Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features

Abstract

Gayal (Bos frontalis) is a semi-wild and endangered bovine species that differs from domestic cattle (Bos taurus and Bos indicus), and its genetic background remains unclear. Here, we performed whole-genome sequencing of one Gayal for the first time, with one Red Angus cattle and one Japanese Black cattle as controls. In total, 97.8 Gb of sequencing reads were generated with an average 11.78-fold depth and >98.44% coverage of the reference sequence (UMD3.1). Numerous different variations were identified, 62.24% of the total single nucleotide polymorphisms (SNPs) detected in Gayal were novel, and 16,901 breed-specific nonsynonymous SNPs (BS-nsSNPs) that might be associated with traits of interest in Gayal were further investigated. Moreover, the demographic history of bovine species was first analyzed, and two population expansions and two population bottlenecks were identified. The obvious differences among their population sizes supported that Gayal was not B. taurus. The phylogenic analysis suggested that Gayal was a hybrid descendant from crossing of male wild gaur and female domestic cattle. These discoveries will provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds and may assist relevant departments with future conservation and utilization of Gayal.

Figure 1. Identified InDels in Gayal.

Variations were annotated using the RefSeq and Ensembl gene sets. Of the total InDels, 1,511,754/76.7% were located in intergenic regions; 442,441/22.5% were located in genic regions, including intronic, splicing sites, exonic and untranslated regions; and the remaining 16,075/0.8% were located in up/downstream regions.

Figure 2. Demographic history of Gayal (Bos frontalis), JBC and RAN (Bos taurus).

Autosomal SNPs of gayal were used to reconstruct demographic history with the pairwise sequentially Markovian coalescent (PSMC) model with the generation time (g = 5), mutation rates (μ = 1 × 10⁻⁸). As is showed above, both of B. frontalis (Gayal) and B. taurus (RAN and JBC) have undergone two population expansions and two population bottlenecks, and gayal could be clearly distinguished from RAN and JBC, which strongly supported that gayal was not a Bos taurus.

Figure 3. Phylogeny of bovine-related species.

Phylogenetic analysis using available data, including (A) 20 randomly selected single ortholog copy genes in Bos taurus, Bos mutus (wild yak) and Bubalus bubalis genomes and (B) the completed mitochondrial genomes of Bos taurus, Bos indicus, Bos gaurus, Bos mutus (wild yak) and Bubalus bubalis downloaded from NCBI, and Equus caballus was used as an outgroup.