| 1. |
- Ibacache Quiroga, Claudia Jimena, et al.
(författare)
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Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle
- 2016
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 133, s. 207-218
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Tidskriftsartikel (refereegranskat)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 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.
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| 3. |
- Mao, Xiaowei, et al.
(författare)
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Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data
- 2016
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Ingår i: Journal of Animal Science. - : Oxford University Press (OUP). - 0021-8812 .- 1525-3163. ; 94, s. 1426-1437
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Tidskriftsartikel (refereegranskat)abstract
- Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins (n = 5,519), Jerseys (n = 1,231), and Red Dairy Cattle (n = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; P-value = 2.8 × 10-32) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene CYP19A1 is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene PLAG1, which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.
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