Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Table 2 The properties of 12 QTL detected in the 99-trait meta-analysis

BTA	Position (bp)	RefSNP id	Annotation	MAF	Effect allele	Ancestral allele	P value	V_EBV	iHS	Trait category	Candidate gene(s)
3	120,211,603	rs109854637	Intergenic	0.34	A	A	1.02 × 10 ^− 11	0.028	–	body conformation	–
5	31,524,629	rs110940367	Downstream gene	0.36	G	G	3.18 × 10⁻²⁷	0.030	−1.65	body conformation	–
5	93,945,655	rs134637616	Intron	0.26	C	C	1.35 × 10⁻⁴³	0.128	1.35	milk production	MGST1
6	87,005,244	rs135679764	Intron	0.18	G	–	1.87 × 10⁻¹⁵	0.041	–	milk production	Casein genes
6	90,486,780	rs41654962	Intergenic	0.20	G	G	2.35 × 10⁻³⁷	0.088	2.49	body conformation, milking speed	RASSF6
11	103,302,351	rs110186753	Intron	0.33	G	–	6.64 × 10⁻¹⁰	0.020	–	milk production	PAEP
14	2,534,899	rs109673915	Intron	0.25	G	G	1.33 × 10⁻¹⁶	0.045	–	milk production	GPIHBP1
17	62,697,699	rs137563207	Intergenic	0.24	C	C	2.35 × 10⁻³⁷	0.042	0.19	body conformation	TBX5, RBM19
20	29,987,376	rs133636599	Intergenic	0.14	A	C	8.24 × 10⁻⁹	0.033	1.21	milk production	GHR
21	913,715	rs108992215	Intergenic	0.15	A	–	1.30 × 10⁻²⁷	0.042	–	calving	MAGEL2
25	1,455,150	rs133315098	Intergenic	0.44	A	A	9.72 × 10⁻³³	0.046	–	body conformation, calving, longevity	IGFALS
26	22,133,617	rs42088986	Intron	0.24	A	A	8.59 × 10⁻¹⁶	0.035	−0.57	body conformation	BTRC

The positions of the QTL correspond to the UMD3.1 assembly of the bovine genome
BTA Bos Taurus autosome
MAF minor allele frequency
RefSNP id Reference SNP ID
V_EBV maximum proportion of the variance in estimated breeding value (EBV) explained by the QTL across traits
Trait category Trait group with which the QTL were associated
iHS integrated haplotype score (not available for SNPs located at the beginning and the end of the chromosome)
- not available

ISSN: 1471-2164