Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS

Abstract

Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM.

The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato

“…We have shown here that a loss-of-function allele of the cucumber two of which occurred in (rather) DM-resistant cucumber accessions according to recent data by Liu et al (2020). However, more data (e.g., by screening F 2 populations derived from these accessions) would be required to conclude whether or not these polymorphisms contribute to the observed DM resistance in those accessions.…”

“…Effects of SNPs on the encoded CsAAP2A protein were predicted using SNPeff software (Cingolani et al, 2012). Data on DM susceptibility of the 115 cucumber accessions were downloaded from Liu et al (2020).…”

A Large-Scale Genomic Association Analysis Identifies the Candidate Genes Regulating Salt Tolerance in Cucumber (Cucumis sativus L.) Seedlings

“…The software Plink [ 44 ] was used to calculate the LD coefficient ( r 2 ) between the pairwise high-quality SNPs and the results were used to estimate LD decay [ 16 ]. Manhattan plots and the LD heatmaps were drawn by qqman package in R environment [ 45 ].…”

“…Lee, et al [ 15 ] conducted GWAS analysis of cucumber powdery mildew resistance using 264 accessions from all over the world and predicted two novel candidate genes ( Csa5G453160 and Csa5G471070 ). Liu, et al [ 16 , 17 ] used the core germplasm to predict five downy mildew-related candidate genes ( Csa1G575030 , Csa2G060360 , Csa4G064680 , Csa5G606470 , and Csa7G004020 ) and eight candidate genes that were associated with powdery mildew ( Csa2G030010 , Csa2G030020 , Csa2G030030 , Csa3G414050 , Csa4G022350 , Csa5G48880 , Csa5G603950 , and Csa5G603960 ), respectively. However, no study on the investigation of cucumber salt tolerance via GWAS has been reported.…”

Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber (Cucumis sativus L.)

“…Bo [ 14 , 15 ] found a new locus fsd6.1 associated with spines and two loci, qgf5.1 and qgf3.1 , related to green fruit flesh in cucumber. For cucumber disease-resistance traits, 395 cucumber germplasm resources were used to analyze downy mildew resistance, and 18 loci were related to downy mildew resistance, five candidate genes were predicted at the major effect loci [ 16 , 17 , 18 ]. Jia [ 19 ] used 231 cucumber core germplasm (CG) resources around the world for powdery mildew resistance analysis, detected 12 loci associated with powdery mildew resistance, and predicted 63 candidate genes.…”