Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Abstract

Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

Genomic evidence for climatic adaptation in Fejervarya multistriata

“…Based on the maximum 5% of F ST values and maximum and minimum 5% of π ratio, genes under selection in both the SG group and HGG group were identified. In KOBAS (version 3.0) (Hu et al., 2023), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to conduct functional enrichment analysis to understand the biological processes and pathways involving the selected genes. The p ‐value cut‐off of .05 was considered to be significantly enriched.…”