Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou

Abstract

Weining cattle is a Chinese indigenous breed influenced by complex breeding and geographical background. The multi-ethnic breeding culture makes Weining cattle require more attention as livestock resources for its genetic diversity. Here, we used 10 Weining cattle (five newly sequenced and five downloaded) and downloaded another 48 genome data to understand the aspects of Weining cattle: genetic diversity, population structure, and cold-adapted performance. In the current study, a high level of genetic diversity was found in Weining cattle, and its breed comprised two potential ancestries, which were Bos taurus and Bos indicus. The positive selective sweep analysis in Weining cattle was analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 203 overlapped genes. In addition, we studied the cold adaptation of Weining cattle by comparing with other Chinese cattle (Wannan and Wenshan cattle) by three methods (FST, θπ-ratio, and XP-EHH). Of the top 1% gene list, UBE3D and ZNF668 were analyzed, and these genes may be associated with fat metabolism and blood pressure regulation in cold adaptation. Our findings have provided invaluable information for the development and conservation of cattle genetic resources, especially in southwest China.

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

“…Commercial breeds/populations with a long breeding history, such as East Asian taurine cattle, European taurine cattle and Eurasian taurine cattle, generally have lower nucleotide diversity. At the same time, the nucleotide diversities of North Chinese cattle breeds are all higher than that of these commercial cattle breeds/populations, which is consistent with previous research results (Guan et al., 2022; Li et al., 2023; Liu et al., 2022; Luo et al., 2022; Mei et al., 2018; Xia, Zhang, et al., 2021). In the North Chinese cattle, the nucleotide diversity of Qaidam cattle is higher than that of the other four breeds.…”

Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions

“…This result may be related to the continuous provision of energy for pigs to resist the cold. Some studies found that UBE3D had a relationship with fat composition in sheep, and it was a cold-resistant candidate gene in Weining cattle [ 42 , 43 ]. Therefore, UBE3D may be related to the adaptation of pigs to low temperatures in the northern region.…”

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

“…Major risks include genetic erosion and the loss of breed-specific genetic variation. It is commonly recognized that local cattle, such as those from Bali, have a significant number of favorable features, including the capacity to withstand hot weather conditions, poor fodder quality and resistance to internal parasites and infectious illnesses (Mohamad et al, 2012;Bakae et al, 2022;Liu et al, 2022;Trujano-Chavez et al, 2022;Xu et al, 2020).…”