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Genetic diversity and relatedness of mango cultivars assessed by SSR markers.

ABSTRACT: Assessment of genetic diversity and relatedness is an essential component of germplasm characterization and use. We analyzed 120 mango (Mangifera indica L.) genetic resources in Japan for their parentage, cultivar identification, genetic relatedness, and genetic diversity, using 46 polymorphic simple sequence repeat (SSR) markers. Ten sets of three SSR markers could successfully distinguish 83 genotypes with the exception of synonymous and identical accessions. We successfully assessed parentage, newly identifying or reconfirming both parents of 11 accessions, and revealing over 30 cultivars as offspring of 'Haden'. Genetic relatedness and diversity analyses revealed three distinct clusters. Two clusters correspond to the groups of USA and India, which are closely related. The other includes accessions from Southeast and East Asia. The results agree with the previous identification of genetically distinct Indian and Southeast Asian types, and suggest that the Florida accessions, which originated from hybrids between those two types, are more closely related to the Indian type.

SUBMITTER: Yamanaka S

PROVIDER: S-EPMC6711724 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Genetic diversity and relatedness of mango cultivars assessed by SSR markers.

Yamanaka Shinsuke S Hosaka Fumiko F Matsumura Masato M Onoue-Makishi Yuko Y Nashima Kenji K Urasaki Naoya N Ogata Tatsushi T Shoda Moriyuki M Yamamoto Toshiya T

Breeding science 20190528 2

Assessment of genetic diversity and relatedness is an essential component of germplasm characterization and use. We analyzed 120 mango (<i>Mangifera indica</i> L.) genetic resources in Japan for their parentage, cultivar identification, genetic relatedness, and genetic diversity, using 46 polymorphic simple sequence repeat (SSR) markers. Ten sets of three SSR markers could successfully distinguish 83 genotypes with the exception of synonymous and identical accessions. We successfully assessed pa ...[more]

PMID: 31481843

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Project description:BackgroundThe economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples.ResultsWe investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability.ConclusionsThe comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.

Dataset Information

Genetic diversity and relatedness of mango cultivars assessed by SSR markers.

Publications

Genetic diversity and relatedness of mango cultivars assessed by SSR markers.

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