Abstract
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels). When compared against the reference genome of the inbred cucumber line 9930, a total of 468,616 SNPs and 67,259 indels were identified in SSL508-28, and 537,352 SNPs and 91,698 indels were identified in D8. Of these, 3,014 non-synonymous SNPs and 226 frameshift indels in SSL508-28, and 3,104 non-synonymous SNPs and 251 frameshift indels in D8, were identified. Bioinformatics analysis of these variations revealed a total of 15,682 SNPs and 6,262 indels between SSL508-28 and D8, among which 120 non-synonymous SNPs and 30 frameshift indels in 94 genes were detected between SSL508-28 and D8. Finally, out of these 94 genes, five resistance genes with nucleotide-binding sites and leucine-rich repeat domains were selected for qRT-PCR analysis. This revealed an upregulation of two transcripts, Csa2M435460.1 and Csa5M579560.1, in SSL508-28. Furthermore, the results of qRT-PCR analysis of these two genes in ten PM resistant and ten PM susceptible cucumber lines showed that when exposed to PM, Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines. This indicates that Csa2M435460.1 and Csa5M579560.1 are candidate genes for PM resistance in cucumber. In addition, the non-synonymous SNPs in Csa2M435460.1 and Csa5M579560.1, identified in SSL508-28 and D8, might be the key to high PM-resistance in SSL508-28.
Highlights
IntroductionMany studies have focused on detecting Powdery mildew (PM)-resistant quantitative trait loci (QTLs) in cucumber
Cucumber (Cucumis sativus L., 2n = 2x = 14) is one of the most important vegetable crops worldwide
These results suggest that SSL508-28 introgressed Powdery mildew (PM) resistance genes from JIN5-508 in the D8 genetic background (Fig 2.)
Summary
Many studies have focused on detecting PM-resistant quantitative trait loci (QTLs) in cucumber. Sakata et al [3] first used a population of F7 recombinant inbred lines to map QTLs for PM resistance in cucumber, and detected six QTLs. Liu et al [4] identified five QTLs in two environments, using 130 F2:3 lines. Nie et al [1] used secondary segregating populations to map a 170-kb region PM resistance QTL named pm5.1. Such findings have provided insight into the genetic control of PM resistance in cucumber, the detailed mechanisms underlying PM resistance remain unclear. The molecular markers identified in these studies are not breeder friendly [8]
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