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Genetic diversity of Guatemalan climbing bean collections

Genetic Resources and Crop Evolution volume 68, pages 639–656 (2021)Cite this article

Abstract

Common bean is the most important legume crop for human consumption around the world. For this reason, bean breeders are challenged with increasing bean production while facing new problems like climate change. Guatemalan climbing beans have been suggested to represent a previously undefined race in the Middle American gene pool that may represent an untapped source of alleles for bean improvement that can contribute to solving production problems affecting both developed and developing countries. The genetic diversity, population structure, and genetic differentiation of two Guatemalan climbing bean collections were analyzed with ~ 45,000 SNPs markers and confirmed the existence of race Guatemala in the Middle American gene pool and its differentiation from other races. Further analysis using geospatial data, showed that elevation was an important factor when defining the population structure of race Guatemala beans.

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References

  • Acosta-Gallegos JA, Kelly JD, Gepts P (2007) Prebreeding in common bean and use of genetic diversity from wild germplasm. Crop Sci 47:S44–S59

    Google Scholar 

  • Agreda KA, Villatoro JC, Miranda AN, Moscoso JR, Osorno JM, McClean P (2017) Phenotypic evaluation of native accessions of climbing beans collected in the Guatemalan highlands. In: Poster session presented at: Legume Innovation Lab Grain Legume Research conference. Ouagadougou, Burkina Faso

  • Akibode S, Maredia MK (2012) Global and regional trends in production, trade and consumption of food legume crops. https://impact.cgiar.org/sites/default/files/images/Legumetrendsv2.pdf. Accessed 10 October 2017

  • 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

    Google Scholar 

  • Bitocchi E, Nanni L, Belluci E, Rossi M, Giardini A, Zeuli PS, 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 USA 109:E788–E796

    CAS  PubMed  PubMed Central  Google Scholar 

  • Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-García N, Cook DR (2013) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet 126:535–548

    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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    CAS  PubMed  Google Scholar 

  • Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128

    CAS  Google Scholar 

  • Chacón MI, Pickersgill B, Debouck DG (2005) Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races. Theor Appl Genet 110:432–444

    Google Scholar 

  • Cichy KA, Porch TG, Beaver JS, Cregan P, Fourie D, Glahn RP, Grusak MA, Kamfwa K, Katuuramu D, McClean P, Mndolwa E (2015) A diversity panel for Andean bean improvement. Crop Sci 55:2149–2160

    CAS  Google Scholar 

  • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis A, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, Kernytsky A, Sivachenko A, Cibulskis K, Gabriel S, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498

    CAS  PubMed  PubMed Central  Google Scholar 

  • DeYoung DJ, Reyes B, Osorno JM, Mejia G, Villatoro JC, and Maredia MK (2017) An overview of bean production practices, varietal preferences, and consumption patterns in the milpa system of the Guatemalan highlands: results of a farm household survey. Department of Agricultural, Food and Resource Economics, Michigan State University. Staff Paper Series 268951

  • Diaz 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

    CAS  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379

    CAS  Article  PubMed  PubMed Central  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

    CAS  PubMed  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

    CAS  Google Scholar 

  • Guerra-García A, Suárez-Atilano M, Mastretta-Yanes A, Delgado-Salinas A, Piñero D (2017) Domestication genomics of the open-pollinated scarlet runner bean (Phaseolus coccineus L.). Front Plant Sci 8:1891

    PubMed  PubMed Central  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

    CAS  PubMed  Google Scholar 

  • Lee TH, Guo H, Wang X, Kim C, Paterson AH (2014) SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15:162. https://doi.org/10.1186/1471-2164-15-162

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Loveless MD, Hamrick JL (1984) Ecological determinants of genetic structure in plant populations. Annu Rev Ecol Syst 15:65–95

    Google Scholar 

  • Mamidi S, Rossi M, Moghaddam SM, Annam D, Lee R, Papa R, McClean PE (2013) Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L. Heredity 110:267–276

    CAS  PubMed  Google Scholar 

  • McClean PE, Terpstra J, McConnell M, White C, Lee R, Mamidi S (2012) Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection. Genet Resour Crop Evol 59:499–515

    Google Scholar 

  • Mercati F, Leone M, Lupini A, Sorgona A, Bacchi M, Abenavoli MR, Sunseri F (2013) Genetic diversity and population structure of a common bean (Phaseolus vulgaris L.) collection from Calabria (Italy). Genet Res Crop Evol 60:839–852

    Google Scholar 

  • Mielczarek M, Szyda J (2015) Review of alignment and SNP calling algorithms for next-generation sequencing data. J Appl Genet 57:71–79

    PubMed  Google Scholar 

  • Mina-Vargas A (2015) Molecular analysis of evolutionary relationships of Phaseolus dumosus with the gene pool of common bean. Ph.D. Thesis, University College Cork

  • Moghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE (2014) Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Front Plant Sci 5:185

    PubMed  PubMed Central  Google Scholar 

  • Moghaddam SM, Mamidi S, Osorno JM, Lee R, Brick M, Kelly J, Miklas P, Urrea C, Song Q, Cregan P, Grimwood J (2016) Genome-wide association study identifies candidate loci underlying agronomic traits in a Middle American diversity panel of common bean. Plant Genome 9(3):1–21. https://doi.org/10.3835/plantgenome2016.02.0012

    CAS  Article  Google Scholar 

  • Müller BS, Pappas GJ, Valdisser PA, Coelho GR, de Menezes IP, Abreu AG, Borba TC, Sakamoto T, Brondani C, Barros EG, Vianello RP (2015) An operational SNP panel integrated to SSR marker for the assessment of genetic diversity and population structure of the common bean. Plant Mol Biol Rep 33:1697–1711

    Google Scholar 

  • Myers JR, Kmiecik K (2017) Common bean: economic importance and relevance to biological science research. In: de la Vega M, Santalla M, Marsolais F (eds) The common bean genome. Springer, Cham, pp 1–20

    Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    CAS  PubMed  PubMed Central  Google Scholar 

  • Osorno JM, Mcclean P (2013) Genetic improvement of Middle-American climbing beans in Guatemala (SO1.A1). Feed the future, Legume Innovation Lab. Michigan State University, Michigan. https://legumelab.msu.edu/uploads/files/SO1.A1-FY2015_Annual_Technical_Progress_Report_Leg_Innovation_Lab.pdf. Accessed 10 Oct. 2017

  • Papa R, Gepts P (2003) Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor Appl Genet 106:239–250

    CAS  PubMed  Google Scholar 

  • Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in excel: population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ponciano-Samayoa KM, Villatoro-Mérida JC, Monterroso LGM (2009) Caracterización preliminar con microsatélites de la colección nacional de frijol trepador en Guatemala. Agronomía Mesoamericana 20:245–254

    Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

  • Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T (2017) Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol 18:60

    PubMed  PubMed Central  Google Scholar 

  • Rodriguez M, Rau D, Bitocchi E, Bellucci E, Biagetti E, Carboni A, Gepts P, Nanni L, Papa R, Attene G (2016) Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris. New Phytol 209:1781–1794

    CAS  PubMed  Google Scholar 

  • Rosenberg NA (2004) Distruct: A program for the graphical display of population structure. Mol Ecol Notes 4:137–138

    Google Scholar 

  • Rossi M, Bitocchi E, Bellucci E, Nanni L, Rau D, Attene G, Papa R (2009) Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L. Evol Appl 2:504–522

    PubMed  PubMed Central  Google Scholar 

  • Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707–713

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schröder S, Mamidi S, Lee R, McKain MR, McClean PE, Osorno JM (2016) Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.). Mol Breed 36:6

    Google Scholar 

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

    Google Scholar 

  • Singh SP, Nodari R, Gepts P (1991b) Genetic diversity in cultivated common bean: I Allozymes. Crop Sci 31:19–23

    CAS  Google Scholar 

  • Tello G (2017) ICTA pone a disposición de los agricultores dos nuevas variedades de frijol de enredo. Instituto de Ciencia y Tecnología Agrícolas ICTA Guatemala. https://www.icta.gob.gt/noticias/marzo2017/Liberacion%2520semillas%2520de%2520frijol%2520enredo.pdf. Accessed 04 Dec 2017

  • Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99:9650–9655

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R (2016) Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 17:32

    PubMed  PubMed Central  Google Scholar 

  • Zizumbo-Villarreal D, Flores-Silva A, Colunga-García P (2012) The archaic diet in Mesoamerica: incentive for Milpa development and species domestication. Econ Bot 66:328–343

    Google Scholar 

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Acknowledgments

The research project was supported by the Feed the Future Innovation Lab for Grain Legumes funded by the United States Agency for International Development through Grant number EDH-A-00-07-00005-00 (S01.A1–NDSU: Genetic Improvement of Guatemalan Climbing Beans for Efficient Production in the Highlands). We also thank to ICTA authorities in Guatemala for allowing the use of their germplasm collections.

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Authors and Affiliations

  1. Instituto de Ciencia y Tecnología Agrícolas (ICTA), Villa Nueva, Guatemala

    María Gabriela Tobar Piñón & Julio C. Villatoro Mérida

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, USA

    Samira Mafi Moghaddam, Rian K. Lee, Juan M. Osorno & Phillip E. McClean

  3. Department of Agricultural, Food, and Resource Economics, Michigan State University, East Lansing, MI, USA

    David J. DeYoung & Mywish Maredia

  4. International Center for Tropical Agriculture (CIAT), Palmira, Colombia

    Byron A. Reyes

Authors
  1. María Gabriela Tobar Piñón
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  2. Samira Mafi Moghaddam
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  3. Rian K. Lee
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  4. Julio C. Villatoro Mérida
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  5. David J. DeYoung
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Contributions

MGTP and RKL conducted the laboratory work. SMM, MGTP and PEM completed the statistical analyses, while JCVM provided all the phenotypic data of the bean collections. JMO and PEM contributed with the conception and design of the study as well as the supervision of the project. DJD and BR contributed in the seed samples collection of the GUA-2015 germplasm collection at Guatemala, and together with MKM designed the survey and provided the data of this collection. All authors contributed with the writing and revision process and approved the final manuscript.

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Correspondence to María Gabriela Tobar Piñón.

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Appendix

Appendix

See the Tables 6.

Table 6 InDel Markers used in the intra-accession analysis
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Tobar Piñón, M.G., Mafi Moghaddam, S., Lee, R.K. et al. Genetic diversity of Guatemalan climbing bean collections. Genet Resour Crop Evol 68, 639–656 (2021). https://doi.org/10.1007/s10722-020-01013-3

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Keywords

  • Phaseolus vulgaris
  • Race Guatemala
  • Population structure
  • Milpa system