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Race structure and relationships among ecotypes in cultivated
                             common bean (Phaseolus vulgaris...
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poster8: Race structure and relationships among ecotypes in cultivated common bean (Phaseolus vulgaris L.)


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poster8: Race structure and relationships among ecotypes in cultivated common bean (Phaseolus vulgaris L.)

  1. 1. Race structure and relationships among ecotypes in cultivated common bean (Phaseolus vulgaris L.). Matthew W. Blair, Hector F. Buendía, Lucy Díaz, Juan M. Díaz, Myriam C. Duque, Steve Kresovich, Sharon Mitchell, Maria J. Peloso, Rosana Brondani, Xiaoyan Zhang, Shumin Wang, Teresa Avila, Ximena Rojas, Andrea Davila, Sandra Lorigados Introduction Tables and Figures Results and Discussion Common bean is the third most important grain legume Table 1. Genetic diversity values for microsatellites evaluated across the core Allele sizes were estimated by comparing the in the world produced over an area of 18 million collection. Genomic (n=20) fragment peaks with the internal Genescan-500 LIZ hectares with large amounts of production in developing No. AG01 9 0.590 0.186 0.542 Marker alleles Exp. Het. Obs. Het. PIC BM137 BM139 44 19 0.947 0.749 0.000 0.077 0.945 0.735 size standard in ABI3730 electropherograms and countries of Latin America and Eastern and Southern BM140 29 0.726 0.126 0.713 Gene-based (n=16) BMd01 17 0.896 0.386 0.887 BM141 BM143 35 40 0.864 0.929 0.269 0.138 0.852 0.925 calculated with Genemapper v. 3.7 software. Africa (Broughton et al., 2003). Cultivated common BMd02 BMd08 7 8 0.499 0.460 0.027 0.018 0.387 0.402 BM149 BM156 9 43 0.481 0.856 0.033 0.105 0.434 0.845 bean germplasm is especially diverse due to the BMd15 BMd16 13 15 0.491 0.560 0.325 0.117 0.424 0.467 BM160 BM172 37 41 0.811 0.813 0.091 0.145 0.804 0.805 Raw allele size calls were binned to assign a whole BMd17 7 0.630 0.081 0.565 existence of two genepools in the Mesoamerican and BMd18 BMd20 12 6 0.347 0.590 0.331 0.018 0.338 0.543 BM175 BM183 BM187 24 32 59 0.807 0.809 0.946 0.051 0.113 0.291 0.784 0.790 0.944 integer allele value using the software program Andean centers of diversity. The two genepools can BMd46 BMd47 BMd51 3 5 4 0.507 0.511 0.011 0.009 0.016 0.004 0.386 0.393 0.011 BM188 BM200 38 55 0.859 0.872 0.721 0.186 0.846 0.865 AlleloBin. Allele data was used to estimate simple BM201 15 0.725 0.070 0.693 be morphologically distinguished into various races PV-ctt001 PV-ag003 PV-at003 14 9 10 0.778 0.556 0.545 0.072 0.030 0.126 0.748 0.459 0.441 BM205 GATs54 15 7 0.820 0.453 0.230 0.061 0.800 0.370 matching dissimilarity matrices and to draw Neighbor GATs91 28 0.891 0.082 0.885 (Singh et al., 1991), however the association of these PV-at001 PV-cct001 70 7 0.970 0.087 0.000 0.028 0.969 0.086 BMd56 Total 2 581 0.264 0.018 0.229 Joining (NJ) trees for the genotypes in Darwin software Total 220 phenotypic divisions with genetic structure has not been Average 13 0.527 0.099 0.469 Average Overall Average 29.1 13.8 0.761 0.657 0.150 0.127 0.740 0.620 v. 5.0 and parameters of diversity evaluation were then clear. In the GCP genotyping project for common bean evaluated with PowerMarker v. 3.25. Finally, the we addressed this through a large-scale analysis of Figure 1. Dendrogram DJ1 DJ2-A number of populations (K) was evaluated with the based on dissimilarity software STRUCTURE assuming an admixture model international and national germplasm collections index for the reference M2 DJ2-B representing wide genetic variability from both primary collection of common DJ2-C with K=2 to K=15 and a total of 50,000 iterations each bean showing the and secondary centers of diversity using genomic and subdividisions within each M1 DJ2-D for both MCMC repetitions and burn in times. race. Race abbreviations INT-2 genic microsatellites. For this poster we concentrate on are M: Mesoamerica, DJ: INT-1 All the markers analyzed were polymorphic with the analysis of the CIAT core collection as it was Durango-Jalisco, P: Peru, from 2 to 59 alleles per marker (Table 1). The total NG: Nueva Granada, selected as a broad set of mostly landrace accessions Introg: Introgression INT-3 number of alleles identified was 801 with an average of from primary and secondary centers of diversity. All NG-A P-A 22.3 alleles per locus. The most polymorphic markers major agro-ecologies were covered in the core P-D were Pv-at01, BM187, BM200, BM137 and BM156, all NG-B collection as this was selected using a geographic P-C genomic microsatellites, while the gene-based information systems (GIS) approach taking into account NG-D NG-C microsatellites were correspondingly less polymorphic. P-B rainfall, temperature patterns, soils and maturity period. The genetic diversity based on Nei’s index for the Table 2. Genetic diversity parameters for clusters found within the core collection. entire set of genotypes was 0.657, which was high Materials and Methods Cluster Sample Size Allele No Availability Gene Observed compared to previous studies with microsatellites (Blair Diversity Heterozygosity DJ1 61 6.81 0.93 (He) 0.45 (Ho) 0.15 et al., 2006; Diaz and Blair, 2006). These values were Mesoamerican Genotypes: About half of the CIAT core collection was DJ2 DJ1-2 M1 101 162 52 9.72 10.69 6.14 0.94 0.94 0.96 0.51 0.51 0.40 0.15 0.15 0.10 Genepool even higher for the genomic microsatellites analyzed analyzed (600 genotypes) and included 293 M2 M1-2 54 106 7.39 8.94 0.95 0.95 0.48 0.46 0.11 0.11 alone (0.761) compared to the gene-based INT1 24 6.22 0.92 0.54 0.27 Mesoamerican genepool accessions and 307 Andean INT2 INT3 10 19 4.00 6.69 0.91 0.91 0.48 0.61 0.12 0.22 microsatellites analyzed alone (0.527). Observed genepool accessions. The majority of the accessions NG P 135 144 11.86 12.00 0.92 0.93 0.45 0.49 0.08 0.13 Andean Genepool heterozygosity was low, averaging 0.127 across all Total 600 22 0.93 0.657 0.13 were from the primary center of diversity especially the markers (0.099 for gene based and 0.150 for genomic countries of Mexico (183 genotypes) and Peru (172 markers). Some observed heterozygosity could be genotypes), while the remainder were from Argentina explained by out-crossing (which can range from 1 to (9), Brazil (27), Bolivia (11), Chile (6), Colombia (32), K=2 Figure 2. Structure 5%) while higher Ho may be due to mixed samples or analysis with K=2 to Costa Rica (16), Cuba (2), Dominican Republic (2), K=7 populations for multiple banding patterns observed for some markers. Ecuador (37), El Salvador (8), Germany (2), Guatemala reference collection Clustering results show a primary division between of common beans. (59), Haiti (9), Honduras (8), Nicaragua (6), United K=3 Number codes 1=D1, the Mesoamerican and Andean genepools (Figure 1, States (3). One accession each were from Australia, 2=D2, 3=INT1, orange and blue lines). Within Mesoamerican beans, 4=INT2, 5=INT3, Burundi, France, Jamaica, Japan, Malawi, Rwanda and 6=M1, 7=M2, 8=NG, the division between the Mesoamerica race and the K=4 Uganda. The accessions had the following phaseolin 9=P as described in Durango-Jalisco group was very evident while the Figure 1 and TAble 1 alleles: Mesoamericans (S, Sb, Sd, B and M), Andean genepool there was somewhat less diversity Andeans (T, C, H and A). Control genotypes run K=5 overall and a continuum between the Nueva Granada between all the studies were: Andeans (Calima/G4494 and Peru races (Figure 2, clusters). and Chaucha Chuga/G19833) and Mesoamericans K=6 The Chile race could not be distinguished within the (ICA Pijao/G5773 and Dorado/DOR364). Seed Andean genepool but there was some support for a samples for the core collection are maintained by the K=7 Guatemala race within the Mesoamerican genepool. bean project at CIAT and were originally from the Introgression between the genepools was evident as Genetic Resources Unit. DNA extraction were from 10 was probable introgression between cultivated and seedlings selected at random from each accession with wild common beans. Studies of national collection the method of Afanador et al. (1993). DNA was diluted References germplasm from Bolivia, Brazil, China and Cuba are to 10 ng/ml for further experiments. 1. Afanador L, Hadley S, Kelly JD (1993) Adoption of a mini-prep DNA extraction being used to determine which races are present in method for RAPD marker analysis in common bean (Phaseolus vulgaris L). Bean Molecular Analysis: Microsatellite amplification used Improv Coop 36:10-11 these primary and secondary centers of diversity. 2. Blair MW, Pedraza F, Buendia H, Gaitan-Solis E, Beebe S, Gepts P,Tohme J the fluorescent marker kit that we developed as part of (2003) Development of a genome-wide anchored microsatellite map for common In conclusion, our study has shown that common this project and were based on microsatellites selected bean (Phaseolus vulgaris L). Theor Appl Genet 107:1362-1374. bean has very significant populations structure that 3. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe SE (2006) from those used by Blair et al. (2006). The kit included Microsatellite marker diversity in common bean (Phaseolus vulgaris L.) Theor could help guide the construction of genetic crosses a total of nine four-color marker panels for the analysis Appl Genet 113: 100–109. that maximize diversity as well as serving as a basis 4. Broughton WJ, Hernandez G, Blair MW, Beebe SE, Gepts P, Vanderleyden J of a total of 36 individual microsatellite loci selected (2003) Beans (Phaseolus spp.); Model Food Legumes. Plant & Soil 252: 55-128 for future association studies. based on their polymorphism information content and 5. Díaz LM, Blair MW (2006) Race structure within the Mesoamerican gene pool of amplification signal strength and on their even common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theor Appl Genet 114: 143-54. Acknowledgements distribution in the genome. 6. Singh. S., Gepts. P. & Debouk. D (1991) Races of common bean (Phaseolus Assistance from Cornell University Biotech. Res. Ctr. And funds vulgaris, Fabaceae). Econ. Bot. 45(3): 379-396. from the Generation Challenge Program – SP1 and from CIAT.