Analysis of Genetic Diversity and Population Structure Changes of Dapulian pigs (Sus scrofa) Based on Genomic Information
ZHANG Xin1, ZHANG Ting1, WANG Huai-Zhong2,3, YANG Qing2,3, GAO Shi-Chao2,3, WANG Yan-Ping2,3, WANG Ji-Ying2,3,*
1 Jining Animal Husbandry and Veterinary Development Center, Jining 272004, China; 2 Institute of Animal Science and Veterinary Medicine/Shandong Key Laboratory of Animal Disease Control and Breeding, Shandong Academy of Agricultural Sciences, Jinan 250100, China; 3 Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan 250100, China
摘要由于系谱错误、留种不均衡和杂种个体混入等原因,地方猪保种过程中可能会出现群体近交系数增速过快、个体间亲缘关系不明等问题。为分析大蒲莲猪(Sus scrofa)保种群的遗传多样性和群体结构,监测保种群2017~2022年期间基因组信息变化情况,本研究利用高密度SNP芯片对110头大蒲莲猪全基因组SNP进行扫描,对比分析了2017年和2022年大蒲莲猪保种核心群样本的遗传多样性、近交系数、系统发生树以及与引进猪的关系。结果表明：1) 2022年大蒲莲猪样本的观察杂合度(observe heterozygosity, HO)(0.356 vs 0.292)、期望杂合度(expected heterozygosity, HE)(0.342 vs 0.285)和遗传距离(0.270 vs 0.233)均高于2017年样本,血缘同源(identity by descent, IBD)比例(0.108 vs 0.127)和基于纯合性片段(runs of homozygosity, ROH)计算的基因组近交系数FROH (0.108 vs. 0.163)低于2017年样本,系统发生树结构与2017年样本相似但家系间的均衡性增加,说明2022年核心群的遗传多样性比2017年有所提高,群体结构有所改善。2) 2022年样本的HO和HE比值(1.041 vs. 1.025)高于2017年样本,与引进品种的主成分分析(PCA)中,2022年样本比2017年样本更偏向于引进品种猪,说明大蒲莲猪中混有一定的其他群体血缘,且2022年大蒲莲猪群体中其他品种的血缘比2017年有所增加。本研究分析了大蒲莲猪群体变化趋势,为大蒲莲猪进一步的保种与科学利用提供参考依据。
Abstract：Due to pedigree errors, unbalanced breeding and hybrid individuals introgression, population coefficient of inbreeding may increase too fast and the genetic relationship between individuals may be unclear in the process of local pig (Sus scrofa) conservation. In order to analyze the genetic diversity and population structure of the Dapulian conserved population, and monitor the genomic information changes of the conserved population during the 5 years from 2017 to 2022, in this study, 110 Dapulian pigs were genotyped using high-density SNP array, and the genetic diversity, inbreeding coefficient, phylogenetic tree and the relationship with the imported pigs of Dapulian pigs of 2017 and 2022 were comparatively analyzed based on genome-wide SNP markers. The results showed that: 1) Compared with those of 2017, the samples of 2022 had higher observe heterozygosity (HO) (0.356 vs. 0.292), expected heterozygosity (HE) (0.342 vs. 0.285) and genetic distance (0.270 vs. 0.233), smaller identity by descent (IBD) proportion (0.108 vs. 0.127) and genomic inbreeding coefficients (FROH) based on run of homozygosity (ROH) (0.108 vs. 0.163), similar phylogenetic tree but increased balance between families, indicating the samples of 2022 had higher genetic diversity and improved population structure than those of 2017. 2) The samples of 2022 had higher HO and HE ratio (1.041) than those of 2017 (1.025), and the sample of 2022 were more influenced by the imported pig breeds than 2017 as shown by principal component analysis (PCA) among Dapulian pigs and 5 imported breeds. These results demonstrated that Dapulian pigs had been impacted by other pig breeds, and the impact on the conserved population of 2022 was greater than on that of 2017. This study analyzed the change trend of Dapulian pigs population. It provides scientific reference basis for further conservation and utilization of Dapulian pigs.
张鑫, 张婷, 王怀中, 杨晴, 高世超, 王彦平, 王继英. 基于基因组信息的大蒲莲猪遗传多样性和群体结构变化分析[J]. 农业生物技术学报, 2024, 32(5): 1093-1101.
ZHANG Xin, ZHANG Ting, WANG Huai-Zhong, YANG Qing, GAO Shi-Chao, WANG Yan-Ping, WANG Ji-Ying. Analysis of Genetic Diversity and Population Structure Changes of Dapulian pigs (Sus scrofa) Based on Genomic Information. 农业生物技术学报, 2024, 32(5): 1093-1101.
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