Runs of Homozygosity Analysis Reveals Genomic Diversity and Population Structure of an Indigenous Cattle Breed in Southwest China

SIMPLE SUMMARY: For the reason that the systematic breeding programs and pedigree records are unavailable in the indigenous livestock breeds, it is hard to evaluate their genetic diversity and population structures using the traditional pedigree-based and demographic approaches. The Xieka cattle are an indigenous breed geographically distributed in the southeastern Sichuan, China, and have the long-term evolutionary adaptation to local subtropical highland environments. To explore efficient programs on genetic resources conservation and utilization, the genetic diversity and population structures of Xieka cattle were investigated in this study using genomic information. Our analyses revealed that this indigenous cattle breed have remained a relatively high degree of genetic diversity and have not suffered from the recently generated inbreeding. Furthermore, some candidate genomic regions and genes were suggested to be likely associated with the diverse production traits in cattle. ABSTRACT: In aiming to achieve sustainable development goals in the livestock industry, it is becoming increasingly necessary and important for the effective conservation of genetic resources. There are some indigenous cattle breeds in Sichuan, southwest China, for which, however, the genetic diversity and population structures still remain unknown because of the unavailability of systematic breeding programs and pedigree information. Xieka cattle are an indigenous breed locally distributed in southeastern Sichuan and have a long-term evolutionary adaptation to local environments and climates. In this study, we obtained 796,828 single nucleotide polymorphisms (SNPs) through sequencing the genomes of 30 Xieka cattle and used them for analyzing the genetic diversity and runs of homozygosity (ROH). The mean nucleotide diversity was 0.28 and 72% of SNPs were found to be in the heterozygous states. A total of 4377 ROH were detected with even distribution among all autosomes, and 74% of them were lower than 1 Mb in length. Meanwhile, only five ROH were found longer than 5 Mb. We further determined 19 significant genomic regions that were obviously enriched by ROH, in which 35 positional candidate genes were found. Some of these genes have been previously reported to be significantly associated with various production traits in cattle, such as meat quality, carcass performances, and diseases. In conclusion, the relatively high degree of genetic diversity of Xieka cattle was revealed using the genomic information, and the proposed candidate genes will help us optimize the breeding programs regarding this indigenous breed.