Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle

Abstract

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 autosome (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 × 10(-59) 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 conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships 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 assembly hampered our efforts to pinpoint the causal mutation.

Genome-wide association study for longevity with whole-genome sequencing in 3 cattle breeds

“…Alternatively, animals suffering from mastitis may have low immunity to other infections (Sordillo, 2005), which would increase their chances of being culled. The QTL on chromosome 18 overlaps with calf size and calving difficulty QTL in the same populations (Mao et al, 2015). A large size calf can cause damage of the birth canal of a cow during calving, which may lead to a higher risk of culling.…”

“…The SNP on RDC-CHR6-88MB with highest significance explained 1.4% of the total variance in the deregressed proofs of longevity (Table 1). Mao et al (2015) reported a major QTL affecting birth index in this HOL population, with the most associated SNP at 57,548,213 bp that explained 4.16% of the total genetic variance for birth index. It is possible that this QTL increases calving difficulties by increasing calf size at birth.…”

“…The strongest association signal in HOL was found on chromosome 18 around 58 Mbp (HOL-CHR18-58MB). The most significant SNP on this region was located at 58,118,935 bp (rs521076153), very close to the zinc finger protein 613 gene (ZNF613; 58,115,782-58,117,110 bp) and zinc finger protein 717 gene (ZNF717; 58,130,465-58,141,877 bp), which have been associated with calving difficulties and which have been reported to be associated with calving traits (Mao et al, 2015). It is also very close to the QTL (BTA18: SIGLEC12) reported to be associated with productive life (Ma et al, 2012).…”

Linkage Map ofLissotritonNewts Provides Insight into the Genetic Basis of Reproductive Isolation

“…Maps allow identification of loci determining specific phenotypes, such as genomic regions underlying economically important traits (Mao et al 2015; Royaert et al 2016), or genetic basis of adaptive ecological traits, such as migration (Hale et al 2013) or industrial melanism (van’t Hof et al 2016). In comparative genomics, linkage maps are indispensable to investigate the conservation of chromosomal segments at various evolutionary time scales (Postlethwait et al 2000; Hollenbeck et al 2015).…”

A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications

“…SNPs have been widely used in a variety of genetic studies and applications, such as mapping of QTL (Kim et al ; Höglund et al ; Mao et al ), GWASs (Chan et al ; Macciotta et al ; Schweer et al ) and genomic selection (Wiggans et al ; Okut et al ; Boerner et al ; Lopes et al ) in farm animals. Over the years, ad‐hoc procedures have been used for designing SNP chips.…”