Whole genome SNP identification and validation in Cucumis melo L. cultivars using genome resequencing approach

Identification of polymorphic loci linked to specific trait variations is an important objective of crop genomics studies. We used next generation sequencing techniques (Illumina and Ion torrent) for whole genome resequencing of two melon (Cucumis melo L.) cultivars, Durgapur Madhu (DM) and BS25. After filtering the raw reads, 92% good quality reads obtained were mapped on to the reference melon genome DHL92. A total of 1,709,383 single nucleotide polymorphisms (SNPs-981,560 in DM and 727, 823 in BS25) and 433,459 insertion/deletions (InDels; 199, 972 in DM and 233, 487 in BS25) were identified. Among these 46.56% and 46.07% non-synonymous and 53.43% and 53.92% synonymous SNPs were detected in DM and BS25 cultivars respectively. Based on gene ontology classification, 11,666 annotated genes were assigned to 53 GO terms categorised as related to biological processes (23), molecular functions (16) and cellular components (14). Homology search against Arabidopsis showed SNPs containing sequence similarity with CLCs and AHK1 gene in chromosome 2 and 4 of melon and were related to drought and salt stress traits. The SNPs and InDels identified would facilitate the study of economically important traits through mapping and construction of high density linkage maps since the two cultivars resequenced have contrasting response to water stress. These markers can be effectively used to design SNP markers for large scale genotyping and their validation in diverse mapping populations that will accelerate marker assisted breeding in melons.