Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Abstract

Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of ‘Jingyu’ and ‘Jingmi’ series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.

Genetic Diversity in Peripheral Pedunculate Oak (Quercus robur L.) Provenances—Potential Climate Change Mitigators in the Center of Distribution despite Challenges in Natural Populations

“…Certainly, the correlation would be even higher considering only non-outlier data. A significant correlation between SSR and nonoutlier SNP data is expected, as they both represent neutral diversity [86]. Because the correlation of all SNPs genetic variance with F IS was not significant, this further confirms the effects of selection on outlier SNP loci, as discussed by Temunović et al [10].…”

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

“…Moreover, GBS was applied on 47 accessions belonging to Spanish melon landraces to perform an in-depth study and characterization of this melon germplasm collection [ 146 ]. To examine the genetic diversity of prevailing varieties in China, Target-seq technology was utilized by Zhang et al [ 147 ] to screen out genome-wide SSRs and SNPs from 149 re-sequenced accessions and established the DNA fingerprint of 259 accessions of which 84 were landraces. Two distinct SNP loci were revealed for the identification of the ssp.…”

“…al. [147] to screen out genome-wide SSRs and SNPs from 149 re-sequenced accessions and established the DNA fingerprint of 259 accessions of which 84 were landraces. Two distinct SNP loci were revealed for the identification of the ssp.…”

Chloroplast Genome-Wide Analysis Reveals New Single-Nucleotide Polymorphism Resources for the ARMS-qPCR Identification of Dendrobium brymerianum

“…This study involved sequencing of the complete cp genome of D. brymerianum, while the remaining 39 sequences were obtained from prior publications by this research group and the GenBank public database. The alignment of the 40 complete cp genomes was made possible by using MAFFT v7 software [48], and MEGA 7 software [53] was employed to identify specific nucleotide sites in D. brymerianum's complete cp genome sequence. Primers were designed using MEGA 7 and Vector NTI 10 software, based on specific nucleotide sites identified in D. brymerianum.…”