Acta Veterinaria et Zootechnica Sinica ›› 2023, Vol. 54 ›› Issue (9): 3631-3641.doi: 10.11843/j.issn.0366-6964.2023.09.005

• ANIMAL GENETICS AND BREEDING • Previous Articles     Next Articles

Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs

YUAN Wei1,2,3, BI Huan1,2,3, ZHANG Yudan1,2,3, ZHANG Yiyu1,2,3, GU Xiaolong4, YANG Hongwen5, CHEN Wei1,2,3*   

  1. 1. Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountain Region of Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China;
    2. Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China;
    3. Institute of Xiang Pig Research, Guizhou University, Guiyang 550025, China;
    4. Guizhou Dekang Agriculture and Animal Husbandry Co. Ltd., Guiyang 550025, China;
    5. Guizhou Provincial Station for Animal Genetic Resources Management, Guiyang 550025, China
  • Received:2023-03-17 Published:2023-09-22

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Abstract: The purpose was to unveil the genetic disparities between the Jianbai and Congjiang Xiang pigs breeds, enhance the understanding of their conservation status, genetic diversity, population structure, and adaptive evolution through whole-genome selection signal analysis. The 2-year-old Congjiang and Jianbai Xiang pigs were randomly selected and divided into two groups of 5 pigs each. Whole-genome resequencing was performed on Jianbai and Congjiang Xiang pigs, and the sequencing data was aligned to the pig reference genome Sscrofa 11.1 using the bwa software. Subsequently, the GATK software was used for variant detection and filtering of SNPs and INDELs. Additionally, population genetic diversity analysis, including effective population size, proportion of polymorphic loci, observed heterozygosity, and expected heterozygosity, was carried out using Plink and SNeP software. The population selection signals were analyzed using the vcftools software, and the selected genomic regions were subjected to KEGG and GO pathway analyses. After SNP and INDEL analysis, it was found that there were 16 158 002 common SNPs in the populations of Jianbai and Congjiang Xiang pigs, with 6 863 992 SNPs unique to Congjiang and 4 275 660 unique to Jianbai. The common INDELs were 3 275 375, with 1 674 081 INDELs unique to Congjiang and 1 114 248 unique to Jianbai. Starting from the sampling time point, the effective population size of both Congjiang and Jianxiang pig populations could be traced back to 18 individuals 13 generations ago. The Congjiang breed displayed a higher proportion of polymorphic loci, with a value of 0.875 7, whereas both populations had observed heterozygosity values exceeding the expected heterozygosity.Nucleotide diversity was less than 0.5% for both breeds, and Tajima's D was greater than 0, with ROD values of 0.553 1 and Fst values of 0.736 2. KEGG and GO enrichment analyses showed that the genetic differences between Jianbai and Congjiang Xiang pigs involved multiple pathways and gene functions, including axon guidance, ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, lipoic acid metabolism, cGMP-PKG signaling pathway, MAPK signaling pathway, nucleotide excision repair, aspirin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. There are a certain loss of population polymorphism and a high degree of population divergence between the Jianbai and Congjiang pig populations. There is clear population differentiation between the two breeds, and both genomes exhibit a substantial number of alleles at intermediate frequencies. It is necessary to enhance the genetic diversity within the Congjiang and Jianbai Xiang pig populations and reduce the risk of decreased purity due to the introduction of foreign lineages.

Key words: whole genome, selection signals, Xiang pig, genetic differences

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