Abstract
Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, ‘SCNU1154’, ‘Edisto47’, ‘MR-1’, and ‘PMR5’. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs), 1.9 million InDels, and 182,398 putative structural variations (SVs). Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.
Highlights
Melon (Cucumis melo L.) is a highly diversified eudicot diploid species (2n = 2x = 24) from the Cucurbitaceae family, which includes cucumber, watermelon, and squash
Young leaves were inoculated with Podosphaera xanthii (PM pathogen) and disease severity was measured for each line using disease index scores (0 to 5)
Further confirmation of disease severity was accessed using Wilcoxon t-test with Bonferroni correction, where a visual cutoff range was fixed based on lesion area infection, 10% (-), 10% to 30% (+), and more than 31% (++) on each sample (S1 Fig)
Summary
Melon (Cucumis melo L.) is a highly diversified eudicot diploid species (2n = 2x = 24) from the Cucurbitaceae family, which includes cucumber, watermelon, and squash. Melon was previously classified into two subspecies, C. melo ssp. Melo, which were differentiated based on pubescence on the hypanthium [1] and later divided into several edible and wild varieties [2]. Melon is an important vegetable/fruit crop cultivated worldwide and highly valued for its fruit quality. More than 31 million tons of melons were produced. Identification of Powdery Mildew Disease Associated Resistant Gene Using Whole Genome Re-Sequencing.
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