SNP marker assay and candidate gene identification for sex expression via genotyping-by-sequencing-based genome-wide associations (GWAS) analyses in Oriental melon (Cucumis melo L.var.makuwa)

Abstract

The Oriental melon is an important delicious fruit crop across East Asia. Single-nucleotide polymorphisms (SNPs) are considered to be a useful genotyping tool both to detect genetic diversity and to protect breeder rights. This study used genotyping-by-sequencing (GBS) to detect genome-wide SNPs by analyzing 48 commercial Oriental melon varieties to generate 5640 filtered SNPs. Based on the high polymorphism information content (PIC), genetic and physical distances, a subset of 192 SNPs was selected as putative SNPs for validation via the Fluidigm JunoTM system. Of these, 164 SNPs were successfully validated in 87 Oriental melon varieties with a validation ratio of 85.41 %. Furthermore, these 87 Oriental melon varieties were classified into ten distinct groups, based on 164 SNP markers. Therefore, these large set of SNP markers detected here has several application, such as genetic diversity studies, varietal identification and marker-assisted selection (MAS) in the Oriental melon. Genome-wide associations (GWAS) analyses detected significant 18 SNPs associated with various morphological traits, including two novel SNPs for sex expression on chromosomes 1 and 8 that were not colocalized with previous studies. The four potential candidate genes such as MELO3C015898, MELO3C015904, MELO3C024563, and MELO3C024565 were predicted within the GWAS-SNPs regions for sex expression in the Oriental melon. Hence, identification of these candidate genes has provided the foundation to study the molecular genetic mechanism of sex expression trait in the Oriental melon.