Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS

Abstract

Background Downy mildew (DM) is one of the most serious diseases in cucumber and brings the loss of yield and profit. Multiple QTLs for DM resistance have been detected, however, no loci related to resistance was reported using genome-wide association analysis (GWAS). In this study, the core germplasm (CG) of cucumber lines that had been constructed and resequenced were used to identify DM resistance Loci using GWAS technology. Results Thirteen loci (dmG1.1, dmG1.2, dmG2.1, dmG2.2, dmG3.1, dmG4.1, dmG4.2, dmG5.1, dmG5.2, dmG6.1, dmG6.2, dmG7.1 and dmG7.2) associated with DM resistance were detected on all the seven chromosomes. Among these loci, dmG2.1 and dmG7.1 were novel loci compared with previous studies. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlations, Csa1G575030 could be the most likely candidate gene of dmG1.2; Csa2G059820 and Csa2G060360 could be the candidate gene of dmG2.1. A WRKY transcription factor Csa5G606470 could be the candidate gene of dmG5.2. Csa7G004020 could be the candidate gene of dmG7.1. Conclusions These results identify five candidate genes for four loci related to DM resistance in cucumber which provide theoretical basis for gene cloning and genetic breeding of DM resistance in cucumber.

Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm

“…In this CG population, a significant association between resistances to PM and DM was observed ( Supplementary Figure S2 ). We detected 13 loci for PM resistance in this study and 18 loci for DM resistance in our previous study [ 34 ]. A number of loci are colocalized, including pmG1.1 and dmG1.1 , pmG2.2 and dmG2.2 , pmG5.2 , and dmG5.1 , as well as pmG5.3 and dmG5.2 ( Figure 11 ).…”

“…In order to verify the potential link between these S genes and the QTLs, we analyzed the effect of SNPs in these S genes on PM DI of the CG lines. We also included the DM data of this CG population in our previous study [ 34 ] since it has been often reported that resistance to PM and DM is linked in cucumber [ 21 ], which is supported by the significant correlation between the DIs of PM and DM in this CG population ( Supplementary Figure S2 ). Based on the SNPs variation in the PMR genes ( Supplementary File S6 ), only SNPs in CsaPMR6-10 showed a significant difference on DI of PM (the average of spring 2013, spring 2014, and autumn 2014), but not on DI of DM (the average of spring 2014, autumn 2014, and autumn 2015) ( Figure 10 a).…”

“…In a review, Schouten et al, (2014) mapped a set of cucumber orthologues of plant S-genes reported for PM and DM [ 27 ]. As we demonstrated for the MLO and PMR genes, allelic variants of these cucumber S genes could be identified and their effect on PM and DM resistance/susceptibility may be discovered with the disease phenotypes of the CG lines for PM (this study) and for DM [ 34 ]. Further, colocalization of these S genes with PM/DM QTLs mapped in other studies ( Table 1 ) may indicate that mutations in the colocalized S-genes contribute to the QTL effect, as it is the case for the mutant allele of CsaMLO8 in this study as well as other studies [ 23 , 27 , 28 ].…”

“…In our cucumber CG germplasm, resistance to both PM (this study) and DM resistance [ 34 ] was identified, which are associated with many genetic loci scattered all over the seven cucumber chromosomes. Some loci are located in chromosomal regions where QTLs and plant S gene for PM and DM have been reported in previous studies.…”

“…For PM resistance, we showed in this study that previously cloned candidate genes contributed to PM resistance in this CG population, including CsaMLO8 , CsaM622830 , and CsPMR6-10 . While, the DM resistance could not be attributed to the previously cloned genes, including Sgr , CsLRK10L2 , and CsAAP2A [ 34 ]. Some QTLs for DM and PM are clustered together in certain chromosomal regions, which supported the significant correlation between PM and DM resistance in this CG germplasm.…”