Molecular genetic variation in the African wild rice Oryza longistaminata A. Chev. et Roehr. and its association with environmental variables

Molecular markers, complemented by appropriate Geographical Information System (GIS) software packages are powerful tools in mapping the geographical distribution of genetic variation andassessing its relationship with environmental variables. The objective of the study was therefore to investigate the relationship between genetic diversity and eco-geographic variables using Oryzalongistaminata as a case study. The methodology used was a novel technique that combined hierarchical cluster analysis of both molecular diversity generated using Amplified Fragment Length Polymorphism (AFLP) and climate data available in a GIS software. The study clearly established that there is a close relationship between genetic diversity and eco-geographic variables. The study also revealed that genetic diversity is a function of annual rainfall, and peak diversity occurs in intermediate rainfall areas reflecting the ‘curvilinear theory’ of clinal relationship between the level of genetic diversity and rainfall. The clear association of genetic diversity with rainfall allows the extrapolation ofthe potential impacts of global warming on diversity when empirical data on predicted climate models, particularly rainfall, are available. This knowledge would therefore be useful in the development ofconservation measures to mitigate the effects of genetic erosion through climate change

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

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

Assessment of the genetic diversity and pattern of relationship of West African sorghum accessions using microsatellite markers

An understanding of the extent, distribution and patterns of genetic variation is useful for estimation of any possible loss of genetic diversity and assessment of genetic variability and its potential use in breeding programs, including establishment of heterotic groups. This study assessed patterns of genetic diversity and relationships among 30 West African sorghum accessions using 22 microsatellite markers. Population structure and within population genetic diversity was also assessed using the same markers. Genotypic data was generated using the ABI Prism 3730 and alleles called and sized using genemapper software version 3.7. Molecular data was analyzed using DARwin 4.0, powermarker 3.0 and Arlequin version 3.11. The average marker quality index was 0.27 while a mean PIC of 0.54 was observed across the 22 SSR markers. Among the 30 accessions, the markers detect a total of 146 alleles with an average of 6.6 alleles per marker. Results from the various statistical analyses performed revealed a wide range of polymorphism from 22.7 to 86.4%. The mean heterozygosity was relatively low at 0.28 while the average Nei’s genetic diversity among the 30 populations was 0.57. The within population Nei’s genetic diversity assessed from 49 individuals in 10 populations was lower at 0.54 and the average heterozygosity was also lower at 0.21. Cluster and principal coordinate analysis of the 30 populations revealed two distinct groups independent of their geographic origins The examination of the hierarchical partitioning of genetic variation by AMOVA demonstrated that genetic differentiation was significant at P < 0.00. Of the total diversity, 8.9% was attributed to country differences, 54.11% was attributed to population differences within the countries while 36.99% was attributed to differences within populations. The FST value (0.63) indicated a very high genetic differentiation as expected for selfing species. This study demonstrates the utility of SSR markers in detecting polymorphism, estimating genetic diversity and establishment of genetic clusters for heterotic studies.Keywords: Genetic diversity, heterozygosity, SSR microsatellites, heterotic grouping, alleles, polymorphismAfrican Journal of Biotechnology, Vol 13(14), 1503-151

Molecular genetic variation in the African wild rice Oryza longistaminata A. Chev. et Roehr. and its association with environmental variables

Molecular markers, complemented by appropriate Geographical Information System (GIS) software packages are powerful tools in mapping the geographical distribution of genetic variation and assessing its relationship with environmental variables. The objective of the study was therefore to investigate the relationship between genetic diversity and eco-geographic variables using Oryza longistaminata as a case study. The methodology used was a novel technique that combined hierarchical cluster analysis of both molecular diversity generated using Amplified Fragment Length Polymorphism (AFLP) and climate data available in a GIS software. The study clearly established that there is a close relationship between genetic diversity and eco-geographic variables. The study also revealed that genetic diversity is a function of annual rainfall, and peak diversity occurs in intermediate rainfall areas reflecting the 'curvilinear theory' of clonal relationship between the level of genetic diversity and rainfall. The clear association of genetic diversity with rainfall allows the extrapolation of the potential impacts of global warming on diversity when empirical data on predicted climate models, particularly rainfall, are available. This knowledge would therefore be useful in the development of conservation measures to mitigate the effects of genetic erosion through climate change