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Background <p>The genetic basis of the phenotypic diversity of pigs is regulated by variants across the genome, especially the trait of early puberty, which is a crucial trait for enhancing the reproductive ability of pigs and the economy of the pig industry. However, the genetic basis of the early puberty trait in pigs remains largely unknown.</p> Results <p>Here, we report a comprehensive genomic variation map for pigs based on the resequencing of 493 accessions representing 59 different pig breeds or populations, which included 5,211,469 single-nucleotide polymorphisms (SNPs) and 487,725 small insertion/deletion structure variants (InDels). This sets included 45,640 high-quality structural variants (SVs). Our results suggested that Hanjiang black (HJB) pigs cluster with Jianghai-type pigs at the genetic level and that the genome characteristics of some HJB individuals exhibit a certain degree of European pig features. Using introgression and signature selection analysis, we identified several candidate genes associated with bone development and early puberty traits, such as <i>TBX5</i>, <i>PAPPA2</i>, <i>IGFBP3</i>, and <i>MKRN3</i>. Additionally, the GWAS and differential expression analysis results suggested that the <i>PAPPA2</i> gene is associated with early puberty in pigs. </p> Conclusions <p>This study revealed that past introgression events could impact the agronomical traits of pigs and contribute raw material of genetics and breeding in pig. Moreover, our results suggest that the <i>PAPPA2</i> gene is a candidate gene associated with early sexual maturity in pigs and the genomic analysis provided important reference value for studying economic traits for pigs.</p>

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Whole-genome resequencing reveals positive selection and introgression signatures and genetic loci associated with early puberty traits in Chinese indigenous pigs

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年6月10日

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  • Minghao Cao,
  • Tiantian Yuan,
  • Dong Li,
  • Yulong Wang,
  • Lin Zhang,
  • Jingchun Sun,
  • Guangquan Lv,
  • Rongrong Ding,
  • Taiyong Yu

摘要

Background

The genetic basis of the phenotypic diversity of pigs is regulated by variants across the genome, especially the trait of early puberty, which is a crucial trait for enhancing the reproductive ability of pigs and the economy of the pig industry. However, the genetic basis of the early puberty trait in pigs remains largely unknown.

Results

Here, we report a comprehensive genomic variation map for pigs based on the resequencing of 493 accessions representing 59 different pig breeds or populations, which included 5,211,469 single-nucleotide polymorphisms (SNPs) and 487,725 small insertion/deletion structure variants (InDels). This sets included 45,640 high-quality structural variants (SVs). Our results suggested that Hanjiang black (HJB) pigs cluster with Jianghai-type pigs at the genetic level and that the genome characteristics of some HJB individuals exhibit a certain degree of European pig features. Using introgression and signature selection analysis, we identified several candidate genes associated with bone development and early puberty traits, such as TBX5, PAPPA2, IGFBP3, and MKRN3. Additionally, the GWAS and differential expression analysis results suggested that the PAPPA2 gene is associated with early puberty in pigs.

Conclusions

This study revealed that past introgression events could impact the agronomical traits of pigs and contribute raw material of genetics and breeding in pig. Moreover, our results suggest that the PAPPA2 gene is a candidate gene associated with early sexual maturity in pigs and the genomic analysis provided important reference value for studying economic traits for pigs.