Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome.

Amir Sherman,Ravit Eshed,David Saada,Ron Ophir,Mazal Ish-Shalom,Michal Sharabi-Schwager,Miri Benita,Yuval Cohen,Ada Rozen,Mor Rubinstein

doi:10.1186/s12870-015-0663-6

Abstract

BackgroundGermplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers.ResultsWe describe a de novo transcriptome assembly from mango cultivar ‘Keitt’. Variation discovery was performed using Illumina resequencing of ‘Keitt’ and ‘Tommy Atkins’ cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1 %) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5 % were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS = −0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST = 0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background.ConclusionsWhole-transcriptome reconstruction was used to significantly broaden the mango’s genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0663-6) contains supplementary material, which is available to authorized users.

Highlights

Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period
We have established a sequence for the mango transcriptome from a pool of tissues
It was used as a reference to align resequencing of two commercially important mango accessions, ‘Keitt’ and ‘Tommy Atkins’, constituting a resource for genetic variation discovery

Summary

Introduction

Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. The genus Mangifera has approximately 70 members which are located mostly on the Malay peninsula, in the Indonesian archipelago, in Thailand and in the Philippines [1, 2] Some of these species have edible fruit which are locally cultivated. A secondary mango center flourished in Florida during the late nineteenth century and early twentieth century, and many new Floridian cultivars were promoted [3]. These cultivars are adapted to the taste of the Western consumer by breeding to a red blush coloration, mild taste and mild aroma idoetype. There is still some demand for cultivar improvement, and several breeding programs are active in Australia, South Africa, Brazil and Israel [4]

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