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

Xiaoping Liu,Han Miao,Panna Liu,Hongwei Lu,Xingfang Gu,Shengping Zhang,Yuling Bai

doi:10.3390/plants9121659

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.

Highlights

Cucumber (Cucumis sativus L.) is an economically important vegetable crop produced all over the world
The core germplasm (CG) lines were scored for Downy mildew (DM) resistance in the spring of 2014, the autumn of 2014, the autumn of 2015, and the spring of
In the cucumber CG germplasm, DM resistance was identified, and it is associated with 18 genetic loci, of which 16 were located in chromosomal regions where QTLs have been reported in previous studies

Summary

Introduction

Cucumber (Cucumis sativus L.) is an economically important vegetable crop produced all over the world. Downy mildew (DM), caused by the obligate biotrophic oomycete Pseudoperonospora cubensis ((Berkeley and Curtis) Rostovzev), is one of the most serious diseases threatening cucumber production [1,2]. The symptoms of cucumber DM mainly appear on the upper side of infected leaves starting with chlorotic (yellow) lesions that are restricted by major leaf veins. Symptom development is sensitive to environmental conditions and in favor of wet and humid conditions, since the pathogen needs moisture for germination and starting of a new infection. Within days following the infection under appropriate environmental conditions, chlorotic lesions become necrotic and sporulation (with a brownish gray downy appearance) may be seen on the lower side of infected leaves. With the disease growth, infected leaves will eventually collapse, leading to losses of cucumber production due to lack of photosynthetic leaves

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Discussion

Conclusion