Genetic diversity and population structure of common bean ( Phaseolus vulgaris L . ) landraces from the East African highlands (original) (raw)
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TAG Theoretical and …, 2010
The Great Lakes region of Central Africa is a major producer of common beans in Africa. The region is known for high population density and small average farm size. The common bean represents the most important legume crop of the region, grown on over a third of the cultivated land area, and the per capita consumption is among the highest in the world for the food crop. The objective of this study was to evaluate the genetic diversity in a collection of 365 genotypes from the Great Lakes region of Central Africa, including a large group of landraces from Rwanda as well as varieties from primary centers of diversity and from neighboring countries of Central Africa, such as the Democratic Republic of Congo and Uganda, using 30 fluorescently labeled microsatellite markers and automated allele detection. In addition, the landraces were evaluated for their seed iron and zinc concentration to determine if genetic diversity influenced nutritional quality. Principal coordinate and neighbor-joining analyses allowed the separation of the landraces into 132 Andean and 195 Mesoamerican (or Middle American) genotypes with 32 landraces and 6 varieties intermediate between the gene pools and representing inter-gene pool introgression in terms of seed characteristics and alleles. Genetic diversity and the number of alleles were high for the collection, reflecting the preference for a wide range of seed types in the region and no strong commercial class preference, although red, red mottled and brown seeded beans were common. Observed heterozygosity was also high and may be explained by the common practice of maintaining seed and plant mixtures, a coping strategy practiced by Central African farmers to reduce the effects of abiotic and biotic stresses. Finally, nutritional quality differed between the gene pools with respect to seed iron and zinc concentration, while genotypes from the intermediate group were notably high in both minerals. In conclusion, this study has shown that Central African varieties of common bean are a source of wide genetic diversity with variable nutritional quality that can be used in crop improvement programs for the region.
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.
French bean (Phaseolus vulgaris L.) in Kenya is cultivated predominantly in the Central, Eastern and Rift Valley provinces. Despite its importance as an export commodity, there has been little breeding effort devoted to its improvement and no much focus on gaining an understanding of the genetic diversity of the germplasm used in cultivation. The present objective was to evaluate the genetic diversity of a set of 36 Kenyan French bean accessions, based on a combination of morpho-agronomic and simple sequence repeat markers (SSRs). For the former, 20 morpho-agronomic traits were measured in two growing seasons, while for the latter; the germplasm was genotyped at 26 SSR loci. The accessions varied significantly (P≤ 0.05) with respect to pod diameter, pod length, pod number per plant, pod weight per plant and seed weight, but not with respect to the number of days taken to reach flowering, leaf length, leaf width or plant height. There was a large influence of season over flowering ti...
Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project
Plant Breeding
Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market-driven approaches to develop client-demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender-responsive participatory variety selection, market-demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics. K E Y W O R D S breeding tools, common bean, demand-led, micronutrient content, production constraints 1 | INTRODUCTION Common bean (Phaseolus vulgaris L.) is grown on about 30 million hectares globally and on 7.6 million ha in Africa annually where it is consumed and traded by more than 100 million households (Buruchara et al., 2011; FAOSTAT, 2014). Being a major staple, common bean contributes to health, food and nutritional security as it is wellendowed with starch, protein, fibre and minerals such as iron, zinc, potassium, selenium, molybdenum and vitamins (thiamine, vitamin B6) and folate. It is an ideal crop for the smallholder farming systems due to its capability to fix N, short maturity period (≤3 months), easily converted to cash to meet urgent household needs, relatively long storage and convenience of handling the harvest and its compatibility with other crops (maize, cassava, banana, etc.), in many low-input production systems. Three East African countries, Kenya, Tanzania and Uganda, are among the global leaders of common bean production (Akibode & Maredia, 2011; FAOSTAT, 2016). The per capita consumption of 40-60 kg/year in Rwanda, Kenya and Uganda is the highest in the world (Beebe, Rao, Blair, & Acosta-Gallegos, 2013; Broughton et al., 2003). A unique partnership model involving CIAT and its research partners, together with effective breeding and seed delivery strategies, have helped to reach millions of beneficiaries with improved bean varieties (Buruchara et al., 2011). There is a notable increase in bean production in most African countries in the
Journal of Plant Breeding and Crop Science, 2015
French bean (Phaseolus vulgaris L.) in Kenya is cultivated predominantly in the Central, Eastern and Rift Valley provinces. Despite its importance as an export commodity, there has been little breeding effort devoted to its improvement and no much focus on gaining an understanding of the genetic diversity of the germplasm used in cultivation. The present objective was to evaluate the genetic diversity of a set of 36 Kenyan French bean accessions, based on a combination of morpho-agronomic and simple sequence repeat markers (SSRs). For the former, 20 morpho-agronomic traits were measured in two growing seasons, while for the latter; the germplasm was genotyped at 26 SSR loci. The accessions varied significantly (P≤ 0.05) with respect to pod diameter, pod length, pod number per plant, pod weight per plant and seed weight, but not with respect to the number of days taken to reach flowering, leaf length, leaf width or plant height. There was a large influence of season over flowering time, pod diameter, pod length, plant height and seed weight, and a significant (P≤ 0.05) interaction between accession and season for pod diameter, pod length, pod weight per plant, number of pods per plant and seed weight. The variation in the morpho-agronomic traits split the 36 accessions into four clusters. Shannon-Weaver diversity indices for qualitative, pseudo-qualitative and four selected quantitative traits ranged from 0.23 to 0.88. Of the 26 SSR primer pairs, which successfully amplified all 36 DNAs, 18 were informative, producing a mean of 2.17 alleles per SSR locus and a PIC value between 0.17 and 0.41. The level of gene diversity ranged from 0.19-0.50 (mean 0.36). The low observed mean heterozygosity reflected the predominantly autogamous habit of French bean. The modest amount of genotypic variation uncovered can be attributed to the effect of intensive selection for pod quality. A phylogeny based on the informative SSR loci revealed three major clusters, each representing a different pod diameter class. Combining the morpho-agronomic and DNA-based markers in this assessment of germplasm provides a way of taking advantage of the best features of both marker types that can be useful for identification of French bean varieties and applications of molecular markers to breeding.
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.
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.
Molecular Biology Reports
Introduction Common bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies. Materials Two hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers. Results The overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the impr...
Journal of Experimental Biology and Agricultural Sciences, 2017
In order to provide essential information for plant breeding and crop improvement programs, genetic diversity assessment is a prerequisite. In this study, starch gel electrophoresis of 9 enzyme systems encoding 19 putative loci was used to assess allozyme diversity of 13 cultivated common bean (Phaseolus vulgaris) accessions from Cameroon and 21 from Kenya. Results of genetic variation among the studied accessions revealed 26.32% as proportion of polymorphic loci (P), 1.263 as average number of alleles per locus (A), 0.007 as observed heterozygosity (HO) and 0.079 as the total expected heterozygosity (HT). The level of genetic diversity within and among the various accessions were HS= 0.014 ± 0.003 and DST = 0.065 ± 0.013 respectively. G-statistics estimation indicated a high level of genetic heterogeneity between accessions (GST=0.825 ± 0.021), suggesting that cultivated P.vulgaris maintains about 82.5 % of its genetic variation among accessions. This distribution was more pronounced in Kenyan accessions (89.2 %) compared to Cameroonian accessions (69.9%). Important deviation from Hardy-Weinberg expectations was reported in this study (FIT = 0.903 ± 0.018). This genetic disequilibrium is likely due to either high genetic differentiation between accessions (FST=0.861 ± 0.023) or significant nonrandom mating within accessions (FIS = 0.233 ± 0.096). There was no significant gene flow among cultivated P.vulgaris accessions in Cameroon (Nm = 0.058 ± 0.029) and in Kenya (Nm = 0.045 ± 0.041).