Identification of QTLs and candidate genes associated with seed germination capacity under heat stress in watermelon

Background Heat stress (HS) severely inhibits seed germination of direct-seeded crops such as watermelon. However, the genetic basis governing germination capacity under HS remains largely unclear. Methods An F2 population consisting of 132 individuals was developed from a cross between the heat-tolerant inbred line 8R098 (high germination under HS) and the heat-sensitive line 8R122 (low germination under HS). SNP-trait association analysis and linkage mapping were employed to dissect the genetic basis of seed germination capacity under HS. Germination-stage RNA-seq of high- and low-germination accessions under HS was performed to screen the DEGs. Results Heat tolerance for seed germination segregated at a high-to-low ratio of 1: 3, indicating a nearly recessive genetic nature. A major QTL for HS germination tolerance was fine-mapped to the interval of 29.05~33.41 Mb on chromosome 10, harboring 472 annotated genes. RNA-seq identified 1,519 HS-responsive DEGs enriched in plant hormone signal transduction and metabolic pathways. A total of 101 putative functional non-synonymous SNPs (nsSNPs) were found in 76 protein-coding genes within this QTL region. Integrative analysis of DEGs and nsSNP-containing genes, followed by filtering genes with inconsistent expression trends, retained four candidate genes with allelic variations, namely Cla97C10G205480, Cla97C10G205850, Cla97C10G204760 , and Cla97C10G203920 . Conclusion Our findings reveal candidate genes regulating thermotolerance during watermelon seed germination and provide useful genetic resources for breeding watermelon varieties with improved heat tolerance at the germination stage.