Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

Abstract

Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, FST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.

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.…”

Assessing the Role of Ancestral Fragments and Selection Signatures by Whole-Genome Scanning in Dehong Humped Cattle at the China–Myanmar Border

“…The WASF2 gene was a downstream effector molecule that involved signal transductions from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. promoting actin filament formation [ 48 , 49 ]. The gene can respond to changes in the external environment by reregulating its expression or distribution to further influence the cytoskeleton arrangement [ 50 ].…”

Whole‐genome resequencing uncovers diversity and selective sweep in Kazakh cattle

“…Owing to the decreased resequencing costs, resequencing is a promising tool for identifying genomic diversity, phylogenetic reconstruction and segments under selection in multiple cattle breeds. In fact, whole‐genome resequencing of 23 Xiangxi cattle revealed 40 million variants with reduced linkage disequilibrium (Luo et al., 2022). Similarly, Chen et al.…”

“…under selection in multiple cattle breeds. In fact, wholegenome resequencing of 23 Xiangxi cattle revealed 40 million variants with reduced linkage disequilibrium (Luo et al, 2022). Similarly, Chen et al (2018) utilized whole-genome analysis to reveal the geographic origins of the East Asia cattle breed, resulting in five geographical ancestors.…”