Integrated Meta-QTL analysis and transcriptomic profiling reveal genomic regions for fruit quality, abiotic and biotic stress resilience in cucumber (Cucumis sativus L.).
TL;DR
This study conducted a comprehensive Meta-QTL analysis by integrating 647 initial QTLs from 40 independent studies published between 2003 and 2024, identifying 38 robust mQTLs associated with fruit quality, biotic and abiotic stress tolerance and key drivers of fruit quality.
Abstract
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.