Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

Abstract

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.

Variability and genetic structure of yellow passion fruit (Passiflora edulis f. flavicarpa Degener) in Colombia using microsatellite DNA markers

“…Bootstrap analysis with 1000 replicates (Felsenstein, 1985) was performed to get the confidence level of the tree. Additionally, all alleles per locus were georeferenced for spatial distribution following van Zonneveld et al (2012). A grid for allelic richness parameter was generated using the DIVA-GIS 7.5 software with a cell size grid of 0.05 minutes (which corresponds to approximately 0.1 km in the study area) and applying a circular neighborhood with a 0.5 degrees diameter (corresponding to approximately 55.5 km).…”

Conservation and Use of Genetic Resources of Underutilized Crops in the Americas—A Continental Analysis

“…An important step towards improving the on-farm conservation of any species is having data about its current (and potential) distribution and cultivation. In addition to individuals' knowledge on these aspects, publicly available georeferenced data is a powerful starting point for studies on a crop's agroecological potential and adaptive capacity which in turn are useful for planning in situ conservation initiatives [33][34][35]. Searches performed in the data portal of the GBIF resulted in retrieval of georeferenced data for almost all the species.…”

Value Chains of Cherimoya (Annona Cherimola Mill.) in a Centre of Diversity and its on-Farm Conservation Implications

“…Based on a subset of 9 simple sequence repeats (SSRs), selected from 52 polymorphic SSR markers from cherimoya [9], in combination with Geographic Information Systems (GIS) techniques, van Zonneveld et al [19] studied spatial patterns of genetic diversity of semi-cultivated and wild cherimoya trees in the Ecuadorian, Peruvian and Bolivian Andes. The latter authors found that allelic richness, locally common alleles and expected heterozygosity are high in the putative centre of origin (southern Ecuador and northern Peru).…”