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DOI: https://doi.org/10.5713/ajas.20.0339    [Accepted] Published online October 19, 2020.
HD-SNP chip-based conservation genetic analysis of indigenous pig breeds from Shandong Province, China
Yanping Wang1  , Xueyan Zhao1  , Cheng Wang1  , Wenwen Wang2  , Qing Zhang2  , Ying Wu1,3  , Jiying Wang1,* 
1Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
2Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai' an 271018, China
3Shandong Xinji Animal Husbandry Co., Ltd, Tai' an 271018, China
Correspondence:  Jiying Wang, Tel: +86-0531-88611680, Fax: +86-0531-88611680, Email: jnwangjiying@163.com
Received: 16 May 2020   • Revised: 10 July 2020   • Accepted: 18 October 2020
Abstract
Objective
Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme.
Methods
Here, an HD-SNP chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds.
Results
The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics (FST) value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (FST values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the PCA scatterplot and small population differentiation (average of 0.1253) among them.
Conclusion
Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.
Keywords: Pig; Indigenous Breeds; Genetic Diversity; Population Structure; Conservation


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