Abstract
Lima bean (Phaseolus lunatus L.) is a crop that stands out for its economic and social importance throughout the world, including in Northeast Brazil. Evidence points to high levels of genetic diversity in this crop in this region. Monitoring the levels of genetic diversity in lima beans is necessary for predicting the possible processes of genetic erosion. In this study, we compared the genetic diversity of 12 lima bean genotypes collected in the 1980s with that of 42 genotypes collected in 2014–2016 in Northeast Brazil, using eight microsatellite loci (SSRs), to assess the occurrence of genetic erosion. The genetic diversity (HE) for the genotypes collected in 2014–2016 ranged from 0.144 to 0.47, indicating a wide diversity among the lima bean germplasms cultivated in Northeast Brazil. The Garza–Williamson index showed values below 0.70 for both the periods (1980s and 2014–2016). Moreover, the results obtained suggest a recent genetic bottleneck for the 2014–2016 genotypes, which may be related to the management and production techniques used by farmers owing to the growing market demand for improved lima bean varieties in recent years.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All data are available from the corresponding author on reasonable request.
References
Alves AU, Cardoso EA, Alixandre TF, Cavalcante IHL, Beckmann-Cavalcante MZ (2014) Emergência de plântulas de fava em função de posições e profundidades de semeadura. Biosci J 30:33–42. https://doi.org/10.5039/agraria.v12i4a5472
Assunção-Filho JR, Costa MF, Pinheiro JB, Carvalho LCB, Gomes RLF, Lopes AC (2022) Selection of superior genotypes of lima bean landraces by multivariate approach. Rev Caatinga 35(1):87. https://doi.org/10.1590/1983-21252022v35n109rc
Assunção-Neto WV, Medeiros AM, Carvalho LCB, Ferreira CS, Lopes ACA, Gomes RLF (2022) Selection of landraces of lima bean for family agriculture. Rev Caatinga 35(1):137–147. https://doi.org/10.1590/1983-21252022v35n114rc
Bassam BJ, Caetanoanollés G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83. https://doi.org/10.1016/0003-2697(91)90120-I
Beardmore JA (1983) Extinction, survival, and genetic variation. In: Schonewald-Cox CM, Chambers SM, MacBryde B, Thomas WL (eds) Genetics and conservation. The Benjamin/Cummings Publ. Co, Menlo Park, pp 125–131
Ben Ayed R, Ercişli S, Hanana M, Rebai A, Moreau F (2021) Assessment of population structure, genetic diversity and relationship of Mediterranean olive accessions using SSR markers and computational tools. Biotechnol Lett. https://doi.org/10.1007/s10529-021-03204-z
Brazilian Institute of Geography and Statistics—IBGE (2019) Reports availably in the website http://www.ibge.gov.br/home/
Brito-Silva V, Gomes RLF, Lopes ACA, Dias CTS, Oliveira-Silva RN (2015) Genetic diversity and promising crosses indication in lima bean (Phaseolus lunatus) accessions. Semina 36(2):683–692. https://doi.org/10.5433/1679-0359.2015v36n2p683
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. https://doi.org/10.1007/s00122-010-1350-5
Camacho-Pérez L, Martínez-Castillo J, Mijangos-Cortés JO, Ferrer-Ortega MM, Baudoin JP, Andueza-Noh RH (2018) Genetic structure of Lima bean (Phaseolus lunatus L.) landraces grown in the Mayan area. Genet Resour Crop Evol 65:229–241. https://doi.org/10.1007/s10722-017-0525-1
Caruso G, Broglia V, Pocovi M (2015) Diversidad genética. Importancia y aplicaciones en el mejoramiento vegetal. Publicación Del Instituto De Ecología y Ambiente Humano 4:45–50
Castiñeiras et al (2007) AFLPs and morphological diversity of Phaseolus lunatus L. in Cuban home gardens: approaches to recovering the lost ex situ collection. Biodivers Conserv 16:2847–2865. https://doi.org/10.1007/s10531-006-9025-x
Chacón-Sánchez MI, Martínez-Castillo J (2017) Testing domestication scenarios of lima bean (Phaseolus lunatus L.) in mesoamerica: insights from genome-wide genetic markers. Front Plant Sci 8:1551. https://doi.org/10.3389/fpls.2017.01551
Chacón-Sánchez MI, Motta-Aldana JR, Serrano-Serrano ML, Debouck DG (2012) Domestication of Lima Beans: a new look at an old problem. In: Gepts P, Famula TR, Bettinger RL, Brush SB, Damania AB, McGuire PE, Qualset CO (eds) Biodiversity in agriculture: domestication, evolution and sustainability. Cambridge University Press, Cambridge, pp 330–343
Cornille A, Feurtey A, Gelin U, Ropars J, Misvanderbrugge K, Gladieux P, Giraud T (2015) Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples. Evol Appl 8(4):373–384
Das A, Yadav RK, Choudhary H, Lata S, Singh S, Kumar C, Kumari S, Boopalakrishnan G, Bhardwaj R, Talukdar A (2021) Population structure, gene flow and genetic diversity analyses based on agro-morphological traits and microsatellite markers within cultivated and wild germplasms of okra [Abelmoschus esculentus (L.) Moench.]. Genet Resour Crop Evol 69:771–791. https://doi.org/10.1007/s10722-021-01263-9
Debnath SC (2016) Genetic diversity and erosion in berries. In: Ahuja MR, Jain SM (eds) Genetic diversity and erosion in plants, sustainable development and biodiversity. Case histories, vol 2. Springer, Berlin, pp 75–129. https://doi.org/10.1007/978-3-319-25954-3_3
Delfni J, Moda-Cirino V, dos Santos NJ et al (2021) Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm. Sci Rep. https://doi.org/10.1038/s41598-021-82437-4
Doyle JJ, Doyle JL (1987) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Are AK, Ortiz R (2016) Landrace germplasm for improving yield and abiotic stress adaptation. Trends Plant Sci 21:31–42
Earl DA, Vonholdt BM (2012) Structure Harvester: a website and program for visualizing Structure output and implementing the Evanno method. Conserv Genet Res 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
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. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Excoffier L, Laval G, Schneider S (2006) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50. https://doi.org/10.1177/117693430500100003
FAO (1996) Report of the conference of FAO. Twenty-second session. Food and Agriculture Organization of the United Nations, Rome
Gadissa F, Abebe M, Worku B (2021) Assessment on the current state of on-farm diversity and genetic erosion in barley (Hordeum vulgare L.) landraces from bale highlands, southeast Ethiopia. BioMed Res Int 1:6677363. https://doi.org/10.1155/2021/6677363
Garcia T, Duitama J, Zullo SS, Gil J, Ariani A, Dohle S, Palkovic A, Skeen P, Bermudez-Santana CI, Debouck G, Martínez-Castillo J, Gepts P, Chacón-Sánchez MI (2021) Comprehensive genomic resources related to domestication and crop improvement traits in lima bean. Nat Commun 12(1):1–17. https://doi.org/10.1038/s41467-021-20921-1
Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318. https://doi.org/10.1046/j.1365-294X.2001.01190.x
Gomes RLF, Costa MF, Alves-Pereira A, Bajay MM, Viana JPG, Valente SES, Lopes ACA, Zucchi MI, Pinheiro JB (2020) A lima bean core collection based on molecular markers. Sci Agric 77(2):e20180140. https://doi.org/10.1590/1678-992x-2018-0140
Guimarães WN, Martins LS, Silva EF, Ferraz GMG, Oliveira FJ (2007) Caracterização morfológica e molecular de acessos de feijão-fava (Phaseolus lunatus L.). Rev Bras Eng Agríc Ambient 11:37–45. https://doi.org/10.1590/S1415-43662007000100005
Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol 2:618–620. https://doi.org/10.1046/j.1471-8286.2002.00305.x
Hartl DL, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer Associates, Sunderland
Hassanpour F, Sahhafi SR (2020) Genetic variation in some Iranian bitter vetch (Vicia ervilia L.) landraces based on agronomic-morphological traits for use in breeding program in Rafsanjan. Genet Resour Crop Evol 67:2087–2100. https://doi.org/10.1007/s10722-020-00962-z
Kumar D, Chhokar V, Sheoran S, Singh R, Sharma P, Jaiswal S et al (2020) Characterization of genetic diversity and population structure in wheat using array based SNP markers. Mol Biol Rep 47:293–306. https://doi.org/10.1007/s11033-019-05132-8
Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J (2017) Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evol Appl. https://doi.org/10.1111/eva.12564
Lioi L, Galazo I (2002) Oligonucleotide DNA fingerprinting revealing polymorphism in Phaseolus lunatus L. Genet Resour Crop Evol 49:53–58. https://doi.org/10.1023/A:1013809915096
Lopes ACA, Gomes RLF, Silva RNO, Costa EMR, Sousa IFS, Santos JO, Sousa THP, Damasceno-Silva KJ (2010) Diversidade genética. In: Araújo ASF, Lopes ACA, Gomes RLF A cultura do feijão-fava no Meio-Norte do Brasil, 1ªedn. Teresina, EDUFPI, pp 45–72
Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv Biol 12:228–237. https://doi.org/10.1111/j.1523-1739.1998.96388.x
Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998) Distortion of allele frequency distributions provided a test for recent population bottlenecks. J Hered 89:238–247. https://doi.org/10.1093/jhered/89.3.238
Luo Z, Brock J, Dyer JM et al (2019) Genetic diversity and population structure of a Camelina sativa spring panel. Front Plant Sci. https://doi.org/10.3389/fpls.2019.00184
Maras M, Susnik S, Sustar-Vozlic J, Meglic V (2006) Temporal changes in genetic diversity of common bean (Phaseolus vulgaris L.) accessions cultivated between 1800 and 2000. Russ J Genet 42:775–782
Martínez-Castillo J, Zizumbo-Villarreal D, Perales-Rivera H, Colunga-GarcíaMarín P (2004) Intraspecific diversity and morpho-phenological variation in Phaseolus lunatus L. from the Yucatan Peninsula, Mexico. Econ Bot 58(3):354–380
Martínez-Castillo J, Zizumbo-Villarreal D, Gepts P, Delgado-Valerio P, Colunga-Garcíamarın P (2006) Structure and genetic diversity of wild population of Lima bean (Phaseolus lunatus L.) from the Yucatan Peninsula. Mex Crop Sci 46:1071–1080
Martínez-Castillo J, Colunga-Garcíamarín P, Zizumbo-Villarreal D (2008) Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center. Genet Resour Crop Evol 55:1065–1077
Martínez-Castillo J, Camacho-Pérez L, Coello-Coello J, Andueza-Noh R (2012) Wholesale replacement of Lima bean (Phaseolus lunatus L.) landraces over the last 30 years in northeastern Campeche, Mexico. Genet Resour Crop Evol 59:191–204
Martínez-Castillo J, Camacho-Pérez L, Villanueva-Viramontes S, Andueza-Noh RH, Chacón-Sánchez MI (2014) Genetic structure withinthe Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: implication for conservation and the domestication of the species. Am J Bot 101(5):1–14
Martínez-Castillo J, May-Pat F, Camacho-Pérez L, Andueza-Noh RH, Dzul-Tejero F (2016) Genetic erosion and in situ conservation of lima bean (Phaseolus lunatus L.) landraces in Mesoamerican Diversity Center. In: Ahuja M, Jain S (eds) Genetic diversity and erosion in plants. Sustainable development and biodiversity, case histories. Springer, Berlin, pp 285–306. https://doi.org/10.1007/s10722-008-9314-1
Maxted N, Guarino L (2006) Genetic erosion and genetic pollution of crop wild relatives. In: Ford-Lloyd BV, Dias SR, Bettencourt E (eds) Genetic erosion and pollution assessment methodologies. Proceedings of PGR forum workshop 5, Terceira Island, Autonomous Region of the Azores, Portugal, 35–45. Published on behalf of the European Crop Wild Relative Diversity Assessment and Conservation Forum, Biodiversity International, Rome, p 100. ISBN: 9789290437109
Montero-Rojas M et al (2013) Genetic, morphological and cyanogen content evaluation of a new collection of Caribbean Lima bean (Phaseolus lunatus L.) landraces. Gen Resour Crop Evol 60:2241–2252. https://doi.org/10.1007/s10722-013-9989-9
Omasheva MY, Flachowsky H, Ryabushkina NA, Pozharskiy AS, Galiakparov NN, Hanke MV (2017) To what extent do wild apples in Kazakhstan retain their genetic integrity? Tree Genet Genomes 13(3):52
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. https://doi.org/10.1093/2Fbioinformatics.2Fbts460
Penha JS, Lopes ACA, Gomes RLF, Pinheiro JB, Assunção-Filho JR, Silvestre EA, Viana JPG, Castilho-Martinez J (2017) Estimation of natural outcrossing rate and genetic diversity in Lima bean (Phaseolus lunatus L. var. lunatus) from Brazil using SSR markers: implications for conservation and breeding. Genet Resour Crop Evol 64:1355–1364. https://doi.org/10.1007/s10722-016-0441-9
Pires CJ, Costa MF, Zucchi MI, Ferreira-Gomes RL, Pinheiro JB, Viana JPG, Bajay MM, Assunção-Filho JR, Lopes ACA (2022) Genetic diversity in accessions of lima bean (Phaseolus lunatus L.) determined from agro-morphological descriptors and SSR markers for use in breeding programs in Brazil. Genet Resour Crop Evol. https://doi.org/10.1007/s10722-021-01272-8
Poh Y-P, Domingues VS, Hoekstra HE, Jensen JD (2014) On the prospect of identifying adaptive loci in recently bottlenecked populations. PLoS ONE 9:e11057. https://doi.org/10.1371/journal.pone.0110579
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1093/genetics/155.2.945
Silva RNO, Burle ML, Padua JG, Lopes ACA, Gomes RLF, Martínez-Castilho J (2017) Phenotypic diversity in lima bean landraces cultivated in Brazil, using the Ward-MLM strategy. Chil J Agric Res 77(1):35–40. https://doi.org/10.4067/S0718-58392017000100004
Silva RNO, Lopes ACA, Gomes RLF, Pádua JG, Burle ML (2019) High diversity of cultivated lima beans (Phaseolus lunatus) in Brazil consisting of one Andean and two Mesoamerican groups with strong introgression between the gene pools. Genet Mol Res 18(4):18441. https://doi.org/10.4238/gmr18441
Soares LADC, Silva JDL, Silva VB, Ferreira CS, Batista de Sousa AMDC, Costa MF, Lopes ACA, Gomes RLF (2022) On-farm conservation in Phaseolus lunatus L: an alternative for agricultural biodiversity. Agroecol Sustain Food Syst 46:1–18. https://doi.org/10.1080/21683565.2021.2016545
Sousa AMCB, Silva VBD, Lopes ACA, Gomes RLF, Carvalho LCB (2020) Prediction of grain yield, adaptability, and stability in landrace varieties of lima bean (Phaseolus lunatus L.). Crop Breed Appl Biotechnol. https://doi.org/10.1590/1984-70332020v20n1a15
Sousa SR, Costa MF, Vasconcelos LFL, Araújo ASF, Castro AAJF, Farias RRS, Ferreira-Gomes RL, Lopes ACA (2021) Assessment of the phenotypic diversity in natural populations of Annona coriacea Mart.: implications for breeding. Genet Resour Crop Evol 12:1–15. https://doi.org/10.1007/s10722-021-01289-z
van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol 4:535–538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
Zargar SA, Wani AA, Saggoo MIS (2021) Analysis of phenotypic diversity of apricot (Prunus armeniaca L) accessions from Jammu and Kashmir India. Plant Genet Res. https://doi.org/10.1017/S147926212121000241
Acknowledgements
The authors thank the Instituto Agronômico de Pernambuco (IPA), specifically Dr. Antônio Félix da Costa; the molecular marker laboratory of the Natural Resources University of the Centro de Investigación Científica de Yucatán, A.C. (CICY), especially Jaime Alejandro Muñoz Lopez and Grecia Montalvo Fernández; and the Universidade Federal do Piauí for academic education and support for research.
Funding
This research was funded by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brazil (CAPES)—Finance Code 001.
Author information
Authors and Affiliations
Contributions
A.C.A.L., J.M.C. and R.L.F.G. designed the experiment. J.D.L.S., L.F.O, M.M.O.G and A.G.S.S conducted the experiment(s) J.D.L.S, G.R.S, L.C.B.C conducted the experiment(s) and analyzed the data J.D.L.S, G.R.S, L.C.B.C, V.B.S, R.L.F.G. M.F.C and A.C.A.L. analyzed the results, discussed, wrote and reviewed the manuscript. All the authors reviewed the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Lustosa-Silva, J.D., Ferreira-Gomes, R.L., Martínez-Castillo, J. et al. Genetic diversity and erosion in lima bean (Phaseolus lunatus L.) in Northeast Brazil. Genet Resour Crop Evol 69, 2819–2832 (2022). https://doi.org/10.1007/s10722-022-01402-w
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10722-022-01402-w