晋南牛遗传结构特征及选择信号分析

doi:10.16431/j.cnki.1671-7236.2024.01.017

Abstract

Abstract: 【Objective】 The purpose of this study was to elucidate the genetic structure characteristics of Jinnan cattle, and explore candidate genes related to economic traits in Jinnan cattle through selection signal detection, in order to explore the selection status during the evolutionary process.【Method】 Whole genome sequencing data of Jinnan cattle and Red Angus cattle were analyzed to identify the single nucleotide polymorphism (SNP) marker of the two populations, and analyze its position and structural characteristics in the genome.Principal component analysis (PCA) and identity by state (IBS) matrix were constructed based on SNP information.A combination of population genetic differentiation index (Fst) and nucleotide diversity ratio (θ_π) was used to screen the highly selected regions in Jinan cattle genome, and quantitative trait locus (QTL), GO function and KEGG pathway enrichment were analyzed for the selected genes.【Result】 The SNPs in Jinnan cattle population were mainly distributed in the intergene region, followed by the intron region.The results of PCA and IBS analysis showed that there was no hybridization between Jinnan cattle and Red Angus cattle, and the genetic distance between individuals in Jinnan cattle was far away.By the combined analysis of Fst and θ_π, a total of 188 potential selected regions were screened.QTL analysis showed that the selection signals of Jinnan cattle were mainly related to growth, meat quality and disease resistance traits.GO function and KEGG pathway enrichment analysis showed that 11 candidate genes related to economic traits were selected strongly in Jinnan cattle, including cathepsin 1 (CATHL1), CATHL3, cathepsin antimicrobial peptide (CAMP), CATHL4, kinase inhibitor of RAS1 (KSR1), Meis homeobox 1 (MEIS1), irregular fragment polar protein 1 (DVL1), polycomb group ring finger 1 (PCGF1), RB transcriptional repressor 1 (RB1), regenerating family member 4 (REG4) and frizzled class receptor 7 (FZD7), and SNP sites were detected in the exon region of the genes.In addition to MEIS1, PCGF1 and FZD7 genes, all other genes had non-synonymous mutation sites, and KSR1 gene had stop gain mutation, and CAMP gene had stop gain and stop loss mutation.Compared with Red Angus cattle, there were 6 unique selected genes (CATHL1, CATHL4, CAMP, MEIS1, PCGF1 and PZD7 genes) in Jinnan cattle, which were mainly related to disease resistance, growth and skeletal muscle development.【Conclusion】 This study explored the genetic structure and selection signal characteristics of Jinnan cattle from the whole genome level, and screened 6 candidate genes that might be related to the economic traits of Jinnan cattle, providing theoretical reference for the subsequent research on conservation and breeding and the molecular mechanism of characteristic trait formation in Jinnan cattle.

Key words: whole genome resequencing; Jinnan cattle; Red Angus cattle; gnetic distance; selection signal

CLC Number:

S823.8

RONG Yanhua, JIA Xuechun, LI Pengfei, TIAN Guofu, ZHU Zhiwei. Analysis of Genetic Structure Characteristics and Selection Signal in Jinnan Cattle[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(1): 160-171.

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Analysis of Genetic Structure Characteristics and Selection Signal in Jinnan Cattle

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