Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

Maria José Gonzalo,Antonio J Monforte,Belén Picó,Narinder P S Dhillon,Umesh K Reddy,Aurora Díaz

doi:10.1186/s12864-019-5784-0

Abstract

BackgroundThe importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data.ResultsA set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17 kb), with more rapid decay in euchromatic (8 kb) than heterochromatic (30 kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59 kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars.ConclusionsThe results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons.

Highlights

The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted
Most of the Indian collections showed a lateral position with the reference accession in the genetic diversity plot, except for the IC collection from North in both Africa and Asia (India) [13]. These results suggested that the IC collection could represent a center of melon diversity, i. e., crop diversified in a divergent way from India to Mediterranean and Far East regions from North India
All the Single Nucleotide Polymorphism (SNP) were integrated before filtering from both datasets in order to retain more SNPs., A total of 8212 common SNPs were found among data sets

Summary

Introduction

The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. A sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data. In the last proposed classification, 19 horticultural groups were defined: agrestis, kachri, chito, tibish, acidulus, momordica, conomon, makuwa, chinensis, flexuosus, chate, dudaim, chandalak, indicus, ameri, cassaba, ibericus, inodorus, and cantalupensis [3]. Molecular diversity analyses cluster cultivars in groups that fit the morphological ones, which indicates that the Mediterranean/ Near East groups (ameri, cassaba, chandalak, ameri, ibericus, inodorus, cantalupensis) are closely related and quite differentiated from Far-East groups (conomon, makuwa, chinensis)

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