Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 266-280 ◽  
Author(s):  
Phillip E McClean ◽  
Rian K Lee ◽  
Phillip N Miklas
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Sequence Data ◽  
Gene Pools ◽  
Specific Primers ◽  
Drift Model ◽  
Intron 1 ◽  
Allele Specific ◽  
Sufficient Variation ◽  
Diversity Studies

Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (π/bp) was 0.0481, a value higher than that reported for introns from other plant species. Tests for significant deviation from the mutation drift model were positive for the population as a whole, the cultivar and landrace subsets, and the Middle American landrace set. Significant linkage disequilibrium extended about 300 nucleotides. Twenty haplotypes were detected among the cultivated genotypes. Seven recombination events were detected for the whole population, and six events for the landraces. Recombination was not observed among the landraces within either the Middle American or Andean gene pools. Evidence for hybridization between the two gene pools was discovered. Five allele-specific primers were developed that could distinguish 56 additional genotypes. The allele-specific primers were used to map duplicate DFR genes on linkage group B8.Key words: Phaseolus vulgaris, intron, diversity, evolution.

scholarly journals Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

2011 ◽  
Vol 38 (12) ◽  
pp. 953 ◽  
Author(s):  
Sujan Mamidi ◽  
Monica Rossi ◽  
Deepti Annam ◽  
Samira Moghaddam ◽  
Rian Lee ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Gene Pool ◽  
Sequence Data ◽  
Gene Pools ◽  
Before Present ◽  
History Of ◽  
Approximate Bayesian ◽  
Population Demographic

Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.

scholarly journals Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Heredity ◽  
2012 ◽  
Vol 110 (3) ◽  
pp. 267-276 ◽  
Author(s):  
S Mamidi ◽  
M Rossi ◽  
S M Moghaddam ◽  
D Annam ◽  
R Lee ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Demographic Factors ◽  
Gene Pools ◽  
Phaseolus Vulgaris L

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 Genetic Diversity and Pathogenic Variation of Colletotrichum lindemuthianum in the Three Centers of Diversity of Its Host, Phaseolus vulgaris

1997 ◽  
Vol 87 (8) ◽  
pp. 807-813 ◽  
Author(s):  
D. Sicard ◽  
Y. Michalakis ◽  
M. Dron ◽  
C. Neema
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Colletotrichum Lindemuthianum ◽  
Population Subdivision ◽  
Gene Pools ◽  
Internal Transcribed Spacer Region ◽  
Mexican Strains

Population subdivision of Colletotrichum lindemuthianum, the causal agent of anthracnose, was studied in three regions located in three centers of diversity of its host, Phaseolus vulgaris. Random amplified polymorphic DNA (RAPD) markers, restriction endonuclease analysis of the amplified ribosomal internal transcribed spacer region, and virulence on a set of 12 cultivars were used to assess the genetic diversity of C. lindemuthianum strains isolated in Mexican, Ecuadorian, and Argentinean wild common bean populations. The three regions were significantly differentiated for molecular markers. For these markers, Mexico was the most polymorphic and the most distant from Ecuador and Argentina. The majority of the RAPD alleles present in Ecuador and Argentina were found in Mexico, suggesting that Andean populations have been derived from the Mesoamerican center. Pathogenicity tests on a set of 12 cultivars showed that all but one of the Mexican strains were virulent exclusively on Mesoamerican cultivars. Argentinean strains were virulent preferentially on southern Andes cultivars, and the Ecuadorian strains, except for one strain, were avirulent on all cultivars. These results suggest an adaptation of strains on cultivars of the same geographic origin. Thus, based on molecular and virulence markers, C. lindemuthianum strains isolated from wild common bean populations were divided into three groups corresponding to host gene pools.

Development of a SCAR marker linked to the I gene in common bean

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1216-1219 ◽  
Author(s):  
M. Melotto ◽  
L. Afanador ◽  
J. D. Kelly
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Rapd Marker ◽  
Bean Common Mosaic Virus ◽  
Gene Pools ◽  
Phaseolus Vulgaris L ◽  
Breeding Programs ◽  
Heat Stable ◽  
Rapd Primer ◽  
I Gene

Two 24-mer SCAR primers (SW13) were developed from a previously identified 10-mer RAPD primer (OW13690) linked to the I gene, which conditions resistance to bean common mosaic virus (BCMV) in common bean. Linkage between SW13 and the I gene was tested in three F2 populations segregating for both SW13 and the I gene: N84004/Michelite (1.0 ± 0.7 cM), Seafarer/UI-114 (1.3 ± 0.8 cM), and G91201/Alpine (5.0 ± 2.2 cM). SW13 proved to be more specific and reproducible than the OW13690 RAPD marker. Using different heat-stable DNA polymerases, SW13 amplified a single 690-bp fragment linked to the I gene that more consistently permitted the identification of resistant plants. In addition, the presence of the I gene was detected using SW13 in genotypes originating from different gene pools of Phaseolus vulgaris L., indicating a broad utility of this marker for bean breeding programs. Key words : Phaseolus vulgaris, SCAR, RAPD, BCMV.

Analysis of the contribution of Mesoamerican and Andean gene pools to European common bean (Phaseolus vulgaris L.) germplasm and strategies to establish a core collection

2007 ◽  
Vol 54 (8) ◽  
pp. 1763-1779 ◽  
Author(s):  
Giuseppina Logozzo ◽  
Rosa Donnoli ◽  
Leonardo Macaluso ◽  
Roberto Papa ◽  
Helmut Knüpffer ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Core Collection ◽  
Gene Pools ◽  
Phaseolus Vulgaris L

scholarly journals Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data

2012 ◽  
Vol 109 (14) ◽  
pp. E788-E796 ◽  
Author(s):  
E. Bitocchi ◽  
L. Nanni ◽  
E. Bellucci ◽  
M. Rossi ◽  
A. Giardini ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Sequence Data ◽  
Phaseolus Vulgaris L ◽  
The Common

scholarly journals SELECTION FOR YIELD AT TWO FERTILIZER LEVELS IN SMALL-SEEDED COMMON BEAN

1989 ◽  
Vol 69 (3) ◽  
pp. 1011-1017 ◽  
Author(s):  
SHREE P. SINGH ◽  
CARLOS A. URREA ◽  
J. ARIEL GUTIERREZ ◽  
JAMES GARCIA
Keyword(s):  
Phaseolus Vulgaris ◽  
Soil Fertility ◽  
Common Bean ◽  
Seed Yield ◽  
Soil Phosphorus ◽  
Low Fertility ◽  
Gene Pools ◽  
High Fertility ◽  
The Mean ◽  
Selection For

Selection for seed yield (visual in the F2, visual and plot yield from the F3 to F5, and yield tests in F6) was carried out in two crosses of common bean (Phaseolus vulgaris L.) in high and low soil fertility environments at CIAT-Quilichao, Colombia. Parents were small-seeded and tolerant to low soil phosphorus, possessed indeterminate bush growth habit, and belonged to lowland tropical gene pools of Middle America. The mean yield of selected lines from low (LFS) and high (HFS) soil fertility environments was significantly higher than the mean of the parents in both crosses when tested in high fertility (HF) but not in low fertility (LF). The highest yielding LFS and HFS lines from A 286 × (G 5059 × A 80) and the LFS line from A 286 × ICA Pijao outyielded the best check cultivar, Carioca, in HF. No line yielded significantly more than A 286, the best parent used in both crosses. The mean effect of fertilizer levels on selection for seed yield was nonsignificant. Lines selected under two environments showed similar but average response and high stability of performance under variable environments. Low soil fertility accelerated maturity and reduced 100-seed weight and seed yield.Key words: Phaseolus vulgaris, bean (small-seeded common), selection for yield, soil fertility, Middle American gene pools, regression coefficient

Genetic architecture of chalcone isomerase non-coding regions in common bean (Phaseolus vulgaris L.)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 203-214 ◽  
Author(s):  
Phillip E. McClean ◽  
Rian K. Lee
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Genetic Architecture ◽  
Sequence Data ◽  
Balancing Selection ◽  
Chalcone Isomerase ◽  
Nucleotide Polymorphisms ◽  
Phaseolus Vulgaris L ◽  
Ancestral Gene ◽  
Coding Regions

Sequence data for 2 non-coding regions of the chalcone isomerase gene were analyzed to study the genetic architecture of common bean ( Phaseolus vulgaris L.). One region corresponded to the first 596 nucleotides (nt) of the 5′-untranslated region (UTR). The other region was the 710 nt intron 3. Data were collected from 67 genotypes representing both landraces and cultivars from the geographical range of the cultivated form of the species. Variability in the 5′-UTR region was represented by single nucleotide polymorphisms (SNPs), whereas intron 3 variation was due to a collection of SNPs and insertion–deletion events. Diversity was greater in the 5′-UTR (π = 0.0175) than in intron 3 (π = 0.0089). For each region, diversity was greater for genotypes of Middle American than Andean origin. A single recombination event was observed, and the hybridization pattern necessary to derive the recombinant genotypes supported the previous observation of an ancestral gene pool from which modern domesticated genotypes are derived. For both regions, a strongly supported Andean group was observed, whereas the presence of 2 Middle American subgroups was also supported. Although a significantly positive Tajima’s D statistic was observed for the 5′-UTR for all genotypes, we conclude that this is more likely the result of a strong demographic effect and that balancing selection is occurring only among the Middle American genotypes.

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