- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
Mao, Xiaowei; Kadri, Naveed Kumar; Thomasen, J. R.; De Koning, Dirk-Jan; Sahana, Goutam; Guldbrandtsen, B.
Decreased calving performance not only directly impacts the economic efﬁciency of dairy cattle farming but also inﬂuences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus auto- some (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, ﬁne mapping of this QTL was performed using imputed high- density SNP chip (HD) genotypes followed by imputed next-generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most signiﬁcantly associated SNP across all seven traits [e.g. p-value = 2.04 x 1059 for birth index (BI)]. To ﬁnely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450- 57 625 355) for associations with direct calving traits and with three con- formation traits. Signiﬁcant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional rela- tionships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assem- bly hampered our efforts to pinpoint the causal mutation.
calving; genome-wide association; Holstein; next-generation sequencing
Journal of Animal Breeding and Genetics
2016, Volume: 133, number: 3, pages: 207-218
Genetics and Breeding