Key message A single recessive gene for complete resistance to powdery mildew and a major-effect QTL for partial resistance to downy mildew were co-localized in a Cucumis hystrix introgression line of cucumber. Downy mildew (DM) and powdery mildew (PM) are two major foliar diseases in cucumber. DM resistance (DMR) and PM resistance (PMR) may share common components; however, the genetic relationship between them remains unclear. IL52, a Cucumis hystrix introgression line of cucumber which has been reported to possess DMR, was recently identified to exhibit PMR as well. In this study, a single recessive gene pm for PMR was mapped to an approximately 468-kb region on chromosome 5 with 155 recombinant inbred lines (RILs) and 193 F plants derived from the cross between a susceptible line 'changchunmici' and IL52. Interestingly, pm was co-localized with the major-effect DMR QTL dm5.2 confirmed by combining linkage analysis and BSA-seq, which was consistent with the observed linkage of DMR and PMR in IL52. Further, phenotype-genotype correlation analysis of DMR and PMR in the RILs indicated that the co-localized locus pm/dm5.2 confers complete resistance to PM and partial resistance to DM. Seven candidate genes for DMR were identified within dm5.2 by BSA-seq analysis, of which Csa5M622800.1, Csa5M622830.1 and Csa5M623490.1 were also the same candidate genes for PMR. A single nucleotide polymorphism that is present in the 3' untranslated region (3'UTR) of Csa5M622830.1 co-segregated perfectly with PMR. The GATA transcriptional factor gene Csa5M622830.1 may be a likely candidate gene for DMR and PMR. This study has provided a clear evidence for the relationship between DMR and PMR in IL52 and sheds new light on the potential value of IL52 for cucumber DMR and PMR breeding program.

Leaf color mutants are the ideal materials to explore the pathways of chlorophyll metabolism, chloroplast development and photosynthesis system. In this study, a new virescent leaf mutant 104Y was identified by spontaneous mutation, whose cotyledon and upper five true leaves were yellow color. The yellow true leaves gradually turned green from top to bottom with increased chlorophyll contents. Genetic analysis indicated that the virescent leaf was controlled by one single recessive gene v-2, which was accurately mapped into 36.0-39.7 Mb interval on chromosome 3 by using BSA-seq and linkage analysis. Fine mapping analysis further narrowed v-2 into 73-kb genomic region including eight genes with BC 1 and F 2 populations. Through BSA-seq and cDNA sequencing analysis, only one nonsynonymous mutation existed in the Csa3G890020 gene encoding auxin F-box protein was identified, which was predicted as the candidate gene controlling virescent leaf. Comparative transcriptome analysis and quantitative real-time PCR analysis revealed that the expression level of Csa3G890020 was not changed between EC1 and 104Y. However, RNA-seq analysis identified that the key genes involved in chlorophyll biosynthesis and auxin signaling transduction network were mainly down-regulated in 104Y compared with EC1, which indicated that the regulatory functions of Csa3G890020 could be performed at post-transcriptional level rather than transcriptional level. This is the first report to map-based clone an auxin F-box protein gene related to virescent leaf in cucumber. The results will exhibit a new insight into the chlorophyll biosynthesis regulated by auxin signaling transduction network.