To Identify Candidate Genes With LRR Domain Governing Powdery Mildew Resistance Based On Whole Genome Re-sequencing In Cucumber(Cucumis Sativus.L)

Cucumber powdery mildew is one of the three major diseases in cucumber(Cucumis sativus L.).It not only reduces the photosynthetic efficiency of plants,but also affects plant yield and fruit quality.When the incidence is serious,it often cause about 30%reduction.Breeding and application of new varieties of powdery mildew resistance in cucumber is the fundamental technical way to overcome the harm of powdery mildew.With the development of genome sequencing and computational biology,it has become possible to use bioinformatics methods to explore resistance genes.In the present study,high-throughput Illumina sequencing technology was used to resequencing the whole genome of a highly resistant powdery mildew-resistant and stable inheritance lineage line SSL508-28 and its recurrent parent D8,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.In a further analysis,15,682 SNPs and 6,262 InDels were obtained by comparing the genome of SSL 508-28 and D8,these SNPs and InDels were tended to be centrally located on chromosome 5.Based on the above results,we have annotated these SNPs and InDels and found that 120 SNPs are non-synonymous mutations and 30 InDels are frameshift mutations.These nonsynonymous SNPs and frameshift InDels are distributed among 94 genes.In order to further validate the contribution of 94 mutant genes to the powdery mildew resistance of SSL508-28,we have classified the 94 genes,among which five genes belong to NBS-LRR(Nucleotide binding site-leucine-rich repeats)genes.The expression levels of Csa2M435460.1 and Csa5M579560.1 were detected by qRT-PCR in D8 and SSL508-28 before and after inoculation with powdery mildew.The results showed that the expression levels of Csa2M435460.1 and Csa5M579560.1 after SSL508-28 inoculation with powdery mildew reached the peak at 48 hours.There was no significant change in the expression of D8 before and after inoculation with powdery mildew.In order to further validate that candidate genes are closely related to resistance to powdery mildew in cucumber,the expression levels of Csa2M435460.1 and Csa5M579560.1 in different resistant and susceptible cucumber lines were analyzed by qRT-PCR.The results showed that Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines and the highest expression level of the two genes was found in the donor JIN5-508.In addition,In addition,we found that a non-synonymous mutation in the coding region of genes Csa2M435460.1 and Csa5M579560.1 in SSL508-28 mutated both cysteine and valine to phenylalanine,so we hypothesized that 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.