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<p>Cold and salinity stresses are major abiotic constraints limiting cucumber (<i>Cucumis sativus</i> L.) productivity worldwide. This study investigated the genetic basis of tolerance to cold and salinity stress using a diverse panel of 134 cucumber accessions. Plants were phenotyped under controlled stress conditions using standardized scoring indices, revealing broad and reproducible variation for both traits. Analysis of variance confirmed highly significant genotypic effects for cold tolerance and salinity stress survival (<i>p</i> &lt; 0.001), demonstrating sufficient phenotypic resolution for association mapping. Genotyping-by-sequencing followed by stringent quality control yielded 18,383 high-confidence SNP markers distributed across the genome. Genome-wide association analyses were conducted using a multilocus mixed-model framework accounting for population structure and kinship, with defined significance thresholds and false discovery rate correction. Seven loci were significantly associated with cold stress tolerance, while three loci were associated with salinity stress tolerance, each explaining moderate proportions of phenotypic variance. Candidate genes underlying cold tolerance loci encode proteins involved in diverse biological functions, including transcriptional regulation, chromatin remodeling, signal transduction, protein turnover, and cellular homeostasis, indicating a multicomponent genetic basis of cold stress adaptation. In contrast, candidate genes associated with salinity tolerance were mainly related to membrane-associated processes and stress signaling pathways. Expression analysis using quantitative RT-PCR in contrasting tolerant and sensitive accessions revealed stress-responsive differential expression patterns for several candidate genes. Notably, cold and salinity tolerance were governed by largely distinct sets of genes, suggesting stress-specific genetic architectures. Overall, this study provides genomic insights into abiotic stress tolerance in cucumber and identifies candidate genes and molecular markers with potential utility for functional validation and breeding applications.</p>

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Genome-Wide Association Study Identifies Candidate Genes for Cold and Salinity Stress Tolerance in Cucumber

  • 期刊论文

  • 发表日期：

    2026年7月14日

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  • Saeed Omrani,
  • Mahdi Badri Anarjan,
  • Shahida Begum,
  • Sanghyeob Lee

摘要

Cold and salinity stresses are major abiotic constraints limiting cucumber (Cucumis sativus L.) productivity worldwide. This study investigated the genetic basis of tolerance to cold and salinity stress using a diverse panel of 134 cucumber accessions. Plants were phenotyped under controlled stress conditions using standardized scoring indices, revealing broad and reproducible variation for both traits. Analysis of variance confirmed highly significant genotypic effects for cold tolerance and salinity stress survival (p < 0.001), demonstrating sufficient phenotypic resolution for association mapping. Genotyping-by-sequencing followed by stringent quality control yielded 18,383 high-confidence SNP markers distributed across the genome. Genome-wide association analyses were conducted using a multilocus mixed-model framework accounting for population structure and kinship, with defined significance thresholds and false discovery rate correction. Seven loci were significantly associated with cold stress tolerance, while three loci were associated with salinity stress tolerance, each explaining moderate proportions of phenotypic variance. Candidate genes underlying cold tolerance loci encode proteins involved in diverse biological functions, including transcriptional regulation, chromatin remodeling, signal transduction, protein turnover, and cellular homeostasis, indicating a multicomponent genetic basis of cold stress adaptation. In contrast, candidate genes associated with salinity tolerance were mainly related to membrane-associated processes and stress signaling pathways. Expression analysis using quantitative RT-PCR in contrasting tolerant and sensitive accessions revealed stress-responsive differential expression patterns for several candidate genes. Notably, cold and salinity tolerance were governed by largely distinct sets of genes, suggesting stress-specific genetic architectures. Overall, this study provides genomic insights into abiotic stress tolerance in cucumber and identifies candidate genes and molecular markers with potential utility for functional validation and breeding applications.