Scholarlink

<p>Cucumber is a globally significant vegetable crop whose production and market value are affected by fruit quality and resilience to diverse environmental stressors. Despite the identification of numerous Quantitative Trait Loci (QTL) over the last two decades, their direct application in breeding has been hindered by inconsistent genomic positions and broad confidence intervals. In this study, we conducted a comprehensive Meta-QTL (mQTL) analysis by integrating 647 initial QTLs from 40 independent studies published between 2003 and 2024. Using a high-density consensus map containing 9,299 markers, we projected 531 QTLs, identifying 38 robust mQTLs associated with fruit quality, biotic and abiotic stress tolerance. The identified mQTLs exhibited a significant reduction in the average confidence interval (CI) by 5.3-fold, compared to the average CI of the original QTLs and phenotypic variance explained values reaching up to 49.81% (mQTL 6.8). Our results identifying specific genomic hotspots on chromosomes 1, 3, 5, and 6 that harbor high-confidence candidate genes responsible for stress tolerance and fruit quality. Comparative analysis with seven independent genome-wide association studies validated 16 mQTL regions, confirming their stability across diverse genetic backgrounds. Biotic stress resilience was linked to immune regulators such as <i>LRK10L2</i> and <i>MLO-like protein 12</i>, while abiotic stress tolerance was anchored by genes like <i>NCED5</i> (cold), <i>ClpB1</i> (heat), and <i>MYB44-like</i> (waterlogging). Furthermore, we identified key drivers of fruit quality, including <i>Expansin-A4</i> and <i>CNR2</i> for dimensions, <i>CsWOX9</i> for epidermal spine initiation, and <i>Hd3a</i> for flowering phenology. Transcriptomic profiling provided robust expression support for these prioritized candidate genes within the target mQTL intervals. The markers linked to these genes serve as robust tools for marker-assisted selection and fine mapping, offering precise targets for the development of climate-resilient, high-quality cucumber cultivars. </p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Integrated Meta-QTL analysis and transcriptomic profiling reveal genomic regions for fruit quality, abiotic and biotic stress resilience in cucumber (Cucumis sativus L.)

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月4日

查看全文
  • Basu Sudhakar Reddy,
  • Sanjay Singh,
  • Sarika Jaiswal,
  • Shyam Sundar Dey,
  • Mir Asif Iquebal

摘要

Cucumber is a globally significant vegetable crop whose production and market value are affected by fruit quality and resilience to diverse environmental stressors. Despite the identification of numerous Quantitative Trait Loci (QTL) over the last two decades, their direct application in breeding has been hindered by inconsistent genomic positions and broad confidence intervals. In this study, we conducted a comprehensive Meta-QTL (mQTL) analysis by integrating 647 initial QTLs from 40 independent studies published between 2003 and 2024. Using a high-density consensus map containing 9,299 markers, we projected 531 QTLs, identifying 38 robust mQTLs associated with fruit quality, biotic and abiotic stress tolerance. The identified mQTLs exhibited a significant reduction in the average confidence interval (CI) by 5.3-fold, compared to the average CI of the original QTLs and phenotypic variance explained values reaching up to 49.81% (mQTL 6.8). Our results identifying specific genomic hotspots on chromosomes 1, 3, 5, and 6 that harbor high-confidence candidate genes responsible for stress tolerance and fruit quality. Comparative analysis with seven independent genome-wide association studies validated 16 mQTL regions, confirming their stability across diverse genetic backgrounds. Biotic stress resilience was linked to immune regulators such as LRK10L2 and MLO-like protein 12, while abiotic stress tolerance was anchored by genes like NCED5 (cold), ClpB1 (heat), and MYB44-like (waterlogging). Furthermore, we identified key drivers of fruit quality, including Expansin-A4 and CNR2 for dimensions, CsWOX9 for epidermal spine initiation, and Hd3a for flowering phenology. Transcriptomic profiling provided robust expression support for these prioritized candidate genes within the target mQTL intervals. The markers linked to these genes serve as robust tools for marker-assisted selection and fine mapping, offering precise targets for the development of climate-resilient, high-quality cucumber cultivars.