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Microsatellite markers reveal promising genetic diversity and seed trait associations in common bean landraces (Phaseolus vulgaris L.) from Nicaragua

Published online by Cambridge University Press:  18 July 2012

O. R. Jiménez  and
H. Korpelainen
O. R. Jiménez
Affiliation:
National Center of Agricultural Research and Biotechnology (CNIAB), Nicaraguan Institute of Agricultural Technology (INTA), Km 14.1 North Highway, Managua, Nicaragua Department of Agricultural Sciences, University of Helsinki, PO Box 27 (Latokartanonkaari 5), FI-00014 Helsinki, Finland
H. Korpelainen*
Affiliation:
Department of Agricultural Sciences, University of Helsinki, PO Box 27 (Latokartanonkaari 5), FI-00014 Helsinki, Finland
*
*Corresponding author. E-mail: [email protected]
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Abstract

Nicaragua is located in the Mesoamerican diversity centre for common beans (Phaseolus vulgaris L.). Yet, there is insufficient knowledge of the molecular characteristics of most common bean landraces in Nicaragua. The objectives of the present study were to investigate the genetic diversity of common bean landraces and to identify promising sources of genetic variation for breeding purposes. Two cultivars and 40 landraces never studied before were selected from a collection based on the geographic origin, seed coloration and information provided by farmers. Fourteen microsatellite markers distributed in different linkage groups were analysed. The study revealed that there is a high genetic diversity (mean 8.9 alleles per locus). The populations showed structuring into three groups where seed weight had a strong relationship with population clustering. At least 20% of the populations hold promising allelic variation and potential for good market acceptance that could be maximized in breeding programmes. Additionally, four markers revealed a high correlation with seed length, width and weight, suggesting that marker-assisted selection for these yield-determinant traits could be straightforward. Nonetheless, more marker–trait associations should be addressed in order to enforce this practice.

Keywords

genetic diversitylandracesmicrosatellite markersPhaseolus vulgarisplant breeding
Type
Research Article
Information
Plant Genetic Resources , Volume 10 , Issue 2 , August 2012 , pp. 108 - 118
Copyright
Copyright © NIAB 2012

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References

Achleitner, A, Tinker, NA, Zechner, E and Buerstmayr, H (2008) Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits. Theoretical and Applied Genetics 117: 1041–1053.CrossRefGoogle ScholarPubMed
Acquaah, G (2007) Principles of Plant Genetics and Breeding. London: Blackwell Publishing, p. 569.Google Scholar
Asfaw, A, Blair, MW and Almekinders, C (2009) Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from East African highlands. Theoretical and Applied Genetics 120: 1–12.CrossRefGoogle ScholarPubMed
Avila, T, Blair, MW, Reyes, X and Bertin, P (2012) Genetic diversity of bean (Phaseolus) landraces and wild relatives from the primary centre of origin of the Southern Andes. Plant Genetic Resources: Characterization and Utilization 10: 83–92.CrossRefGoogle Scholar
Benchimol, LL, De Campos, T, Morais, SA, Colombo, CA, Chioratto, AF, Fernandes, E, Lima, LR and Pereira, A (2007) Structure of genetic diversity among common bean (Phaseolus vulgaris L.) varieties of Mesoamerican and Andean origins using new developed microsatellite markers. Genetic Resources and Crop Evolution 54: 1747–1762.CrossRefGoogle Scholar
Blair, MW, Pedraza, F, Buendia, HF, Gaitán-Solís, E, Beebe, SE, Gepts, P and Tohme, J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 107: 1362–1374.CrossRefGoogle ScholarPubMed
Blair, MW, Giraldo, MC, Buendía, HF, Tovar, E, Duque, MC and Beebe, SE (2006 a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 113: 100–109.CrossRefGoogle ScholarPubMed
Blair, MW, Iriarte, G and Beebe, S (2006 b) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross. Theoretical and Applied Genetics 112: 1149–1163.CrossRefGoogle Scholar
Blair, MW, Buendía, HF, Giraldo, MC, Métais, I and Peltier, D (2008) Characterization of AT-rich microsatellites in common bean (Phaseolus vulgaris L.). Theoretical and Applied Genetics 118: 91–103.CrossRefGoogle ScholarPubMed
Blair, MW, Diaz, LM, Buendia, HF and Duque, MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theoretical and Applied Genetics 119: 955–972.CrossRefGoogle ScholarPubMed
Blair, MW, Prieto, S, Diaz, LM, Buendia, HF and Cardona, C (2010 a) Linkage disequilibrium at the APA insecticidal seed protein locus of common bean (Phaseolus vulgaris L.). BMC Plant Biology 10: 79.CrossRefGoogle ScholarPubMed
Blair, MW, Gonzales, LF, Kimani, PM and Butare, L (2010 b) Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa. Theoretical and Applied Genetics 121: 237–248.CrossRefGoogle ScholarPubMed
Burle, ML, Fonseca, JR, Kami, JA and Gepts, P (2010) Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theoretical and Applied Genetics 121: 801–813.CrossRefGoogle Scholar
Cabral, PDS, Soares, TCB, Lima, ABP, De Miranda, FD, Souza, FB and Gonçalves, LSA (2011) Genetic diversity in local and commercial dry bean (Phaseolus vulgaris) accessions based on microsatellite markers. Genetics and Molecular Research 10: 140–149.CrossRefGoogle ScholarPubMed
Chacón, MI, Pickersgill, B and Debouk, DG (2005) Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races. Theoretical and Applied Genetics 110: 432–444.CrossRefGoogle Scholar
Dalla-Corte, A, Moda-Cirino, V, Arias, CAA, De Toledo, JFF and Destro, D (2010) Genetic analysis of seed morphological traits and its correlations with grain yield in common bean. Brazilian Archives of Biology and Technology 53: 27–34.CrossRefGoogle Scholar
Dellaporta, SJ, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: version II. Plant Molecular Reporter 1: 19–21.CrossRefGoogle Scholar
Díaz, LM and Blair, MW (2006) Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theoretical and Applied Genetics 114: 143–154.CrossRefGoogle ScholarPubMed
Díaz, LM, Buendía, HF, Duque, MC and Blair, MW (2010) Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites. Plant Genetic Resources: Characterization and Utilization 9: 86–96.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Excoffier, L and Lischer, HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564–567.CrossRefGoogle ScholarPubMed
Falconer, DS and Mackay, TFC (1996) Introduction to Quantitative Genetics. Malaysia: Prentice Hall, p. 464.Google Scholar
Gaitán, E, Duque, MC, Edwards, KJ and Tohme, J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris L.): isolation, characterization, and cross-species amplification in Phaseolus spp . Crop Science 42: 2128–2136.CrossRefGoogle Scholar
García, RAV, Rangel, PN, Brondani, C, Martins, WS, Melo, LC, Carneiro, MS, Borba, TCO and Brondani, RPV (2011) The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris . BMC Genetics 12: 41.CrossRefGoogle ScholarPubMed
Gómez, OJ and Frankow-Lindberg, BE (2005) Yield formation in Nicaraguan landraces of common bean compared to bred cultivars. Journal of Agricultural Science 143: 369–375.CrossRefGoogle Scholar
Gómez, OJ, Blair, MW, Frankow-Lindberg, BE and Gullberg, U (2004) Molecular and phenotypic diversity of common bean landraces from Nicaragua. Crop Science 44: 1412–1418.CrossRefGoogle Scholar
Gómez, OJ, Blair, MW, Frankow-Lindberg, BE and Gullberg, U (2005) Comparative study of common bean (Phaseolus vulgaris L.) landraces conserved ex situ in genebanks and in situ by farmers. Genetic Resources and Crop Evolution 52: 371–380.CrossRefGoogle Scholar
ISTA(2004) International Rules for Seed Testing. Glattbrugg: Seed Science and Technology.Google Scholar
Jiménez, OR (2009) Genetic purity of the common bean (Phaseolus vulgaris L. cv. ‘INTA ROJO’) during seed production in Nicaragua Master's Thesis, University of Helsinki, Finland.Google Scholar
Maureira-Butler, IJ, Udall, JA and Osborn, TC (2007) Analyses of a multi-parent population derived from two diverse alfalfa germplasm: test cross evaluations and phenotype-DNA associations. Theoretical and Applied Genetics 115: 859–867.CrossRefGoogle Scholar
Munsell Color (1977) Munsell Color Charts for Plant Tissues. 2nd edn revised. Baltimore, MD: Macbeth Divisions of Kollmorgen Corporation.Google Scholar
Negri, V and Tiranti, B (2010) Effectiveness of in situ and ex situ conservation of crop diversity. What a Phaseolus vulgaris L. landrace case study can tell us? Genetica 138: 985–998.CrossRefGoogle ScholarPubMed
Pereira, HS, Dos Santos, JB, De Souza, TP and Lima, IA (2008) Phenotypic and marker-assisted selection of common bean families with high grain yield. Pesquisa Agropecuaria Brasileira 43: 1551–1558 (In Portuguese).CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of populations structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Rodrigues, TB, Dos Santos, JB, Ramalho, MAP, Amorim, EP and Silva, NO (2007) QTLs identification in common bean through SSR markers affected by natural selection. Ciência e Agrotecnologia 31: 1351–1357 (In Portuguese).CrossRefGoogle Scholar
Rousset, F (2008) Genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8: 103–106.CrossRefGoogle ScholarPubMed
Ruan, CJ (2010) Germplasm-regression-combined marker–trait association identification in plants. African Journal of Biotechnology 9: 573–580.Google Scholar
Ruan, CJ, Li, H and Mopper, S (2009) Characterization and identification of ISSR markers associated with resistance to dried-shrink disease in sea buckthorn. Molecular Breeding 24: 255–268.CrossRefGoogle Scholar
Santalla, M, Fueyo, MA, Rodino, A, Montero, I and De Ron, A (1999) Breeding for culinary and nutritional quality of common bean (Phaseolus vulgaris L.) in intercropping systems with maize (Zea mays L.). Biotechnology, Agronomy, Society and Environment 3: 225–229.Google Scholar
Santalla, M, De Ron, AM and De La Fuente, M (2010) Integration of genome and phenotypic scanning gives evidence of genetic structure in Mesoamerican common bean (Phaseolus vulgaris L.) landraces from the southwest of Europe. Theoretical and Applied Genetics 120: 1635–1651.CrossRefGoogle ScholarPubMed
Tamura, K, Peterson, D, Peterson, N, Stecher, G, Nei, M and Kumar, S (2011) MEGA5: molecular evolutionary genetics analysis using likelihood, distance, and parsimony methods. Molecular Biology and Evolution 28: 2731–2739.CrossRefGoogle ScholarPubMed
Torga, PP, Dos Santos, JB, Pereira, HS, Furtado, D and Leite, ME (2010) Selection of common bean families based on grain type and yield, and QTLs information. Ciência e Agrotecnologia 34: 95–100 (In Portuguese).CrossRefGoogle Scholar
Virk, PS, Ford-Lloyd, BV, Jackson, MT, Pooni, HS, Clemeno, TP and Newbury, HJ (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76: 296–304.CrossRefGoogle Scholar
White, JW and Izquierdo, J (1991) Physiology of the yield potential and stress tolerance. In: van Schoonhoven, A and Voysest, O (eds) Common Beans: Research for Crop Improvement. Wallingford/Cali, Colombia: CABI/CIAT, pp. 287–383.Google Scholar
Yu, K, Park, SJ, Poysa, V and Geps, P (2000) Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). The Journal of Heredity 91: 429–434.CrossRefGoogle ScholarPubMed
Zhang, X, Blair, MW and Wang, S (2008) Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat markers. Theoretical and Applied Genetics 117: 629–640.CrossRefGoogle ScholarPubMed