911	EIPR1	pGWAS	3.39 × 10–5	PWW and LMWW	0.2
2	rs411656768	81968762	NFIB	pGWAS	4.74 × 10–5	PWW	0.11
7	rs430218107 rs419540936	23778602 23939664	EDDM3B, ANG1, RNASE1, RNASE6, RNASE4, ANG2, UQCRFS1, RNASE12, RNASE11, RNASE9, RNASE10, PIP4P1, APEX1, OSGEP, KLHL33, TEP1, PARP2, RPPH1, SNORA79B, CCNB1IP1, TTC5, OR11H4, OR11H7, OR11H6	pGWAS pGWAS	7.42 × 10–5 9.79 × 10–5	PWW PWW	0.42 0.29
2	rs403459195	77075145	RPLP0	pGWAS	7.88 × 10–5	PWW	0.26
13	rs401393221	30320719	PTER, C1ql3, RSU1, CUBN, VIM	pGWAS	9.50 × 10–5	PWW	0.29
3	rs404069303	143726957	SNORA62	pGWAS	1.90 × 10–5	LMWW	0.04
16	rs409558668	39225407	PRLR, AGXT2, DNAJC21, BRIX1, RAD1, TTC23L, RAI14	pGWAS	7.95 × 10–5	LMWW	0.23
25	rs405045517	16553906	CDK1, FTH1, RHOBTB1	pGWAS	9.89 × 10–5	LMWW	0.09

Chr, Chromosome number; pGWAS, GWAS using phenotype; eGWAS, GWAS using EBVs; PWW, Progeny Weaning Weight; TLWW, Total Litter Weight at Weaning; LMWW, Litter Mean Weight at Weaning; MAF, Minor allele frequency. P-values are presented only for the first trait in the Trait(s) column. P-values are adjusted based on the Genomic Control value. Genes with boldface indicate that significant SNPs are located within the gene. SNPs with boldface are significantly associated with genes but otherwise are suggestive SNPs. The regression coefficient of each SNP is provided in Supplementary Table 15.