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基于单核苷酸多态性的民猪保种群遗传结构分析。

Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population.

作者信息

Meng Fanbing, Cai Jiancheng, Wang Chunan, Fu Dechang, Di Shengwei, Wang Xibiao, Chang Yang, Xu Chunzhu

机构信息

College of Life Science, Northeast Agricultural University, Harbin 150030, China.

Lanxi Breeding Farm, Lanxi 151500, China.

出版信息

Anim Biosci. 2022 Dec;35(12):1839-1849. doi: 10.5713/ab.21.0571. Epub 2022 Jun 30.

DOI:10.5713/ab.21.0571
PMID:35798042
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9659443/
Abstract

OBJECTIVE

The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree.

METHODS

We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm.

RESULTS

The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (FPED) was significantly different from those estimated from runs of homozygosity (FROH) and single nucleotide polymorphism (FSNP) based on genome. The Pearson correlation coefficient between FROH and FSNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40<r<1.50) and increased significantly in the last 5 generations (r = 2.6). According to the composition of Chinese lineage, we separated the nucleus conservation population (81 individuals) and the candidate conservation population (13 individuals) of Min pig, then the nucleus conservation population of Min pig was divided into 9 families by genomic information matrix.

CONCLUSION

Our study indicated that the genetic diversity of the Min pig conserved population was inadequate. Due to the introgression of European commercial pig breeds and the unscientific breeding process, it is necessary to construct the molecular pedigree of the nucleus conservation population for the Min pig.

摘要

目的

本研究旨在揭示民猪保种群的遗传多样性和独特遗传结构，划分核心保种群，并构建分子系谱。

方法

我们使用KPS猪育种芯片v1 50K对来自兰溪种猪场的民猪保种群中的94个样本（31♂，63♀）进行单核苷酸多态性（SNP）检测。

结果

多态性标记比例（PN）、观察杂合度（Ho）和期望杂合度（He）分别为0.663、0.335和0.330。基于系谱的近交系数（FPED）与基于纯合子片段（FROH）和单核苷酸多态性（FSNP）估计的基因组近交系数有显著差异。FROH与FSNP之间的Pearson相关系数显著（p<0.05）。有效种群含量（Ne）呈持续下降趋势。下降速率在200代至50代前最慢（r = 0.95），然后在50代至5代前略有加速（1.40<r<1.50），在最后5代显著增加（r = 2.6）。根据中国血统组成，我们分离出了民猪的核心保种群（81头个体）和候选保种群（13头个体），然后根据基因组信息矩阵将民猪核心保种群分为9个家系。

结论

我们的研究表明民猪保种群的遗传多样性不足。由于欧洲商业猪品种的渗入和育种过程的不科学，有必要为民猪构建核心保种群的分子系谱。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2996f6eeddf4/ab-21-0571f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/ff4236cff537/ab-21-0571f1.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/3d5c0ca2ffc0/ab-21-0571f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/42c4566aad82/ab-21-0571f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2ed1784e3758/ab-21-0571f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2c6c1085e135/ab-21-0571f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/cb9f5ddab651/ab-21-0571f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2996f6eeddf4/ab-21-0571f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/ff4236cff537/ab-21-0571f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/c229792bed00/ab-21-0571f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/3d5c0ca2ffc0/ab-21-0571f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/42c4566aad82/ab-21-0571f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2ed1784e3758/ab-21-0571f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2c6c1085e135/ab-21-0571f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/cb9f5ddab651/ab-21-0571f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a3c5/9659443/2996f6eeddf4/ab-21-0571f8.jpg

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