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Background <p><i>Larimichthys crocea</i>, commonly known as large yellow croaker, is a marine species of significant commercial value in East Asia. However, overfishing and long-term artificial breeding have raised concerns about the genetic diversity and adaptive capacity of farmed populations. Understanding the genetic differentiation and environmental adaptation between wild and cultured populations is crucial for conservation efforts and sustainable aquaculture development.</p> Results <p>Whole-genome resequencing of 195 individuals revealed: (1) Significant genetic divergence between wild and farmed populations (764,656 SNPs), with cultured stocks showing 18–22% lower heterozygosity; (2) 153 selective sweep regions containing 739 candidate genes, including <i>hsp40</i> (thermal adaptation) and <i>ndufs6</i> (energy metabolism); (3) Genome-environment association identifying 9,265 loci linked to salinity, temperature, and dissolved oxygen (RDA adj. <i>R²</i>=0.036, <i>P</i> &lt; 0.001); (4) Strong isolation-by-environment patterns (Mantel <i>R²</i>=0.89, <i>P</i> = 0.042) outweighing geographical distance effects.</p> Conclusions <p>Our results demonstrate that environmental factors rather than geography drive genetic differentiation in <i>L. crocea</i>, with aquaculture populations exhibiting signatures of both artificial selection and reduced adaptive potential. These findings provide actionable insights for conservation management and marker-assisted breeding to maintain genetic diversity in cultured stocks.</p>

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Genomic differentiation between wild and domesticated populations of large yellow croaker (Larimichthys crocea): environmental impacts

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月15日

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  • Lihua Jiang,
  • Xingyu Gao,
  • Kaifen Zhang,
  • Kaida Xu,
  • Jialang Zheng,
  • Lifan Liu,
  • Weihua Song,
  • Shun Chen,
  • Xiaojun Yan

摘要

Background

Larimichthys crocea, commonly known as large yellow croaker, is a marine species of significant commercial value in East Asia. However, overfishing and long-term artificial breeding have raised concerns about the genetic diversity and adaptive capacity of farmed populations. Understanding the genetic differentiation and environmental adaptation between wild and cultured populations is crucial for conservation efforts and sustainable aquaculture development.

Results

Whole-genome resequencing of 195 individuals revealed: (1) Significant genetic divergence between wild and farmed populations (764,656 SNPs), with cultured stocks showing 18–22% lower heterozygosity; (2) 153 selective sweep regions containing 739 candidate genes, including hsp40 (thermal adaptation) and ndufs6 (energy metabolism); (3) Genome-environment association identifying 9,265 loci linked to salinity, temperature, and dissolved oxygen (RDA adj. R²=0.036, P < 0.001); (4) Strong isolation-by-environment patterns (Mantel R²=0.89, P = 0.042) outweighing geographical distance effects.

Conclusions

Our results demonstrate that environmental factors rather than geography drive genetic differentiation in L. crocea, with aquaculture populations exhibiting signatures of both artificial selection and reduced adaptive potential. These findings provide actionable insights for conservation management and marker-assisted breeding to maintain genetic diversity in cultured stocks.