Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan

SIMPLE SUMMARY: Similar cattle breeds are difficult to distinguish based on appearance alone, but their price and breeding options vary greatly. In this study, we examined a high level of genomic diversity in Loudi cattle from central Hunan using whole-genome resequencing data. We speculated the origin of Loudi cattle and detected the positive selection signal of its genome by comparison with carefully selected cattle breeds from around the world. These findings will serve as the basis for upcoming conservation and breeding initiatives. ABSTRACT: Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today’s extreme climate environment.