The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.

中文翻译：

---

世界不同牛种中的有害蛋白质编码变体

野生动物的驯化导致有效种群规模的减少，这会影响驯化品种的有害突变负荷。此外，由于家养动物的近亲繁殖率增加，人工选择会导致有害突变的积累。由于创始人种群大小和人工选择因牛而异，它们的有害突变负荷可能会有所不同。我们使用来自全球 54 个牛品种的 432 只动物的全基因组数据调查了这个问题。我们的分析揭示了基因组杂合性与非同义与沉默多样性比率之间的负相关，这表明影响低多样性品种蛋白质的单核苷酸变异 (SNV) 的比例更高。我们的结果还表明，与高多样性品种相比，低多样性品种具有更多数量的高频（衍生等位基因频率 (DAF) > 0.51）有害 SNV。对于低频（DAF ≤ 0.51）有害 SNV，观察到相反的趋势。总体而言，牛磺酸牛品种基因组中高频有害 SNV 的数量比黄牛品种多，而红牛基因组中低频有害 SNV 的数量多于牛磺酸牛。此外，我们观察到牛磺酸品种中有害 SNV 的数量存在显着差异。牛磺酸和indicine品种之间有害突变负荷的变化可归因于驯化前野生祖先的种群规模，而在牛磺酸品种中观察到的差异可能是由于近亲繁殖水平、人工选择强度和/或创始种群规模的差异。我们的研究结果意味着遗传疾病的发生率可能因牛品种而异。