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Background <p>Dengchuan cattle, the only dairy-purpose breed among Chinese indigenous yellow cattle, possesses strong environmental adaptability, tolerance to coarse forage, and excellent disease resistance. Its milk contains high levels of protein, fat, and total solids. However, intensive crossbreeding with high-yield Holstein cattle has drastically shrunk its population and increased inbreeding, pushing this valuable breed to the brink of extinction.</p> Results <p>In the present study, using inter-population selection scans (<i>F</i><sub><i>ST</i></sub> and XP-EHH) based on SNPs and structural variants (SVs), we identified 34 candidate genes under selections between Dengchuan and Dianzhong cattle. Within the Dengchuan population, iHS analysis detected 1,189 selected regions encompassing 790 candidate genes. By integrating SNP- and SV-based cis expression quantitative trait loci (cis-eQTL) analyses, we identified 100 significant SNPs associated with 100 genes and 87 SVs associated with 81 candidate genes. Integration of selection signatures with eQTL results revealed seven overlapping genes (<i>GUCY2C</i>, <i>IFI47</i>, <i>LOC132342100</i>, <i>PNPLA7</i>, <i>RAB19</i>, <i>TMEM132B</i>, and <i>A2M</i>). Functional enrichment and QTL annotation indicated that selected genes and eGenes are mainly involved in immunity, environmental adaptation, and milk-related traits. Collectively, we identified candidate genes associated with key traits, including immunity (e.g., <i>CCDC50</i> and <i>BOLA-DQA5</i>), milk production (e.g., <i>CTNND2</i>, <i>TBC1D5</i>, and <i>A2M</i>), and environmental adaptation (e.g., <i>PLCB4</i> and <i>RRAGA</i>).</p> Conclusions <p>This study reveals the genetics relationship between Dengchuan and Dianzhong cattle, identifies genetic factors associated with immunity, environmental adaptation, and milk quality in Dengchuan cattle. Notably, despite the restricted sample size inherent to studying an endangered breed, our integrative approach yielded highly informative results, demonstrating the power of such strategies for small yet valuable native populations.</p>

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Integrated selection scans and cis-eQTL analyses reveal genes and variants associated with milk quality, immunity, and adaptation in endangered Dengchuan cattle

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月20日

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  • Kunjiang Feng,
  • Yongyan Liu,
  • Yaman Li,
  • Mei Yang,
  • Zongyou Huang,
  • Lingyue Wen,
  • Heng Xiao,
  • Shanyuan Chen

摘要

Background

Dengchuan cattle, the only dairy-purpose breed among Chinese indigenous yellow cattle, possesses strong environmental adaptability, tolerance to coarse forage, and excellent disease resistance. Its milk contains high levels of protein, fat, and total solids. However, intensive crossbreeding with high-yield Holstein cattle has drastically shrunk its population and increased inbreeding, pushing this valuable breed to the brink of extinction.

Results

In the present study, using inter-population selection scans (FST and XP-EHH) based on SNPs and structural variants (SVs), we identified 34 candidate genes under selections between Dengchuan and Dianzhong cattle. Within the Dengchuan population, iHS analysis detected 1,189 selected regions encompassing 790 candidate genes. By integrating SNP- and SV-based cis expression quantitative trait loci (cis-eQTL) analyses, we identified 100 significant SNPs associated with 100 genes and 87 SVs associated with 81 candidate genes. Integration of selection signatures with eQTL results revealed seven overlapping genes (GUCY2C, IFI47, LOC132342100, PNPLA7, RAB19, TMEM132B, and A2M). Functional enrichment and QTL annotation indicated that selected genes and eGenes are mainly involved in immunity, environmental adaptation, and milk-related traits. Collectively, we identified candidate genes associated with key traits, including immunity (e.g., CCDC50 and BOLA-DQA5), milk production (e.g., CTNND2, TBC1D5, and A2M), and environmental adaptation (e.g., PLCB4 and RRAGA).

Conclusions

This study reveals the genetics relationship between Dengchuan and Dianzhong cattle, identifies genetic factors associated with immunity, environmental adaptation, and milk quality in Dengchuan cattle. Notably, despite the restricted sample size inherent to studying an endangered breed, our integrative approach yielded highly informative results, demonstrating the power of such strategies for small yet valuable native populations.