基于全基因组重测序解析皮山红羊群体遗传结构及产羔数候选基因研究

doi:10.16431/j.cnki.1671-7236.2024.02.019

Abstract

Abstract: 【Objective】 Pishan Red sheep is a newly bred prolific breed of sheep distributed in Hotan area of Xinjiang.Based on the whole genome resequencing technology, genetic structure of the population and the selection signal region of litter size traits of Pishan Red sheep were understood at the genome level, and the candidate genes were verified.【Method】 Thirty ewes prolific of Pishan Red sheep with 2-3 lambs born were selected as high fertility group (HF) and 30 prolific Pishan Red sheep ewes with single lambs born were selected as low fertility group (LF).The whole genome of these two populations was re-sequenced.Comprehensive analysis methods such as principal component analysis (PCA), phylogenetic tree, population genetic structure and genome-wide scanning (Fst & θπ) were used to determine candidate regions and further screen candidate genes for lambing traits in Pishan Red sheep.The candidate genes were genotyped by flight mass spectrometry.【Result】 The attenuation curves of linkage disequilibrium (LD) analysis of the high and low fertility groups were similar.The phylogenetic tree showed that the degree of differentiation between the two groups were not obvious.The PCA results showed that the two groups were obviously clustered into a cluster, individuals were out of the group, and their location and relationship were consistent with the evolutionary tree structure and population structure results.The window with both the Top 1% Z(Fst) value and the θπ value were set as the candidate region, and a total of 229 strong selection signals were annotated.The annotated genes in HF and LF groups were 86 and 143, respectively.Among them, 42 candidate genes that might be related to reproductive traits were screened, such as MARF1, CHGA, BMPR1B, IMMP2L, CDK14, ZDHHC3, CCDC71, DSCAML1, LIMK2, P2RY14, etc.Through GO function and KEGG pathway analysis, it was found that the GO significant enrichment terms were in the regulation of sodium ion transmembrane transporter activity, regulation of apoptosis process, sodium ion channel regulator activity, G protein-coupled receptor binding, G protein-coupled purine nucleotide receptor activity and other pathways.The KEGG significant enrichment pathways were mainly related to signal transmission, signal pathway, material metabolism and so on.The results of genotyping showed that 11 SNPs of MARF1 gene existed in the population of Pishan Red sheep and g.14023542 T＞A, g.14036507 A＞G and g.14046123 C＞T loci were significantly associated with the average litter size of the population, and the first two loci showed strong linkage relationship (r²＞0.3), and the TT genotype of g.14023542 T＞A locus had the highest average litter size (1.901±0.675).【Conclusion】 The genetic background of the two groups of high and low fertility groups was similar, and there was a certain degree of differentiation, but the differentiation was not obvious.MARF1, CHGA, BMPR1B, IMMP2L, CDK14, ZDHHC3, CCDC71, DSCAML1, LIMK2, P2RY14 and other genes might be candidate genes affecting the lambing traits in Pishan Red sheep.The three SNPs of MARF1 gene could be used as potential molecular breeding markers for lambing traits of Pishan Red sheep.

Key words: Pishan Red sheep; whole genome resequencing; selection signal; litter size

CLC Number:

S826.8⁺9

SHI Lan, MA Meilan, MUHETAPA Maimaitijiang, YANG Huiguo, YIMING Sulaiman. Study on the Genetic Structure and Litter Size Candidate Genes of Pishan Red Sheep Population Based on Whole Genome Resequencing[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(2): 624-638.

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Study on the Genetic Structure and Litter Size Candidate Genes of Pishan Red Sheep Population Based on Whole Genome Resequencing

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