High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia (original) (raw)
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African Journal of Biotechnology, 2016
The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, which represented different common bean production ecologies and seed types common in the country. This sample was then analyzed with 24 simple sequence repeat (SSR) markers to assess the genetic diversity within and between common bean landraces, classifying them based on SSR clustering, and determining relationships between genetic and agroecological diversity. Representatives of both Andean and Mesoamerican gene pools were identified by STRUCTURE software analysis, as well as a high proportion of hybrid accessions as evidenced by a STRUCTURE K = 2 preset. At the optimum K = 5 preset value, mixed membership of Andean and Mesoamerican genotypes in some of the clusters was also seen, which supported previous findings. Cluster analyses, principal coordinate analysis, and analysis of molecular variance all indicated clustering of accessions from different collection sites, accompanied by high gene flow levels, highlighting the significant exchange of planting materials among farmers in different growing regions in the country. Values of allelic diversity were comparable to those reported in previous similar studies, showcasing the high genetic diversity in the landrace germplasm studied. Moreover, the distribution of genetic diversity across various bean-growing population groups in contrasting geographical/ecological population groups suggests elevated but underutilized potential of Ethiopian germplasm in common bean breeding. In summary, this study demonstrated the geographical, as well as gene pool diversity in common bean germplasm of Ethiopia. This substantial diversity, in turn, should be utilized in future common bean breeding and conservation endeavors in the nation.
Theoretical and Applied Genetics, 2009
The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region.
Advances in Agriculture
This study was conducted on one hundred common bean landraces at the Jimma Agricultural Research Center, Melko, with the objective of assessing genetic variability and association of traits in common bean landraces collected from different parts of Ethiopia. The experiment was laid out in a simple lattice design with two replications. Analysis of variance showed significant differences among genotypes for all traits. This highly significant difference indicates the existence of large variability among genotypes. High phenotypic coefficients of variation and genotypic coefficients of variation were obtained for plant height (19.43, 11.73), pod length (11.27, 10.69), and 100-seed weight (15.42, 12.74). High heritability in the broad sense was found for days to 50% flowering (66.98), days to 90% maturity (87.43), pod length (90.03), pod width (78.23), harvest index (98.67), and 100-seed weight (68.31). High genetic advance as a percentage of mean with high heritability was obtained for...
African Journal of Agricultural Research, 2019
Knowledge of the sources and magnitude of variability among genotypes plays a pivotal role in any crop improvement program to maximize gains from selection. This experiment was conducted at Bako Agricultural Research Center in 2011 cropping season with the objective of studying and estimating the extent of genetic variability in common bean genotypes under sole and mixed cropping systems. Meanwhile, the wider range of variability observed from the mean of various quantitative traits. The genotypes that varied by cropping system depicted the presence of high level of variability. The highest genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) values were recorded for hundred grain weight (29.56 and 35.46 g), biological yield (27.22 and 31.37) and grain yield (26.60 and 31.54 q/ha), whereas the lowest GCV and PCV values were recorded for days to maturity of sole common bean genotypes. Phenotypic variance in both sole and mixed cropping systems was higher than that of genotypic variances. This implies that, considerable contribution of environmental factors to the phenotypic expression of the genotypes. High broad sense heritability as observed under both sole and intercropping systems indicated that, genetic improvement can be obtained through further selection programme. Important agronomic traits: pods per plant, seeds per pod and branches per plant had positive and significant correlation with grain yield in most cases. Path coefficient analysis at genotypic level indicated that all traits except plant height, seeds per pod and hundred grain weights exerted their positive direct effect on grain yield. Hence, the current study identified the presence of wide variability between those common bean genotypes which can be used for further breeding program and selection can be made using those traits associated to yield.
African Journal of Biotechnology, 2014
The knowledge and understanding of the genetic variability of common bean (Phaseolus vulgaris L.) germplasm is important for the implementation of measures addressed to their utilizations and conservation. The objective of this study was to characterize common bean in Uganda using polymorphic molecular markers for use in hybridization and variety development. Genomic DNA was extracted from plants at the first trifoliate leaf stage growing in pots using the modified cetyltrimethylammonium bromide (CTAB) method. The gene pool membership (Andean vs. Mesoamerican) for each accession was established with the phaseolin marker. Simple sequence repeat (SSR) alleles were separated by capillary electrophoresis that provided further information on the organization of genetic diversity. The Andean and Mesoamerican genotypes were present in similar frequencies (51 vs. 49%, respectively). All SSR markers tested were polymorphic with mean polymorphism information content (PIC) of 0.8. The model-based cluster analysis of SSR diversity in the STRUCTURE software found three sub populations (K3.1, K3.2 and K3.3) genetically differentiated with moderate Wrights fixation indices (F ST) values 0.14, 0.12 and 0.09, respectively and many cases of admixture. The STRUCTURE result was confirmed by principal coordinate analysis (PCoA) which also clustered beans in three groups. Most Andean genotypes were included in K3.1 and Mesoamerican genotypes belonged to the K3.2 and K3.3 subgroups. This study sets the stage for further analyses for agronomic traits such as yield, resistance to biotic and abiotic stresses and the need for germplasm conservation.
SINET: Ethiopian Journal of Science, 2021
Lima bean (Phaseolus lunatus L.) is one of the five most important legume crops from the genus Phaseolus though it is one of the neglected crops in Ethiopia. There is no national breeding program for its improvement. As it is true for all crops, understanding the genetic diversity of Lima bean is useful for its improvement and sustainable use. Therefore, the objective of the current study was to investigate genetic diversity of Lima bean landrace collected in Ethiopia using eight issr markers. A total of 96 landrace were collected from five administrative zones of Ethiopia from which 106 clear bands were detected. About 95 (88.7%) of the bands were polymorphic. The genetic diversity analyses result revealed that landrace collected from West Wellega showed the highest (0.1864) genetic diversity. amova demonstrated highly significant (P=0.00) genetic diversity among and within populations. A considerable proportion (66%) of the total genetic diversity was distributed among populations...
Advances in Agriculture
The efficiency of variety development can be determined with variability and genetic progress of released varieties. The aim of this study was to determine the variability and genetic advancement of common bean varieties. Randomized Completed Block Design was used to evaluate 15 varieties at Koga and Chefa in 2013. Cluster, principal, and biplot analysis including genetic parameter estimation were done following analysis of variance. Significant variation was observed among the varieties, and they are clustered into four groups. Seed color and size were found as an important factors for clustering of the varieties. Hawassa Dume and Nasir have red and small seeded, respectively, and clustered in one group. Similarly, Awash 1 and Awash Melka are both small white and clustered in one group. Hawassa Dume was highly similar to Nasir, and Red Wolayta with Dimitu, while a large distance was recorded between Awash Melka and Haramaya. Deme and Haramaya were found the most divergent and uniqu...
Research & Reviews: Journal of Botany , 2021
This experiment was conducted in Guraghe and Siltie Zones of Southern Ethiopia to assess the extents of variability and associations of characters among common bean genotypes. Data were collected on nine quantitative traits. The analysis of variance revealed significant variation among the traits. Moderate genotypic and phenotypic coefficient of variation was observed for 100 seeds' weight, pod length and seed per plant. Highest heritability and genetic advances as percent mean values were observed for 100 seeds' weight and pod length. Seed yield had positive and significant association with most traits at both phenotypic and genotypic levels. The maximum positive direct effects on seed yield were exerted by pods per plant and days to 90% maturity. The moderate positive indirect effect on seed yield was exerted days to 90% maturity through pods per plant. Four major PCs explained 79.72% of total variation. Pod per plant from all PCs, seed yield and days to 90% maturity were from PC1, seed per pod and days to 50% flowering from PC1 and PC2, plant height from PC2 and PC3 and seed per plant from PC1, PC3. Therefore, in future these traits would be used for selection of genotypes as improving seed yield among these common bean genotypes.
Genetic Resources and Crop Evolution
Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a Electronic supplementary material The online version of this article (
Genetic Diversity of Dry Bean (Phaseolus vulgaris L.) Accessions of Kenya Using SSR Markers
American Journal of Experimental Agriculture, 2015
Aims: To determine the genetic diversity existing within the Kenyan dry bean using SSR markers. Place and Duration of Study: This study was conducted in Western Kenya and Bangor University, North Wales, between September 2010 and December 2012. Methodology: Thirty five (35) marketable dry bean samples collected from farmers, market centers as well as seed stockists were subjected to SSR analysis. Data generated was subjected to analysis with the GenAlEx 6.4 software assuming Hardy-Weinberg equilibrium to determine gene diversity index, number of polymorphic loci and alleles, genetic distances, analysis of molecular Original Research Article