Analysis of genetic diversity and selection signals in Chaling cattle of southern China using whole‐genome scan

Abstract

China has diversified resources of indigenous cattle, which are classified into Northern, Central, and Southern groups according to their geographical distribution. Chaling cattle belong to Southern group. This breed is famous for the production of good quality meat with elite meat grades. To analyze the genetic diversity of Chaling cattle, 20 samples were sequenced using whole‐genome resequencing technology, along with 138 published whole‐genome sequencing data of Indian indicine cattle, Chinese indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle as control. It was found that Chaling cattle originated from Chinese indicine cattle. The genetic diversity of Chaling cattle is higher than that of Indian indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle, but lower than that of Chinese indicine cattle and Xiangxi cattle. Annotating the selection signals obtained by composite likelihood ratio, θπ, FST, π‐ratio, and XP‐EHH methods, several genes associated with immunity, heat tolerance, reproduction, growth, and meat quality showed strong selection signals. In general, this study provides a theoretical basis for analyzing the genetic mechanism of Chaling cattle with excellent adaptability, rough feeding tolerance, good immune performance, and good meat quality. This work lays a foundation for genetic breeding of Chaling cattle in future.

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole‐genome re‐sequencing

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Genomic characterization of dryland adaptation in endangered Anxi cattle in China

“…Recently, WGS analysis of domestic cattle revealed that cattle worldwide can be divided into five continental groups: European taurine, Eurasian taurine, East Asian taurine, Chinese indicine, and Indian indicine (Chen et al., 2018). Many studies have employed WGS to analyze the unique adaptability of native Chinese cattle breeds (Chen et al., 2021; Lyu, Guan, et al., 2023; Lyu, Ren, et al., 2023; Shen et al., 2022) and identified a range of representative genes and signaling pathways. In the past, limited research has been performed on the genome diversity and population structure of the Anxi cattle breed's mtDNA and Y chromosomes.…”

Whole‐genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle

“…Whole‐genome sequencing (WGS) is an effective technique/tool for identifying population structures and genetic variations that influence economic traits in livestock (Li et al., 2023). A global analysis of domestic cattle using WGS identified five distinct continental groups: European taurine, Eurasian taurine, East Asian taurine, Chinese indicine and Indian indicine (Chen et al., 2018).…”