Table 3.

Overlapping QTL intervals identified based on single-trait GWAS for milk yield (MY), fat yield (FY) and protein yield (PY)

Chr.	Region	Traits	Genes
2	85393563–86241732	FY, MY	ENSBTAG00000047452, GTF3C3, CCDC150, PGAP1, ANKRD44
5	20035379–20534779	FY, PY	–
5	93703737–93762020	FY, PY, MY	–
5	93762020–94198670	FY,PY	MGST1, SLC15A5
5	93698481–93703737	FY, MY	LMO3
14	1545264–1583427	FY, PY, MY	bta-mir-2308, ARHGAP39
14	1448510–1545264	FY, MY	ZNF16, C14H8orf33, ZNF34, ZNF7, COMMD5, RPL8
14	1549272–2044412	FY, PY, MY	bta-mir-2308, C14H8orf82, LRRC14, RECQL4, GPT, PPP1R16A, KIFC2, VPS28, SLC52A2, TMEM249, SCX, ENSBTAG00000044406, ENSBTAG00000039978, HGH1, MAF1, SHARPIN, CYC1, GPAA1, EXOSC4, ENSBTAG00000015040, GRINA, PARP10, LRRC24, MFSD3, FOXH1, CYHR1, TONSL, SLC39A4, CPSF1, ADCK5, FBXL6, SCRT1, DGAT1, HSF1, MROH1, WDR97, SPATC1, ARHGAP39, BOP1, OPLAH
14	2044412–2049435	FY, MY	–
14	67731848–68231920	FY, MY	KCNS2, STK3, ENSBTAG00000046739
16	31268349–31746789	FY, MY	ENSBTAG00000044816, H3F3C, ENSBTAG00000021109, ENSBTAG00000042363, SCCPDH, TFB2M, SMYD3, CNST
19	27156952–27692965	FY, PY, MY	PSMB6, GLTPD2, VMO1, CXCL16, MED11, ARRB2, bta-mir-2338, ALOX15, ALOX12E, ENSBTAG00000047925, RNASEK, C19H17orf49, bta-mir-497, bta-mir-195, BCL6B, SLC16A13, CLEC10A, ASGR1, ENSBTAG00000042630, ACADVL, bta-mir-324, PHF23, GABARAP, ELP5, CLDN7, SLC2A4, EIF5A, GPS2, NEURL4, ENSBTAG00000045892, ACAP1, KCTD11, PLD2, TM4SF5, ZMYND15, PELP1, ALOX12, SLC16A11, ASGR2, DLG4, DVL2, CTDNEP1, YBX2, MINK1
19	26625240–27156952	FY, PY	ENSBTAG00000025126, MIS12, C1QBP, RPAIN, bta-mir-199c, ENSBTAG00000013906, SPAG7, ENO3, ENSBTAG00000004913, SLC25A11, GP1BA, CHRNE, C19H17orf107, NLRP1, DERL2, DHX33, SCIMP, ZFP3, KIF1C, INCA1, CAMTA2, PFN1, NUP88, RABEP1, MINK1
19	27692965–27773922	FY, MY	PLSCR3, TMEM256, NLGN2, SPEM1, TMEM102, CHRNB1, TNK1, FGF11, ZBTB4