Patterns of genetic diversity in the Andean gene pool of common bean reveal a candidate domestication gene

2012 ◽  
Vol 31 (3) ◽  
pp. 501-516 ◽  
Author(s):  
María De La Fuente ◽  
Ana M. González ◽  
Antonio M. De Ron ◽  
Marta Santalla
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Gene Pool ◽  
Andean Gene Pool

Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites

2011 ◽  
Vol 9 (01) ◽  
pp. 86-96 ◽  
Author(s):  
Lucy M. Díaz ◽  
Héctor F. Buendía ◽  
Myriam C. Duque ◽  
Matthew W. Blair
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Common Bean ◽  
Gene Pool ◽  
Major Gene ◽  
Gene Pools ◽  
Silver Stain ◽  
Fluorescent Marker ◽  
Fluorescent Markers

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgarisL.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescentversusnon-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

Genetic diversity of bean (Phaseolus) landraces and wild relatives from the primary centre of origin of the Southern Andes

2012 ◽  
Vol 10 (1) ◽  
pp. 83-92 ◽  
Author(s):  
Teresa Avila ◽  
Matthew W. Blair ◽  
Ximena Reyes ◽  
Pierre Bertin
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Gene Pool ◽  
Morphological Characteristics ◽  
Germplasm Collection ◽  
Genetic Distances ◽  
Phaseolus Lunatus ◽  
Group Method ◽  
Common Beans ◽  
Southern Andes

The Southern Andes, especially the inter-Andean valleys of south Bolivia, is thought to be a probable point of domestication within the primary centre of diversity for Andean common beans (Phaseolus vulgaris L.). The national Phaseolus germplasm collection of Bolivia is maintained by the Pairumani Foundation and consists of 449 accessions where most of the accessions are of common bean but some are of related cultivated and wild species. The goal of this study was to determine the genetic diversity of this collection by sampling 174 accessions of P. vulgaris and an outgroup of eight Phaseolus augusti, two Phaseolus lunatus and one Phaseolus coccineus genotype. The genetic diversity and population structure were estimated using 29 microsatellite markers. High levels of polymorphism were found, with a total of 311 alleles identified and an average of 10.7 alleles per marker. Correspondence analysis and an unweighted pair group method with arithmetic mean-based dendrogram distinguished P. vulgaris from the other species of Phaseolus. Common bean accessions were separated into two groups: the first one including Andean controls and most accessions from high altitudes with morphological characteristics and growth habits typical of this gene pool; the second one including Mesoamerican controls and accessions from low altitudes. Inside the Andean gene pool, the wild accessions were diverse and separated from the weedy and cultivated accessions. Low geographical distances between collection sites (up to 100 km) were shown to be related to low genetic distances. These results are important for the conservation of common beans in the Southern Andes.

RFLP diversity of common bean (Phaseolus vulgaris) in its centres of origin

Genome ◽  
1994 ◽  
Vol 37 (2) ◽  
pp. 256-263 ◽  
Author(s):  
Viviana L. Becerra Velasquez ◽  
Paul Gepts
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Gene Pool ◽  
Geographical Area ◽  
Rflp Markers ◽  
Gene Pools ◽  
Restriction Fragment Length

Eighty-five wild and cultivated accessions of common bean (Phaseolus vulgaris L.), representing a wide geographic area in the centres of domestication were tested for restriction fragment length polymorphisms (RFLPs). Genomic DNA was digested with one of three restriction enzymes (EcoRI, EcoRV, and HindIII) and hybridized to 12 probes distributed throughout the common bean genome. Accessions could be classified into two major groups with a distinct geographical distribution in Middle America and the Andes. Within each gene pool, cultivated accessions clustered together with wild forms from the same geographical area supporting the multiple domestications hypothesis for this crop. Estimates of Nei's genetic distances among the cultivated races from the two different gene pools varied from 0.12 to 0.56 and among races from the same gene pool from 0.04 to 0.12, suggesting that the divergence in Phaseolus vulgaris has reached the subspecies level. The level of genetic diversity (Ht = 0.38) was twice the value obtained with isozyme analysis. Genetic diversity within races (Hs = 0.27) was four to five times higher compared with isozymes, but genetic diversity between races (Dst = 0.11) was similar for both categories of markers. These results corroborate previous studies on the characterization of genetic diversity in common bean that clearly showed two distinct gene pools, Middle American and Andean. Moreover, RFLP markers are superior to isozymes because they provide better coverage of the genome and reveal higher level of polymorphisms.Key words: common bean, restriction fragment length polymorphism, domestication, genetic diversity.

scholarly journals Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0205363 ◽  
Author(s):  
Muhammad Azhar Nadeem ◽  
Ephrem Habyarimana ◽  
Vahdettin Çiftçi ◽  
Muhammad Amjad Nawaz ◽  
Tolga Karaköy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Gene Pool ◽  
Whole Genome ◽  
Marker Information

scholarly journals Population structure and genetic diversity in common bean accessions from Northeast Brazil

2021 ◽  
Vol 12 (1) ◽  
pp. 287-297
Author(s):  
Maria da Conceição Martiniano-Souza ◽  
Maria Celeste Gonçalves-Vidigal ◽  
Giseli Valentini ◽  
Julio Cesar Ferreira Elias ◽  
Larissa Fernanda Sega Xavier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Pool ◽  
Northeast Brazil ◽  
Tropical Regions ◽  
High Quality Snps ◽  
Population Structure Analysis ◽  
Great Relevance ◽  
Bioclimatic Conditions

Common bean is of great relevance for several countries, especially those located in tropical regions. Common bean in Brazil has a wide genetic diversity, which is used by breeders to improve this crop. In this study, we used GBS methodology to genotype common bean accessions from Northeast Brazil, and to study its population structure and genetic diversity. After a filtering process, we identified 30,529 high-quality SNPs distributed in 11 linkage groups. The number of SNPs per chromosome ranged from 1,731 to 3,853. The population structure analysis separated the accessions into two subpopulations, according to K=2, one subpopulation with 26 Andean and the other with 60 Middle American accessions. Considering K=3, Middle American accessions were divided into two subpopulations with presence of allele mixture between these two groups. Based on the PCA, we were able to verify a narrow genetic base of accessions belonging to the Andean gene pool, as well as a vast genetic diversity among the accessions from the Middle American gene pool. The knowledge on the genetic diversity among the accessions is of extreme importance to subsidize the common bean breeding programs in Northeast Brazil, and to explore the variability existing in cultivars adapted to the specific bioclimatic conditions.

scholarly journals Examination of Genetic Diversity of Common Bean from the Western Balkans

2015 ◽  
Vol 140 (4) ◽  
pp. 308-316 ◽  
Author(s):  
Marko Maras ◽  
Barbara Pipan ◽  
Jelka Šuštar-Vozlič ◽  
Vida Todorović ◽  
Gordana Đurić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Common Bean ◽  
Gene Pool ◽  
Molecular Data ◽  
Gene Pools ◽  
Western Balkans ◽  
Mesoamerican Gene Pool ◽  
Information Index ◽  
Large Clusters

In this study, genetic diversity of 119 accessions of common bean (Phaseolus vulgaris) from five former Yugoslav republics constituting the western Balkans was assessed by 13 microsatellite markers. This set of markers has proven before to efficiently distinguish between bean genotypes and assign them to either the Andean or the Mesoamerican gene pool of origin. In this study, 118 alleles were detected or 9.1 per locus on average. Four groups (i.e., Slovene, Croatian, Bosnian, and Serbian) showed similarly high levels of genetic diversity as estimated by the number of different alleles, number of effective alleles, Shannon’s information index, and expected heterozygosity. Mildly narrower genetic diversity was identified within a group of Macedonian accessions; however, this germplasm yielded the highest number of private alleles. All five germplasms share a great portion of genetic diversity as indicated by the analysis of molecular variance (AMOVA). On the basis of the scored number of migrants, we concluded that the most intensive gene flow in the region exists in Bosnia and Herzegovina. Cluster analysis based on collected molecular data classified the accessions into two large clusters that corresponded to two gene pools of origin (i.e., Andean and Mesoamerican). We found that Andean genotypes are more prevalent than Mesoamerican in all studied countries, except Macedonia, where the two gene pools are represented evenly. This could indicate that common bean was introduced into the western Balkans mainly from the Mediterranean Basin. Bayesian cluster analysis revealed that in the area studied an additional variation exists which is related to the Andean gene pool. Different scenarios of the origin of this variation are discussed in the article.

Patterns of resistance to angular leaf spot, anthracnose and common bacterial blight in common bean germplasm

2002 ◽  
Vol 42 (4) ◽  
pp. 481 ◽  
Author(s):  
F. M. A. Islam ◽  
K. E. Basford ◽  
R. J. Redden ◽  
C. Jara ◽  
S. Beebe
Keyword(s):  
Common Bean ◽  
Leaf Spot ◽  
Gene Pool ◽  
Bacterial Blight ◽  
Insect Pests ◽  
Angular Leaf Spot ◽  
Common Bacterial Blight ◽  
The Andes ◽  
Andean Gene Pool ◽  
Resistance Patterns

Diseases and insect pests are major causes of low yields of common bean (Phaseolus vulgaris L.) in Latin America and Africa. Anthracnose, angular leaf spot and common bacterial blight are widespread foliar diseases of common bean that also infect pods and seeds. One thousand and eighty-two accessions from a common bean core collection from the primary centres of origin were investigated for reaction to these three diseases. Angular leaf spot and common bacterial blight were evaluated in the field at Santander de Quilichao, Colombia, and anthracnose was evaluated in a screenhouse in Popay�n, Colombia. By using the 15-group level from a hierarchical clustering procedure, it was found that 7 groups were formed with mainly Andean common bean accessions (Andean gene pool), 7 groups with mainly Middle American accessions (Middle American gene pool), while 1�group contained mixed accessions. Consistent with the theory of co-evolution, it was generally observed that accessions from the Andean gene pool were resistant to Middle American pathogen isolates causing anthracnoxe, while the Middle American accessions were resistant to pathogen isolates from the Andes. Different combinations of resistance patterns were found, and breeders can use this information to select a specific group of accessions on the basis of their need.

Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool

2003 ◽  
Vol 108 (2) ◽  
pp. 243-252 ◽  
Author(s):  
F. M. Amirul Islam ◽  
S. Beebe ◽  
M. Muñoz ◽  
J. Tohme ◽  
R. J. Redden ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Common Bean ◽  
Gene Pool ◽  
Andean Gene Pool

scholarly journals Genetic diversity of common bean accessions from former Yugoslav Republic of Macedonia as revealed by molecular and morphological markers

Genetika ◽  
2016 ◽  
Vol 48 (2) ◽  
pp. 729-742 ◽  
Author(s):  
Marko Maras ◽  
Afrodita Ibusoska ◽  
Suzana Kratovalieva ◽  
Rukie Agic ◽  
Jelka Sustar-Vozlic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Gene Pool ◽  
Morphological Traits ◽  
High Capacity ◽  
Morphological Markers ◽  
Mesoamerican Gene Pool ◽  
Republic Of Macedonia ◽  
Upgma Dendrogram ◽  
Yugoslav Republic

Cultivation of common bean has a long tradition in the Former Yugoslav Republic of Macedonia (FYROM) and is still nowadays important part of the human diet. In a study reported here 71 accessions from the FYROM were assessed for genetic diversity with the aim to provide information on genetic structure of Macedonian common bean germplasm and to depict its peculiarities. A total of 71 accessions were assessed using 13 microsatellite and 16 morphological markers. The average number of alleles per microsatellite was 5.8, and ranged from three to 16 alleles. High capacity of selected markers for distinguishing genotypes was identified by the calculation of a very low value of probability of identity. The relationship among 71 studied accessions was assessed by hierarchical cluster analysis. A very clear separation of accessions into two groups was observed in the UPGMA dendrogram. The larger represented Andean gene pool and contained 40 accessions (56% of total), while the other 31 accessions (44% of total) composed Mesoamerican gene pool. The two groups were successfully discriminated by eight morphological traits. Within the larger Andean cluster in the UPGMA dendrogram a sub-group of 16 climbing accessions was separated from 24 bush accessions. The absence of the string in the pods of the climbers suggests that this sub-group comprises snap beans grown primarily for their fresh pods. There were eight morphological traits in total that distinguished the two Andean sub-groups. Assessment of genetic relationship among accessions, their classification into respective gene pool and identification of morphological peculiarities provided valuable information for the management of plant gene bank and Macedonian bean breeding program.

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