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

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

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Genome Sequence of Venturia oleaginea, the Causal Agent of Olive Leaf Scab

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0070-a ◽

2020 ◽

Vol 33 (9) ◽

pp. 1095-1097

Author(s):

Mohammed Y. Jaber ◽

Jiandong Bao ◽

Xiuqin Gao ◽

Limei Zhang ◽

Dou He ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Population Genetic ◽

Whole Genome Sequence ◽

Whole Genome ◽

Olive Leaf ◽

Spot Disease ◽

Host Interaction ◽

Fungal Biology

Olive leaf scab, also known as peacock spot disease, caused by Venturia oleaginea (syn. Spilocaea oleaginea and Fusicladium oleagineum) is the most widespread and economically important fungal disease attacking olive in production countries. Here, we report the first highly contiguous whole-genome sequence (46.08 Mb) of one isolate, YUN35, of V. oleaginea. The described genome sequence and annotation resource will be useful to study the fungal biology, pathogen-host interaction, characterization of genes of interest, and population genetic diversity.

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

Plant Genetic Resources ◽

10.1017/s1479262110000420 ◽

2011 ◽

Vol 9 (01) ◽

pp. 86-96 ◽

Cited By ~ 17

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.

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Recombinants of Bean common mosaic virus (BCMV) and Genetic Determinants of BCMV Involved in Overcoming Resistance in Common Bean

Phytopathology ◽

10.1094/phyto-08-13-0243-r ◽

2014 ◽

Vol 104 (7) ◽

pp. 786-793 ◽

Cited By ~ 22

Author(s):

Xue Feng ◽

Alan R. Poplawsky ◽

Olga V. Nikolaeva ◽

James R. Myers ◽

Alexander V. Karasev

Keyword(s):

Common Bean ◽

Mosaic Virus ◽

Resistance Genes ◽

Bean Common Mosaic Virus ◽

Whole Genome ◽

Genetic Determinant ◽

Genetic Determinants ◽

Resistance Factors ◽

Pro Region

Bean common mosaic virus (BCMV) exists as a complex of strains classified by reactions to resistance genes found in common bean (Phaseolus vulgaris); seven BCMV pathotypes have been distinguished thus far, numbered I to VII. Virus genetic determinants involved in pathogenicity interactions with resistance genes have not yet been identified. Here, we describe the characterization of two novel field isolates of BCMV that helped to narrow down these genetic determinants interacting with specific P. vulgaris resistance factors. Based on a biological characterization on common bean differentials, both isolates were classified as belonging to pathotype VII, similar to control isolate US10, and both isolates exhibited the B serotype. The whole genome was sequenced for both isolates and found to be 98 to 99% identical to the BCMV isolate RU1 (pathotype VI), and a single name was retained: BCMV RU1-OR. To identify a genetic determinant of BCMV linked to the BCMV pathotype VII, the whole genome was also sequenced for two control isolates, US10 and RU1-P. Inspection of the nucleotide sequences for BCMV RU1-OR and US10 (both pathotype VII) and three closely related sequences of BCMV (RU1-P, RU1-D, and RU1-W, all pathotype VI) revealed that RU1-OR originated through a series of recombination events between US10 and an as-yet-unidentified BCMV parental genome, resulting in changes in virus pathology. The data obtained suggest that a fragment of the RU1-OR genome between positions 723 and 1,961 nucleotides that is common to US10 and RU1-OR in the P1-HC-Pro region of the BCMV genome may be responsible for the ability to overcome resistance in bean conferred by the bc-22 gene. This is the first report of a virus genetic determinant responsible for overcoming a specific BCMV resistance gene in common bean.

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

Plant Genetic Resources ◽

10.1017/s1479262112000020 ◽

2012 ◽

Vol 10 (1) ◽

pp. 83-92 ◽

Cited By ~ 9

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.

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

Genome ◽

10.1139/g94-036 ◽

1994 ◽

Vol 37 (2) ◽

pp. 256-263 ◽

Cited By ~ 115

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.

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

Molecular Breeding ◽

10.1007/s11032-012-9806-8 ◽

2012 ◽

Vol 31 (3) ◽

pp. 501-516 ◽

Cited By ~ 6

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

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The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L.)

Acta agriculturae Slovenica ◽

10.2478/v10014-008-0009-2 ◽

2008 ◽

Vol 91 (1) ◽

Cited By ~ 15

Author(s):

Marko Maras ◽

Jelka Šuštar-Vozlič ◽

Branka Javornik ◽

Vladimir Meglič

Keyword(s):

Genetic Diversity ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Ssr Markers ◽

Gene Pool ◽

Phaseolus Vulgaris L

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

World Journal of Advanced Research and Reviews ◽

10.30574/wjarr.2021.12.1.0532 ◽

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.

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Examination of Genetic Diversity of Common Bean from the Western Balkans

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.4.308 ◽

2015 ◽

Vol 140 (4) ◽

pp. 308-316 ◽

Cited By ~ 14

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.

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