First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree

Abstract

Platonia insignis is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for P. insignis. We used Roche 454 GS FLX sequencing platform of a single P. insignis genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of P. insignis that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (H E ) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (H O ) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of P. insignis in clusters and we can conclude that the primers can estimate the genetic diversity of P. insignis populations.

Nuclear and chloroplast microsatellites reveal high genetic diversity and structure in Platonia insignis Mart., an endangered species native to the Brazilian Amazon

“…Ten specific microsatellite primers developed by Paraense et al (2020) were tested (Tab. S1 in supplementary material).…”

“…Only two studies have been developed so far based on microsatellite markers. Paraense et al (2020) developed primers for the bacurizeiro, while Pena (2016) used these primers to characterize the germplasm bank of Embrapa Amazônia Oriental. It is worth mentioning that although there are two studies with ncSSR markers described for P. insignis, no information is available on cpSSR markers for this species.…”

Low Diversity and High Genetic Structure for Platonia insignis Mart., an Endangered Fruit Tree Species

“…Few studies on population genetics have been carried out so far regarding the bacurizeiro tree [1,[20][21][22], with most of them using ISSR (Inter Simple Sequence Repeat) markers. Paraense et al [23] developed 22 microsatellite markers (nSSRs) for bacurizeiro. Of these, eight nSSRs, in addition to three chloroplast microsatellites (cpSSRs), were used by Nascimento et al [24] to evaluate seven populations of the species, originating from two Brazilian biomes (Amazon and Cerrado).…”

Genômica populacional do bacurizeiro (>i<Platonia insignis>/i< Mart.)

“…No contexto do estudo de genética populacional com espécies arbóreas e frutíferas, o bacurizeiro foi estudado utilizando marcadores ISSR (Inter-Simple Sequence Repeat) e SSR (Simplesequence repeats), que são limitados no sentido de quantidade de marcadores e locos amostrados (Souza et al, 2013;Pena, 2016;Pontes et al, 2017;Paraense et al, 2020;Pena et al, 2020;Nascimento et al, no prelo). Nesse sentido a genômica populacional amplia a escala de amostragem do genoma, demonstrando representatividade em termos de quantidade de marcadores e de regiões genômicas (Ellegren, 2014).…”

“…Os diferentes tipos de marcadores moleculares utilizados em genética de populações, para o estudo da estrutura populacional de P. insignis, revelaram padrões e características importantes para o entendimento da evolução dessa planta arbórea (Souza et al, 2013;Pena, 2016;Pontes et al, 2017;Paraense et al, 2020;. Marcadores ISSR foram utilizados para a caracterização molecular do bacurizeiro por Souza et al (2013) (2016).…”