Bacterial soft rot (BSR) caused by Pectobacterium carotovorum subsp. brasiliense (Pcb) is a serious bacterial disease which negatively impact yield and quality in cucumber. However, the genetic mechanism of BSR resistance in cucumber has not been reported. Here, we investigated the BSR resistance of 119 cucumber core germplasm worldwide at the seedling stage and identified 26 accessions highly resistant to BSR. A total of 1 642 740 single-nucleotide polymorphisms (SNPs) were used to conduct GWAS, and five loci associated with BSR resistance were detected on four chromosomes: gBSR2.1, gBSR2.2, gBSR3.1, gBSR4.1 and gBSR5.1. Based on haplotype analysis, sequence polymorphisms, functional annotation and qRT-PCR analysis, six candidate genes were identified within the five loci. CsaV3_2G014450, CsaV3_2G014490, CsaV3_2G016000, CsaV3_3G000850, CsaV3_4G033150, and CsaV3_5G000390 each had nonsynonymous SNPs, and were significantly up-regulated in the resistant genotypes after inoculation. And CsaV3_5G000390 in the susceptible genotype was significantly up-regulated after inoculation. The identification of these candidate genes lays a foundation for understanding the genetic mechanism of BSR resistance in cucumber. Generally, our study mined genes associated with BSR resistance in cucumber seedlings and will assist the breeding of BSR-resistant cucumber cultivars.

Heat stress causes overgrowth, leaf dryness and fruit malformation, which negatively impacts cucumber quality and yield. Yet, in spite of the devastating consequences of this abiotic stress, few genes for heat tolerance in cucumber have been identified. Here, the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments, with naturally occurring high temperatures over two years. Seventeen of the 88 accessions were identified as highly heat-tolerant. Using a genome-wide association study, five loci (gHII3.1, gHII3.2, gHII3.3, gHII4.1 and gHII6.1) on three chromosomes associated with heat tolerance were detected. Pairwise linkage disequilibrium correlation, sequence polymorphisms, and qRT-PCR analyses at these loci, identified five candidate genes predicted to be casual for heat stress response in cucumber. CsaV3_3G04883, CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs, and were significantly up-regulated by heat stress in the heat-tolerant genotypes. CsaV3_3G031890 was also induced by heat stress, but in the heat-sensitive genotypes, and sequence polymorphism was only found in the promoter region. Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms. Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge. It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.

Gummy stem blight (GSB), caused by Didymella bryoniae, is a serious fungal disease that leads to decline in cucumber yield and quality. The molecular mechanism of GSB resistance in cucumber remains unclear. Here, we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages. A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified, of which some are co-localized to previously mapped Quantitative trait loci (QTLs) for GSB resistance (gsb3.2/gsb3.3, gsb5.1, and gsb-s6.2). Based on haplotype analysis and expression levels after inoculation, four candidate genes were identified within the region identified by both Genome-wide association study (GWAS) and previous identified QTL mapping, including Csa3G129470 for gsb3.2/gsb3.3, Csa5G606820 and Csa5G606850 for gsb5.1, and Csa6G079730 for gsb-s6.2. The novel GSB resistant accessions, significant SNPs, and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.

Cucumber is one of the most widely consumed vegetables worldwide, and the fruit spine is an important fruit quality trait. Expansins play critical roles in fruit development; however, the regulation of expansins in cucumber fruit spine development has not been reported. In this study, 33 expansin genes were identified in the cucumber genome V3; additionally, expansin genes in Citrullus lanatus, Cucumis melo, Cucurbita maxima, Lagenaria siceraria, and Benincasa hispida were also identified. Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species. Phylogenetic analysis showed that C. maxima was derived earlier than the other five Cucurbitaceae species. The expression of CsEXPA2, CsEXPA14, and CsEXLA3 varied in cucumber lines with different fruit spine densities. A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene (ns) interacts with CsEXLA2, which may be involved in the development of the numerous spines in cucumber. These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.