Accumulation of deleterious mutations in the domestic yak genome

Abstract

Deleterious mutations play an important functional role, affecting trait phenotypes in ways that decrease the fitness of organisms. Estimating the frequency of occurrence and abundance has been a topic of much interest, especially in crops and livestock. The processes of domestication and breeding allow deleterious mutations to persist at high frequency, and identifying such deleterious mutations is particularly important for breed improvement. Here, we assessed genome-wide patterns of deleterious variation in 59 domestic and 13 wild yaks using genome resequencing data. Based on the intersection of results given by three methods (provean, polyphen2 and sift4g), we identified 3187 putative deleterious mutation sites affecting 2586 genes in domestic yaks and 2067 affecting 1701 genes in wild yaks. Multiple lines of evidence indicate a significant increase in the load of deleterious mutations in domesticated yaks compared to wild yaks. Private deleterious genes were found to be associated with the perception of smell and detection of chemical stimulus. We also identified 36 genes related to Mendelian genetic diseases involved in sensory perception, skeletal development and the nervous and immune systems. This study not only adds to the understanding of the genetic basis of yak domestication but also provides a rich catalog of variants that will facilitate future breeding-related research on the yak genome and on other bovid species.

Deleterious mutation load in diverse cattle breeds of the world

“…This is due to the role of genetic drift that elevates the frequency of SNVs due to bottleneck, inbreeding and artificial selection. Previous studies on dog breeds and yaks showed a higher number of homozygous deleterious SNVs in domesticated canines or yaks than those present in their respective wild relatives [6,15]. Since homozygous SNVs represents high frequency variants, our results are in consensus with those reported by the above-mentioned studies.…”

“…This was confirmed by a previous study that compared the exomes of dog breeds and wild wolves and found a higher proportion of homozygous deleterious SNVs in dogs than wolves [6]. Similarly, domesticated yak populations were reported to have higher number of homozygous deleterious amino acid changing SNVs than those estimated for wild yaks [15]. High frequency deleterious variants causing diseases such as retinal degeneration in European cattle breeds has been attributed to the process of domestication and artificial selection [16].…”

“…This is because those studies showed that the diversity of the domesticated breeds or varieties were always smaller than those of their wild relatives. Analysis based on the actual number of deleterious nonsynonymous SNVs revealed a higher number of high-frequency deleterious SNVs in breeds with low diversity [6,15]. This is due to the role of genetic drift that elevates the frequency of SNVs due to bottleneck, inbreeding and artificial selection.…”

Evolution and domestication of the Bovini species

“…2015; Xie et al . 2018). Several of these genes are related to smell perception and chemical stimuli (Hu 2012).…”

Characteristics of pulmonary microvascular structure in postnatal yaks

“…With the development of modern biotechnology, increasing numbers of researchers are conducting molecular biology research pertaining to the environmental adaptability of this mammal. In the last few years, high-throughput studies on yaks, such as genome and miRNA sequencing and transcriptome analysis, have become popular 13 – 15 . In fact, there are still many unexplored areas of basic research in this animal.…”