Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method

David N Kuhn,Natalie Dillon,Ian Bally,Amy Groh,Jordon Rahaman,Emily Warschefsky,Barbie Freeman,David Innes,Alan H Chambers

doi:10.1016/j.scienta.2019.03.037

David N Kuhn, Natalie Dillon + Show 7 more

Open Access

https://doi.org/10.1016/j.scienta.2019.03.037

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Abstract

Mango is a globally important tropical fruit but lacks genomic tools to support cultivar identification and to enable breeding efforts. Assessing the genetic diversity and relatedness of mango germplasm is essential for identifying genetically distant parents with favorable agronomic traits to produce hybrid populations enabling selection of improved cultivars. We thus genotyped 1915 mango accessions from the United States, Senegal, Thailand, and Australia with 272 single nucleotide polymorphism (SNP) markers identifying over 520,000 genotypes. These accessions represent the available diversity from both public and private germplasm collections in these countries, as well as accessions from smaller international collections. The study included Mangifera indica, other Mangifera species, and accessions from half sibling populations. Genotype data were analyzed using an affinity propagation method to define 258 groups. Using a simple visual method, no more than 30 SNPs are needed to distinguish a single cultivar of interest from all other cultivars in the dataset enabling the accurate identification of important commercial cultivars. As these SNP markers provided accurate genotype data for accessions from different genera as well as half siblings, the majority of the genetic diversity of the mango germplasm and related species that were genotyped has been captured. The dataset contains a large collection of open-pollinated half siblings from known maternal parents. A simple visual method can also be used to identify self-pollinated individuals among the half siblings of known maternal parents and, in some cases, to infer likely candidates for the paternal parent. Identification of self-pollinated individuals is particularly important in terms of selection of improved cultivars, as due to high levels of heterozygosity, self-pollinated progeny are likely to uncover deleterious recessive alleles. Genotyping of progeny at the seedling stage and removal of self-pollinated progeny can increase the efficiency and decrease the costs of selection of improved cultivars from open-pollinated populations.

Highlights

Mango (Mangifera indica) is a tropical tree species valued for the nutritional and organoleptic qualities of its fruit
We selected a subset of mango single nucleotide polymorphism (SNP) markers that were initially developed to produce a genetic map (Kuhn et al, 2017), and used these markers to genotype as much of the world’s mango germplasm as could be obtained for this study
The generation of the largest mango SNP genotype database derived from diverse germplasm accessions ranging from different genera to half sibling hybrids provides a tool that is useful to mango breeders and researchers worldwide

Summary

Introduction

Mango (Mangifera indica) is a tropical tree species valued for the nutritional and organoleptic qualities of its fruit. Mango is imbedded in the cultural backgrounds of many tropical nations including major producers such as India, Mexico, China, Thailand, Indonesia, and Pakistan (Mahato et al, 2016). The center of origin for mango is believed to be somewhere in Northeastern India, Bangladesh, and Nepal, perhaps stretching into Northern Myanmar and Thailand, though current distributions of wild M. indica are not well known (Kostermans and Bompard, 1993; Litz, 2009; Singh et al, 2016). Mangos from South East Asia comprise a tropical, polyembryonic group that contain seeds with both zygotic and nucellar embryos.

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