基于单倍型肉牛屠宰性状全基因组关联分析研究

doi:10.11843/j.issn.0366-6964.2022.12.010

Abstract

Abstract: Haplotypes have a stronger linkage disequilibrium (LD) relationship with quantitative trait loci (QTLs). Haplotypes tend to have higher application value in gene mapping and searching for causal mutations. In order to evaluate the role of haplotype markers in genome studies, a total of 1 478 individuals in Huaxi cattle with an average age of 24 months, including 1 333 bulls and 145 cows, were slaughtered from 2008 to 2021. The LD thresholds was set at r²>0.3 and the number of fixed-SNPs was 5 for haploblock construction with 770K chip data, GWAS using GCTA with mixed linear model based on SNP and haplotype (a total of 3 markers were used: SNP marker and two types of haplotype marker) were performed on Huaxi cattle to detect the significant SNPs, haploblocks and candidate genes associated with LW and DP traits. In addition, the GWAS results of the 3 markers were compared to evaluate the advantages and disadvantages of the 3 markers. The results showed that 16 significant SNPs and haploblocks were detected in the whole genome, mainly distributed on chromosome 1, 5, 6, 14, 16, 17 and 28. A total of 10 candidate genes, such as FAM184B,PPM1K,LCORL,RIMS2 were identified, which significantly associated with the slaughter traits. And 3 candidate genes identified by SNP markers could also be identified by haplotype method, most of the significant loci or regions identified by haplotype were located within the gene. Among the two haplotype construction methods, the LD-based construction method identified more candidate genes than the one based on the fixed-SNPs for GWAS. In this study, the results showed that haplotype-based GWAS can comprehensively consider the LD between SNPs and can better reveal the genetic structure of complex traits.

Key words: beef cattle, haplotype, SNP, genome-wide association study, linkage disequilibrium

CLC Number:

S823.2

LI Hongwei, XU Lingyang, WANG Zezhao, CAI Wentao, ZHU Bo, CHEN Yan, GAO Xue, ZHANG Lupei, GAO Huijiang, LI Junya. Genome-wide Association Study of Slaughter Traits Based on Haplotype in Beef Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4232-4243.

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Genome-wide Association Study of Slaughter Traits Based on Haplotype in Beef Cattle

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