全基因组重测序探究晋南牛优势性状的分子基础OACSTPCD

[Objective]The aim of this study was to investigate the genetic basis on which the phenotypic advantage of Jinnan cattle were based and provide a reference for the subsequent utilization of germplasm resources and molecular breeding in Jinan cattle.[Method]12 healthy purebred Jinnan cattle ear margin tissues were collected,and genomic DNA was extracted for whole genome resequencing.Compare the sequencing data and the genome data of 12 Red Angus cattle in NCBI database to the bovine reference genome(ARS-UCD1.2),and detect the SNPs loci in the population,and annotate the mutation sites using ANNOVAR software.The variant genes of Jinnan cattle and Red Angus cattle were analyzed by Venn method to screen for specific variant genes of Jinnan cattle,and conduct GO function and KEGG pathway enrichment analysis.The functional interaction of significantly enriched variant genes were analyzed by Cytoscape software.[Result]A total of 2 621 153 222 clean reads were sequenced from the Jinnan cattle genome,with an average Q30 value of 93.5％.The base distribution was uniform and without significant bias,and the average sequencing depth of 11.19×and an average coverage rate(≥4×)of 92.64％were obtained.A total of 117 773 201 SNPs loci were detected.A total of 405 506 non-synonymous,stopgain/stoploss SNPs were obtained by annotating the exon region,covering 16 690 genes,and 5 289 specific variant genes were screened out in Jinnan cattle.GO and KEGG analysis showed that genes were widely enriched in mitochondrial,ribosome,organelle membrane related biological processes,as well as oxidative phosphorylation and cytochrome P450(CYP)metabolic pathways.Mitochondrial respiratory chain protein(NDU),cytochrome C oxidase(COX),and glucuronic acid transferase(UGT)were widely enriched in the oxidative phosphorylation pathway.The CYP1A1,CYP2E1,UGT1A6,and UGT1A1 genes were enriched in multiple metabolic pathways related to cytochrome P450.The GSTM2,GSTT1,GSTT2,and GSTK1 genes were enriched in the glutathione(GST)metabolic pathway and cytochrome P450 related pathways.The sub network of mitochondrial ribosomal protein(MRP)and ribosomal protein(RP)gene families were enriched in the process of ribosomal protein formation.[Conclusion]The cattle-specific variant genes were significantly associated with cellular energy metabolism.It was inferred that they had a potential genetic effect on the feed efficiency of Jinan cattle.The results provided direction for screening SNPs markers that significantly affect fattening traits and breeding Jinnan cattle with high feed conversion.