Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip

DENG Yuan; CUI Qingming; CHEN Sihai; ZUO Jianbo; LIU Yingying; ZHU Ji; REN Huibo; HU Xionggui; LI Huali; YU Guojun; CHEN Chen; PENG Yinglin

doi:10.19303/j.issn.1008-0384.2023.11.007

Volume 38 Issue 11

Nov. 2023

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Article Navigation > Fujian Journal of Agricultural Sciences > 2023 > 38(11): 1312-1320

DENG Y, CUI Q M, CHEN S H, et al. Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip [J]. Fujian Journal of Agricultural Sciences，2023，38（11）：1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007

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DENG Y, CUI Q M, CHEN S H, et al. Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip [J]. Fujian Journal of Agricultural Sciences，2023，38（11）：1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007

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Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip

doi: 10.19303/j.issn.1008-0384.2023.11.007

1.
Hunan Institute of Animal and Veterinary Science, Changsha, Hunan　410131, China
2.
Animal Husbandry and Aquatic Products Affairs Center of Luxi County, Luxi, Hunan　416100, China

Received Date: 2023-02-03
Rev Recd Date: 2023-05-14

Available Online: 2023-12-21

Publish Date: 2023-11-28

Abstract

Abstract

Objective Genetic diversity and family structure of a preserved population of Pushi black pig were analyzed using the SNP bead chip for resource conservation. Method SNPs of 79 adult Pushi black pigs consisting of 10 boars and 69 sows were determined using Porcine 50K SNP Beadchips. Software, including Plink, Gmatix, and Mega X, was used to analyze the genetic diversity and phylogenetic relationships to construct phylogenetic structure of the pig population. Result A total of polymorphic 57466 SNP loci were found with an average genotype detection rate of 99.15%. The population showed evidence of inbreeding as the effective Ne was merely 1.5 and the average observed heterozygosity slightly below the expected level. The average distance of IBS was (0.2949±0.0726) and that for the boars (0.277 1±0.091 8). A total of (29.60±16.12) ROHs were detected with 40.5% of them between 0 and 100 Mb in length. The average inbreeding coefficient based on ROH was 0.108. The analysis on IBS distance matrix, G matrix, and population ROHs indicated a close genetic relationship among the individual animals. Based on the evolutionary tree, the population was divided into two families containing boars and one without. Conclusion The population of Pushi black pigs under study had only a few families, which varied greatly in number of members in each family and showed a high degree of inbreeding. Consequently, introducing or creating new lineages to expand the gene pool and reduce inbreeding coefficient for the population seemed imperative.
- Pushi black pig,
- preserved population,
- SNP chip,
- genetic diversity,
- phylogenetic relationship

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References(36)

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