Genome-wide association study identifies candidate genes for bacterial soft rot resistance in cucumber seedlings

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.