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Population Structure and Genetic Diversity of Common Bean Accessions from Brazil

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Abstract

Brazil can be considered a secondary center of common bean diversification (Phaseolus vulgaris L.), and the landraces grown throughout Brazil are valuable sources of genes for breeding programs and evolutionary studies. The objective of this study was to evaluate the population structure of 109 accessions of common bean, including cultivars and landraces from southern and central-western regions of Brazil. The population structure analysis based on simple sequence repeat markers demonstrates that the accessions can be separated into two distinct subpopulations—the Andean and the Mesoamerican—with some admixtures observed according to Delta K = 2 groups. The optimal number of groups was found at K = 4, a level at which the Andean accessions were divided into two subpopulations and the Mesoamerican accessions into two subpopulations. Accordingly, the accessions preserved in the current collection maintained by the Universidade Estadual de Maringá are an important source of genes for germplasm conservation programs and the development of common bean cultivars.

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References

  • Afanador LK, Haley SD, Kelly JD (1993) Adoption of a ‘mini-prep’ DNA extraction protocol for RAPD marker analysis in common bean (Phaseolus vulgaris L.). Ann Rep Bean Improv Coop 36:10–11

    Google Scholar 

  • Barbosa L (2010) Food and sociability on the contemporary Brazilian plate. Etnográfica 14:567–586

    Article  Google Scholar 

  • Beebe S, Skroch PW, Tohme J, Duque MC, Pedraza F, Nienhuis J (2000) Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD. Crop Sci 40:264–273

    Article  Google Scholar 

  • Bertoldo JG, Coimbra JLM, Guidolin AF, Andrade LRB, Nodari RO (2014) Agronomic potential of genebank landrace elite accessions for common bean. Sci Agric 71:120–125

    Article  Google Scholar 

  • Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, Zeuli SP, Logozzo G, Stougaard J, Mcclean P, Attene G, Papa R (2012) Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proc Natl Acad Sci U S A 109:788–796

    Article  Google Scholar 

  • Blair MW, Pedraza F, Buendia H, Gaitán-Solís E, Beebe S, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374

    Article  CAS  PubMed  Google Scholar 

  • Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe S (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109

    Article  CAS  PubMed  Google Scholar 

  • Blair MW, Díaz LM, Buendía HF, Duque MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119:955–972

    Article  CAS  PubMed  Google Scholar 

  • Blair MW, Brondani RVP, Díaz LM, Del Peloso MJ (2013) Diversity and population structure of common bean from Brazil. Crop Sci 53:1983–1993

    Article  Google Scholar 

  • Botstein D, White RL, Skolmick H, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • Burle ML, Fonseca JR, Kami JA, Gepts P (2010) Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor Appl Genet 121:801–813

    Article  PubMed  PubMed Central  Google Scholar 

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 19:233–257

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cichy KA, Porch TG, Beaver JS, Cregan PB, Fourie D, Glahn RP, Grusak MA, Kamfwa K, Katuuramu DN, McClean P, Mndolwa E, Nchimbi-Msolla S, Pastor-Corrales MA, Miklas PN (2015) A Phaseolus vulgaris diversity panel for Andean bean improvement. Crop Sci 55:1–12

    Article  Google Scholar 

  • Díaz LM, Blair MW (2006) Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theor Appl Genet 114:143–154

    Article  PubMed  Google Scholar 

  • Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Ashok KA, Ortiz R (2016) Landrace germplasm for improving yield and abiotic stress adaptation. Trends Plant Sci 21:3–42

    Article  Google Scholar 

  • Earl DA, vonHoldt BM (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  PubMed Central  Google Scholar 

  • Freitas FO (2006) Evidências genético-arqueológicas sobre a origem do feijão comum no Brasil. Pesq Agropec Bras 41:1199–1203

    Article  Google Scholar 

  • Gaitán-Solís E, Duque MC, Edwards KJ, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42:2128–2136

    Article  Google Scholar 

  • Gepts P, Bliss FA (1986) Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia. Econ Bot 40:439–478

    Google Scholar 

  • Gepts P, Bliss FA (1988) Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from Phaseolin electrophoretic variability. II. Europe and Africa. Econ Bot 42:86–104

    Article  Google Scholar 

  • Gepts P, Osborn TC, Rashka K, Bliss FA (1986) Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. Econ Bot 40:451–468

    Article  CAS  Google Scholar 

  • Gepts P, Kmiecik K, Pereira P, Bliss FA (1988) Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from Phaseolin electrophoretic variability. I. The Americas. Econ Bot 42:73–85

    Article  Google Scholar 

  • Grisi MCM, Blair MW, Gepts P, Brondani C, Pereira PAA, Brondani RPV (2007) Genetic mapping of a new set of microsatellite markers in a reference common bean (Phaseolus vulgaris) population BAT93 × Jalo EEP558. Genet Mol Res 6:691–706

    CAS  PubMed  Google Scholar 

  • Kelly JD, Kolkman JM, Schneider K (1998) Breeding for yield in dry bean (Phaseolus vulgaris L.). Euphytica 102:343–356

    Article  Google Scholar 

  • Kwak M, Gepts P (2009) Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor Appl Genet 118:979–992

    Article  CAS  PubMed  Google Scholar 

  • Lin L-Z, Harnly JM, Pastor-Corrales MA, Luthria DL (2008) The polyphenolic profiles of common bean (Phaseolus vulgaris L.). Food Chem 107:399–410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R, Mcclean P (2010) Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet 121:1103–1116

    Article  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pereira PA, Souza CRB (1992) Tipos de faseolina em “raças” de feijão no Brasil. Pesq Agropec Bras 27:1219–1221

    Google Scholar 

  • Pereira T, Coelho SMM, Bogo A, Guidolin AF, Miquelluti DJ (2009) Diversity in common bean landraces from South Brazil. Acta Bot Croat 68:79–92

    Google Scholar 

  • Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ramalho MAP, Silva GS, Dias LAS (2009) Genetic plant improvement and climate changes. Crop Breed Appl Biot 9:189–195

    Article  Google Scholar 

  • Rezende AA, Pacheco MTB, Silva VSN, Ferreira TAPC (2018) Nutritional and protein quality of dry Brazilian beans (Phaseolus vulgaris L.). Food Sci Technol 38:421–427

    Article  Google Scholar 

  • Schmutz J, Mcclean PE, Mamidi S, Wu GA et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh SP, Gepts P, Debouck DG (1991) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45:379–396

    Article  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  • Yu K, Park SJ, Poysa V, Gepts P (2000) Integration of single sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered 91:429–434

    Article  CAS  PubMed  Google Scholar 

  • Zeven AC (1989) Landraces: a review of definitions and classifications. Euphytica 104:127–139

    Article  Google Scholar 

Download references

Funding

The authors thank the National Council for Scientific and Technological Development (CNPq) for financial support and scholarship grants and the Coordination for the Improvement of Higher Education Personnel (CAPES) for scholarship grants.

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Authors and Affiliations

  1. Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, PR, 87020-900, Brazil

    Giseli Valentini, Maria Celeste Gonçalves-Vidigal & Julio Cesar Ferreira Elias

  2. Faculdade de Engenharias e Arquitetura, FEITEP, Av. Paranavaí 1164, Maringá, PR, 87070-30, Brazil

    Giseli Valentini

  3. Instituto de Investigação Agrária de Mozambique, Av. das FPLM, Km 7, Via Corrane, 662, Nampula, Mozambique

    Leonel Domingos Moiana

  4. Associação Nacional de Extensão Rural (AENA), Rua dos continuadores, 723, Nampula, Mozambique

    Noimilto Nicolau Augusto Mindo

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  1. Giseli Valentini
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  2. Maria Celeste Gonçalves-Vidigal
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  3. Julio Cesar Ferreira Elias
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  5. Noimilto Nicolau Augusto Mindo
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Correspondence to Giseli Valentini.

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Valentini, G., Gonçalves-Vidigal, M.C., Elias, J.C.F. et al. Population Structure and Genetic Diversity of Common Bean Accessions from Brazil. Plant Mol Biol Rep 36, 897–906 (2018). https://doi.org/10.1007/s11105-018-1129-4

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