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

Area of Science:

• Horticultural Science
• Molecular Genetics
• Plant Breeding

Background:

• Melon (Cucumis melo) is a vital crop, but distinguishing its numerous, similar varieties is challenging for breeding and innovation.
• Molecular markers, specifically simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), offer a reliable method for variety identification.

Purpose of the Study:

• To elucidate the genetic structure and diversity of melon varieties using molecular markers.
• To establish DNA fingerprints for a wide range of cultivated melon varieties.
• To identify core sets of markers for efficient melon variety identification and protection.

Main Methods:

• Screening of 136 perfect SSRs and 164 perfect SNPs from resequencing data of 149 accessions.
• DNA fingerprinting of 259 widely-cultivated melon varieties using Target-seq technology.
• Classification of varieties into five subgroups and analysis of genetic diversity and gene exchange.

Main Results:

• Established DNA fingerprints for 259 melon varieties, classifying them into five subgroups.
• Identified ssp. agrestis varieties as having a narrow genetic background, at risk of genetic erosion.
• Demonstrated a high linear correlation (R² = 0.9722) between SSR and SNP genotyping methods for variety identification.
• Selected 23 SSRs and 40 SNPs as core marker sets for practical applications.

Conclusions:

• The developed DNA fingerprinting method using SSRs and SNPs is effective for melon variety identification and authentication.
• Conservation strategies should address the genetic erosion risk in ssp. agrestis by promoting gene exchange with ssp. melo.
• The selected core marker sets provide an efficient tool for variety monitoring and intellectual property protection in melon breeding programs.