Melon, Cucumis melo L., is an important horticultural crop with abundant morphological variability, but the genetic diversity and relationships within wild and cultivated melons remain unclear to date. In this study, thick-skinned (TC) (cultivated subspecies melo), thin-skinned (TN) (cultivated subspecies agrestis), and wild accessions were analyzed for genetic diversity and relationships using 36 microsatellite markers. A total of 314 alleles were detected with a mean allelic number of 8.72 and polymorphism information content of 0.67. Cluster analysis of the accessions resulted in four distinct clusters (I, II, III, and IV) broadly matching with the TC, TN, and wild groups. Cluster I contained only two Indian wild accessions. Cluster II was consisted of 49 South Asian accessions, 34 wild accessions, and 15 TN accessions. Cluster III was a typical TC group including 51 multiorigin TC accessions and one wild accession. The remaining 88 accessions, including 75 TN accessions, 6 wild accessions, and 7 TC accessions, formed the cluster IV, and all the TN and wild accessions in this cluster were from China. These findings were also confirmed by Principal component analysis and STRUCTURE analysis. The South Asian subspecies agrestis accessions, wild and cultivated, had close genetic relationships with a distinctive genetic background. Chinese wild melons showed closeness to cultivated subspecies agrestis landraces and could be a return from the indigenous cultivated melons. The AMOVA and pairwise F statistics (FST) presented genetic differentiation among the three groups, with the strongest differentiation (FST = 0.380) between TC and TN melons. These results offer overall information on genetic diversity and affiliations within a variety of melon germplasms and favor efficient organization and utilization of these resources for the current breeding purpose.
Low temperature is an important abiotic stress that negatively affects morphological growth and fruit development in melon (Cucumis melo L.). Chilling stress at the seedling stage causes seedling injury and poor stand establishment, prolonging vegetative growth and delaying fruit harvest. In this study, association mapping was performed for chilling tolerance at the seedling stage on an expanded melon core collection containing 212 diverse accessions by 272 SSRs and 27 CAPSs. Chilling tolerance of the melon seedlings was evaluated by calculating the chilling injury index (CII) in 2016 and 2017. Genetic diversity analysis of the whole accession panel presented two main groups, which corresponded to the two subspecies of C. melo, melo, and agrestis. Both the subspecies were sensitive to chilling but with agrestis being more tolerant. Genome-wide association study (GWAS) was conducted, respectively, on the whole panel and the two subspecies, totally detecting 51 loci that contributed to 74 marker-trait associations. Of these associations, 35 were detected in the whole panel, 21 in melo, and 18 in agrestis. About half of the associations identified in the two subspecies were also observed in the whole panel, and seven associations were shared by both the subspecies. CMCT505_Chr.1 was repeatedly detected in different populations with high phenotypic contribution and could be a key locus controlling chilling tolerance in C. melo. Nine loci were selected for evaluation of the phenotypic effects related to their alleles, which identified 11 elite alleles contributing to seedling chilling tolerance. Four such alleles existed in both the subspecies and six in either of the two subspecies. Analysis of 20 parental combinations for their allelic status and phenotypic values showed that the elite alleles collectively contributed to enhancement of the chilling tolerance. Tagging the loci responsible for chilling tolerance may simultaneously favor dissecting the complex adaptability traits and elevate the efficiency to improve chilling tolerance using marker-assisted selection in melon.
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