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| 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 |
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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.
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Received: 23 May 2023
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Corresponding Authors:
*jnwangjiying@163.com
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