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

Caroline Bertocco Garcia; Allison Vieira da Silva; Igor Araújo Santos de Carvalho; Wellington Ferreira do Nascimento; Santiago Linorio Ferreyra Ramos; Doriane Picanço Rodrigues; Maria Imaculada Zucchi; Flaviane Malaquias Costa; Alessandro Alves-Pereira; Carlos Eduardo de Araújo Batista; Dario Dantas Amaral; Elizabeth Ann Veasey

doi:10.3390/plants13071033

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

Plants (Basel). 2024 Apr 6;13(7):1033. doi: 10.3390/plants13071033.

Authors

Affiliations

¹ Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil.
² Science Center of Chapadinha, Federal University of Maranhão, Chapadinha 65500-000, MA, Brazil.
³ Exact Sciences and Technology Institute, Federal University of Amazonas, Itacoatiara 69103-128, AM, Brazil.
⁴ Genetics Department, Federal University of Amazonas, Manaus 69067-005, AM, Brazil.
⁵ São Paulo Agency for Agribusiness and Technology, Piracicaba 13400-970, SP, Brazil.
⁶ Museu Paraense Emílio Goeldi, Belém 66040-170, PA, Brazil.

Abstract

Platonia insignis is a fruit tree native to Brazil of increasing economic importance, with its pulp trading among the highest market values. This study aimed to evaluate the structure and genomic diversity of P. insignis (bacurizeiro) accessions from six locations in the Brazilian States of Roraima, Amazonas, Pará (Amazon biome), and Maranhão (Cerrado biome). A total of 2031 SNP markers were obtained using genotyping-by-sequencing (GBS), from which 625 outlier SNPs were identified. High genetic structure was observed, with most of the genetic variability (59%) concentrated among locations, mainly between biomes (Amazon and Cerrado). A positive and significant correlation (r = 0.85; p < 0.005) was detected between genetic and geographic distances, indicating isolation by distance. The highest genetic diversity was observed for the location in the Cerrado biome (H_E = 0.1746; H_O = 0.2078). The locations in the Amazon biome showed low genetic diversity indexes with significant levels of inbreeding. The advance of urban areas, events of burning, and expansion of agricultural activities are most probably the main factors for the genetic diversity reduction of P. insignis. Approaches to functional analysis showed that most of the outlier loci found may be related to genes involved in cellular and metabolic processes.

Keywords: Amazonian fruits; SNPs; bacurizeiro trees; conservation genetics; genotyping-by-sequencing.

Grants and funding

This research was funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, 2019/04100-6). Scholarships were provided by FAPESP (2019/15544-2 to IASC and 2021/04698-9 to FMC), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), (309445/2020-5 to EAV; 305280/2022-8 to SLFR] and by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (to CBG). Thanks go to Fundação de Estudos Agrários Luiz de Queiroz (FEALQ), for the financial support of this publication.