东湖杂交羊产羔性状的GWAS分析及候选基因GRID2的验证

doi:10.11843/j.issn.0366-6964.2023.11.018

Abstract

Abstract: The experiment aimed to study the key genes affecting lambing traits in East Friesian and Hu crossbred sheep and select the mutation loci of the key genes for validation, to provide molecular markers for the selection and breeding of multiple lambing traits in East Friesian and Hu crossbred sheep. In this study, 168 healthy and disease-free East Friesian and Hu crossbred sheep were collected from the Jinchang Milk Sheep Experimental Demonstration Base of Northwest Agriculture and Forestry University for whole-genome resequencing, genome-wide association study was performed by GEMMA and SnpEff softwares, enrichment analysis of annotated genes was conducted by KOBAS 3.0 database, and analysis of the chain region around the most significant SNPs with LDBlockShow software. Linkage disequilibrium analysis was performed on the linkage regions around the SNPs by LDBlockShow. SNPs were typed in the GRID2 gene using kompetitive allele-specific PCR (KASP), and the genetic diversity parameters of the two polymorphic loci of the gene were counted and analyzed in association with lambing traits. The results showed that genome-wide association analysis identified 1 163 SNP loci at the significance level on chromosome 6, and candidate genes BMPR1B, PDLIM5, PDHA2, UNC5C, GRID2, NFKB1, TSPAN5, STPG2, and PPP3CA were identified as associated with lambing traits through the annotation of the candidate loci. The two SNPs on GRID2 (g.35685218A>G and g.35685499C>T) were also selected as candidate loci by combining the existing reports and annotations of the most strongly associated regions. Statistical analysis revealed that both loci involved in this study were in Hardy-Weinberg equilibrium at P>0.05, indicating that neither locus had been subjected to over-selection and that both loci were significantly associated with lambing traits in East Friesian and Hu crossbred sheep, with wild-type being dominant at both loci and the means of the two loci increasing with the increasing parities. In summary, the two SNPs in the GRID2 gene have significant effects on lambing number traits in East Friesian and Hu crossbred sheep and can be used as candidate loci for molecular marker-assisted selection. This study provides a solid theoretical basis for improving the lambing rate of East Friesian and Hu crossbred sheep and promoting the progress of genetic breeding of milk sheep.

Key words: East Friesian and Hu crossbred sheep, litter size, genome-wide association studies, GRID2 gene

CLC Number:

S826.2

ZHAO Xueyang, LI Danni, WANG Yuchen, GUO Lei, WANG Li, HUANG Jie, JIAO Yiqiang, AN Xiaopeng, ZHANG Xiyun, ZHANG Lei, SONG Yuxuan. GWAS Analysis of Lambing Traits in East Friesian and Hu Crossbred Sheep and Verification of Candidate Gene GRID2[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4625-4635.

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GWAS Analysis of Lambing Traits in East Friesian and Hu Crossbred Sheep and Verification of Candidate Gene GRID2

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