基于简化基因组测序的永登七山羊遗传多样性分析

doi:10.11843/j.issn.0366-6964.2023.05.016

Abstract

Abstract: The aim of this study was to analyze the genetic diversity and population structure of Yongdeng Qishan sheep by specific-locus amplified fragment sequencing (SLAF-seq), and to provide support for the declaration of Yongdeng Qishan sheep as a newly discovered resource. Four local sheep populations (10 adult healthy ewes randomly selected from each population) in Gansu Province were taken as the research object. Single nucleotide polymorphisms(SNPs) within the whole genome were detected by SLAF technology. Five genetic diversity indexes, such as observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), Shnnon Wiener index (SHI) and Nei diversity index (Nei), were calculated by Perl software. The linkage disequilibrium of each breed was analyzed by PopLDdecay software. elgensoft software was used for principal component analysis (PCA); mega x software was used to build phylogenetic trees of 4 sheep breeds; The structure software was used to analyze the genetic structure of the population; gcta software was used for kinship analysis. A total of 1 658 596 SNPs were detected in 40 sheep individuals, most of which were located in the intergenic region. The Ho, He, PIC, SHI, and Nei values of Yongdeng Qishan sheep were 0.082, 0.277, 0.221, 0.411, and 0.305, respectively. The higher linkage disequilibrium coefficient and slower decay rate in Yongdeng Qishan sheep indicate the low genetic diversity in the population of Yongdeng Qishan sheep. The genetic differentiation coefficients (F_st) between Yongdeng Qishan sheep and Tan sheep, Lanzhou fat tail sheep and Minxian black fur sheep were 0.090 6, 0.098 0 and 0.104 5, respectively, which indicated a high differentiation degree between Yongdeng Qi-shan sheep and the other 3 breeds. Principal component analysis showed obvious differences in clustering patterns among groups, which could distinguish Yongdeng Qishan sheep from Lanzhou fat tail sheep, Tan sheep and Minxian black fur sheep; The results of phylogenetic tree showed that Lanzhou fat tail sheep was clustered as one big branch alone, Yongdeng Qishan sheep and Tan sheep were clustered as another big branch, and the kinship was relatively close, subsequently Yongdeng Qishan sheep was gradually separated into one small branch alone. The structure analysis showed that K=2 was the optimal number of subpopulations, with 4 populations from two original ancestors. As the K value gradually increased, some QS individuals segregated and differed significantly from the genetic background of other breeds. The kinship heat map showed low kinship between individuals of each group. These results indicated that there was low genetic diversity in Yongdeng Qishan sheep and Lanzhou fat tail sheep, and that there was obvious differentiation between Yongdeng Qishan sheep and Tan sheep, Lanzhou fat tail sheep and Minxian black fur sheep. This provides theoretical data for further mining the characteristics of Yongdeng Qishan sheep germplasm resources.

Key words: Yongdeng Qishan sheep, germplasm resources, genetic diversity, population structure, specific-locus amplified fragment sequencing

CLC Number:

MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1939-1950.

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Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing

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