In the last decade, there has been an enormous increase worldwide in the use of molecular marker methods to assess genetic variation in trees. These approaches can provide significant insights into the defining features of different taxa and this information may be used to define appropriate management strategies for species
Tag: genetic markers
Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing
Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted. © 2016 Published by NRC Research Press.
Genetic diversity and gene flow revealed by microsatellite DNA markers in some accessions of African Plum (Dacryodes edulis) in Cameroon
Dacryodes edulis is a multipurpose tree integrated in the cropping system of Central African region still dominated by subsistence agriculture. Some populations grown are wild which can provide information on the domestication process, and could also represent a potential source of gene ow. Leaves samples for DNA extraction were collected from wild forms in Mbakwa supe region and from cultivated forms in Yaounde and Santchou region. Six microsatellites DNA markers were employed in genotyping to analyze population structure and gene flow. Amplification rate was high and genotyping revealed high level of genetic variation. The overall polymorphic level at the six loci was also high with average expected heterozygosity of 0.53; polymorphism of 0.46; mean allelic diversity of 0.5 and mean allele number of 8.33. There were no clear differences with only 1% variation among the three populations and 6% variation among individuals within populations. In contrast, the rate of heterozygosis was high in all the three populations. Both the number of migrant per generation (Nm=20) and the Wright’s F-statistics (FST=0.012) suggest that there was substantial gene ow among the populations. These findings indicate that D. edulis possess a great potential of pollen dispersal and dominant cross-pollination within populations. Most of the loci with private alleles (45%) were found in wild individuals which could be a source of pollen for crossing their cultivated relatives.