Evaluating genomic inbreeding of two Chinese yak (Bos grunniens) populations

Abstract

Background: Yaks are a vital livestock in the Qinghai-Tibetan Plateau area for providing food products, maintaining sustainable ecosystems, and promoting cultural heritage. Because of uncontrolled mating, it is impossible to estimate inbreeding level of yak populations using the pedigree-based approaches. With the aims to accurately evaluate inbreeding level of two Chinese yak populations (Maiwa and Jiulong), we obtained genome-wide single nucleotide polymorphisms (SNPs) by DNA sequencing and calculated five SNP-by-SNP estimators ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]), as well as two segment-based estimators of runs of homozygosity (ROH, [Formula: see text]) and homozygous-by-descent (HBD, [Formula: see text]). Functional implications were analyzed for the positional candidate genes located within the related genomic regions.

Results: A total of 151,675 and 190,955 high-quality SNPs were obtained from 71 Maiwa and 30 Jiulong yaks, respectively. Jiulong had greater genetic diversity than Maiwa in terms of allele frequency and nucleotide diversity. The two populations could be genetically distinguished by principal component analysis, with the mean differentiation index (Fst) of 0.0054. The greater genomic inbreeding levels of Maiwa yaks were consistently supported by all five SNP-by-SNP estimators. Based on simple proportion of homozygous SNPs ([Formula: see text]), a lower inbreeding level was indicated by three successfully sequenced old leather samples that may represent historical Maiwa yaks about five generations ago. There were 3304 ROH detected among all samples, with mean and median length of 1.97 Mb and 1.0 Mb, respectively. A total of 94 HBD segments were found among all samples, whereas 92 of them belonged to the shortest class with the mean length of 10.9 Kb. Based on the estimates of [Formula: see text] and [Formula: see text], however, there was no difference in inbreeding level between Maiwa and Jiulong yaks. Within the genomic regions with the significant Fst or enriched by ROH, we found several candidate genes and pathways that have been reported to be related to diverse production traits in farm animals.

Conclusions: We successfully evaluated the genomic inbreeding level of two Chinese yak populations. Although different estimators resulted in inconsistent conclusions on their genomic inbreeding levels, our results may be helpful to implement the genetic conservation and utilization programs for the two yak populations.

Keywords: Genetic diversity; Jiulong yaks; Maiwa yaks; ROH; Runs of homozygosity.

Fig. 1

Genomic distribution and genetic diversity of SNPs. (A) The genomic distribution is shown for the SNPs found in Maiwa yaks (outside circle), Jiulong yaks (middle circle), and their common SNPs (inner circle). The distribution density of minor allele frequencies within each population and their pairwise correlations between Maiwa and Jiulong yaks are shown in (B) and (C), respectively. The nucleotide diversity of SNPs is shown by the boxplot (D)

Fig. 2

Sample clustering and population differentiation index Fst. (A) The top three principal components (PC1, PC2, and PC3) derived from the genome-wide SNPs are used for clustering Maiwa (blue) and Jiulong (red) yaks. The threshold of Fst is denoted by the horizontal dashed line in (B)

Fig. 3

Estimates of genomic inbreeding estimators

Fig. 4

Numbers of runs of homozygosity (ROH) on each autosome (A), and their length distribution (B) and sample enrichment (C).