Hostname: page-component-cd9895bd7-p9bg8 Total loading time: 0 Render date: 2024-12-24T01:00:58.442Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity and structure analysis of Vigna unguiculata L. (Walp.) landraces from southeastern Mexico using ISSR markers

Published online by Cambridge University Press:  04 November 2020

L. F. C. dos Santos Open the ORCID record for L. F. C. dos Santos [Opens in a new window] ,
M. M. Ferrer ,
M. R. Ruenes-Morales ,
P. I. Montañez-Escalante ,
R. H. Andueza-Noh  and
J. Jiménez-Osornio
L. F. C. dos Santos
Affiliation:
Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, 97315Mérida, Yucatán, México
M. M. Ferrer
Affiliation:
Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, 97315Mérida, Yucatán, México
M. R. Ruenes-Morales
Affiliation:
Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, 97315Mérida, Yucatán, México
P. I. Montañez-Escalante
Affiliation:
Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, 97315Mérida, Yucatán, México
R. H. Andueza-Noh
Affiliation:
Conacyt-División de Estudios de Posgrado e Investigación, Instituto Tecnológico de Conkal, Avenida Tecnológico S/N CP 97345Conkal, Yucatán, México
J. Jiménez-Osornio*
Affiliation:
Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, 97315Mérida, Yucatán, México
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Cowpea (Vigna unguiculata L. Walp.) is an important grain legume in tropical and subtropical regions. It requires low resource inputs and has a high nutritional value. Therefore, cowpea can play an important role in the development of agriculture. In southern Mexico, Mayan farmers have conserved and developed cowpea landraces for centuries. Nevertheless, information on their genetic diversity, conservation status and potential use is minimal. To generate information toward sustainable use, management and conservation of this species, we evaluated the genetic diversity and structure of 20 cowpea landraces from southeast Mexico using 10 inter-simple sequence repeat (ISSR) molecular markers. These ISSR markers generated 68 loci with a 67.7% polymorphism rate and average polymorphic information content of 0.36. The results of Bayesian assignation and the UPGMA analysis suggest the formation of two main groups defined by their genetic origin in southeast Mexico. High levels of genetic structure were found with a moderate level of genetic diversity distributed mainly between landraces. Low levels of intra-landrace variability were observed. Two landraces (P5 and P12) from Calakmul resulted in the high levels of genetic diversity. The selected markers were efficient at assessing genetic variability among Mexican cowpea landraces, providing valuable information that can be used in local conservation and participatory breeding programmes.

Keywords

Cowpeagenetic resourceslandrace conservationmolecular markerspolymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 4 , August 2020 , pp. 201 - 210
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Ali, ZB, Yao, KN, Odeny, DA, Kyalo, M, Skilton, R and Eltahir, IM (2015) Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] accessions from Sudan using simple sequence repeat (SSR) markers. African Journal of Plant Science 9: 293–304. doi: 10.5897/ajps2015.1313.CrossRefGoogle Scholar
Anatala, TJ, Mandavia, MK, Gajera, HP, Savaliya, DD and Golakiya, BA (2014) Comparison of ISSR and SSR markers for characterization of cowpea (Vigna unguiculata L.) genotypes. Indian Journal of Agricultural Biochemistry 27: 145–150.Google Scholar
Araújo, LBR, Fiege, LBC, Silva, ABA and Bertini, CHCM (2019) Genetic diversity in cowpea landraces analyzed by ISSR markers. Genetics and Molecular Research 18: gmr18082.10.4238/gmr18082CrossRefGoogle Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RM (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Brody, JR and Kern, SE (2004) Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36: 214–216.10.2144/04362BM02CrossRefGoogle ScholarPubMed
Camacho, VTC, Maxted, N, Scholten, M and Ford-Lloyd, B (2005) Defining and identifying crop landraces. Plant Genetic Resources 3: 373–384. doi: 10.1079/PGR200591.Google Scholar
Carvalho, M, Muñoz-Amatriaín, M, Castro, I, Lino-Neto, T, Matos, M, Egea-Cortines, M, Rosa, E, Close, T and Carnide, V (2017) Genetic diversity and structure of Iberian Peninsula cowpeas compared to worldwide cowpea accessions using high density SNP markers. BMC Genomics 18:891. doi: 10.1186/s12864-017-4295-0.CrossRefGoogle ScholarPubMed
Castillo-Caamal, JB (2006) Evaluación de leguminosas herbáceas como coberteras asociadas al maíz de temporal durante tres ciclos agrícolas en Yucatán. Tesis grado doctor en ciencias. Facultad de Medicina Veterinaria y Zootecnia. Mérida, Yucatán México.Google Scholar
Cázares, ES and Duch, JG (2004) La diversidad genética de variedades locales de maíz, frijol, calabaza y chile, y su relación con características culinarias. In: Chávez-Servia, JL, Tuxill, J and Jarvis, DI (eds) Manejo de la Diversidad de los Cultivos en los Agroecosistemas Tradicionales. Cali, Colombia: Instituto Internacional de Recursos Fitogenéticos, pp. 250–255.Google Scholar
Chen, H, Chen, H, Hu, L, Wang, L, Wang, S, Wang, ML and Chen, X (2017) Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. The Crop Journals 5: 363–372. http://dx.doi.org/10.1016/j.cj.2017.04.002.CrossRefGoogle Scholar
Earl Dent, A and vonHoldt, BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361. doi: 10.1007/s12686-011-9548-7.CrossRefGoogle Scholar
Etminan, A, Pour-Aboughadare, A, Mohammadi, R, Ahmadi-Rad, A, Noori, A, Mahdavian, Z and Moradi, Z (2016) Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnology & Biotechnological Equipment 30: 1075–1108. http://dx.doi.org/10.1080/13102818.2016.1228478.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: 2611–2620.10.1111/j.1365-294X.2005.02553.xCrossRefGoogle ScholarPubMed
Falcón, LI and Valera, A (2007) Extracción de ácidos nucleico. In: Eguiarte, LE, Souza, V and Aguirre, X (eds) Ecología Molecular. México: INE, SEMARNAT and CONABIO Distrito federal, pp. 506–509.Google Scholar
Felsenstein, J (2005) PHYLIP (Phylogeny inference package), version 3.6. Computer program distributed by the author, Department of Genome Sciences, University of Washington, Seattle, USA.Google Scholar
Fikiru, E, Tesfaye, K and Bekele, E (2010) A comparative study of morphological and molecular diversity in Ethiopian lentil (Lens culinaris Medikus) landraces. African Journal of Plant Science 4: 242–254.Google Scholar
Gajera, HP, Domadiya, RK, Patel, SV and Golakiya, BA (2014) Appraisal of RAPD and ISSR markers for genetic diversity analysis among cowpea (Vigna unguiculata L.) genotypes. Journal of Crop Science and Biotechnology 17: 79–88. doi: 10.1007/s12892-013-0062-1.CrossRefGoogle Scholar
Ghalmi, N, Malice, M, Jacquemin, J-M, Ounane, S-M, Mekliche, L and Baudoin, J-P (2010) Morphological and molecular diversity within Algerian cowpea (Vigna unguiculata (L.) Walp.) landraces. Genetic Resources and Crop Evolution 57: 371–386. doi: 10.1007/s10722-009-9476-5.CrossRefGoogle Scholar
Gómez, LM, Latournerie, ML, Arias, RLM, Canul, KJ and Tuxill, J (2004) Sistema informal de abastecimiento de semillas de los cultivos de la milpa de Yaxcabá, Yucatán. In: Chávez-Servia, JL, Tuxill, J and Jarvis, DI (eds) Manejo de la Diversidad de los Cultivos en los Agroecosistemas Tradicionales. Cali, Colombia: Instituto Internacional de Recursos Fitogenéticos, pp. 250–255.Google Scholar
Henareh, M, Dursun, A, Mandoulakani, BA and Haliloglu, K (2016) Assessment of genetic diversity in tomato landraces using ISSR markers. Genetika 48: 25–35. doi:10.2298/gensr1601025h.CrossRefGoogle Scholar
Hernández, FC and Delgado, AS (1992) Recursos genéticos de frijoles en el oriente de Yucatán. In: Zizumbo, VD, Rasmussen, CH, Arias, RLA and Terán, CS (eds) La Modernización de la Milpa en Yucatán: Utopía o Realidad. Mérida, México: Centro de Investigación Científica de Yucatán (CICY), pp. 147–159.Google Scholar
Herniter, I (2019) Genetics of Consumer-Related Traits in Cowpea (Vigna unguiculata [L.] Walp.) PhD Thesis, University of California Riverside. pp. 12–20. https://escholarship.org/uc/item/5ph2v3g7.Google Scholar
Huynh, BL, Close, TJ, Roberts, PA, Hu, Z, Wanamaker, S, Lucas, MR, Chiulele, R, Cissé, N, David, A, Hearne, S, Fatokun, C, Diop, NN and Ehlers, JD (2013) Gene pools and the genetic architecture of domesticated cowpea. The Plant Genome 6: 1–8. doi: 10.3835/plantgenome2013.03.0005.CrossRefGoogle Scholar
Igwe, DO, Afiukwa, CA, Ubi, BE, Ogbu, KI, Ojuederie, OB and Ude, DN (2017) Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers. BMC Genetics 18: 98. doi:10.1186/s12863-017-0567-6.CrossRefGoogle ScholarPubMed
Kumar, D, Golakia, BA and Parakhia, AM (2017) Characterization and genetic diversity of cowpea (Vigna unguiculata L.) genotypes linked to cowpea yellow mosaic virus. Legume Research 41: 27–33. doi: 10.18805/lr.v0iOF.9101.Google Scholar
Kumar, S, Stecher, G, Li, M, Knyaz, C and Tamura, K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35: 1547–1549.10.1093/molbev/msy096CrossRefGoogle ScholarPubMed
Lagunes-Espinoza, LC, Gallardo-López, F, Becerril-Hernández, H and Bolaños-Aguilar, ED (2007) Diversidad cultivada y sistema de manejo de Phaseolus vulgaris Y Vigna unguiculata en la región de la Chontalpa, Tabasco. Revista Chapingo Serie Horticultura 14: 13–21.10.5154/r.rchsh.2006.11.047CrossRefGoogle Scholar
Liu, K and Muse, SV (2005) Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics (Oxford, England) 21: 2128–2129.10.1093/bioinformatics/bti282CrossRefGoogle ScholarPubMed
López, CL, Garruña, HR, Castillo, AC, Martínez-Hernández, A, Ortiz-García, MM and Andueza-Noh, RH (2019) Structure and genetic diversity of nine important landraces of capsicum species cultivated in the Yucatan Peninsula, Mexico. Agronomy 9: 376. doi:10.3390/agronomy9070376.CrossRefGoogle Scholar
Lynch, M and Milligan, BG (1994) Analysis of population genetic structure with RAPD markers. Molecular Ecology 3: 91–99.10.1111/j.1365-294X.1994.tb00109.xCrossRefGoogle ScholarPubMed
Martínez-Castillo, J, Zizumbo-Villarreal, D, Perales-Rivera, H and Colunga-GarcíaMarín, P (2004) Intraspecific diversity and morpho-phenological variation in Phaseolus lunatus L. from the Yucatan Peninsula, Mexico. Economic Botany 58: 354–380.10.1663/0013-0001(2004)058[0354:IDAMVI]2.0.CO;2CrossRefGoogle Scholar
Martínez-Castillo, J, Colunga-GarcíaMarín, P and Zizumbo-Villarreal, D (2008) Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center. Genetic Resources Crop Evolution 55: 1065–1077. doi: 10.1007/s10722-008-9314-1.CrossRefGoogle Scholar
Martínez-Castillo, J, Camacho-Pérez, L, Villanueva-Viramontes, S, Andueza-Noh, RH and Chacón-Sánchez, MI (2014) Genetic structure within the Mesoamerican gene pool of wild Phaseolus lunatus (Fabaceae) from Mexico as revealed by microsatellite markers: implications for conservation and the domestication of the species. American Journal of Botany 101: 851–864. doi:10.3732/ajb.1300412.CrossRefGoogle ScholarPubMed
Menssen, M, Linde, M, Omondi, EO, Abukutsa-Onyango, M, Dinssa, FF and Winkelmann, T (2017) Genetic and morphological diversity of cowpea (Vigna unguiculata (L.) Walp.) entries from East Africa. Scientia Horticulturae 226: 268–276. http://dx.doi.org/10.1016/j.scienta.2017.08.003.CrossRefGoogle Scholar
Morales-Morales, AE, Andueza-Noh, RH, Márquez-Quiroz, C, Benavides-Mendoza, A, Tun-Suarez, JM, González-Moreno, A and Alvarado-López, CJ (2019) Caracterización morfológica de semillas de frijol caupí (Vigna unguiculata L. Walp) de la Península de Yucatán. Ecosistemas y Recursos Agropecuarios 6: 463–475.Google Scholar
Peakall, R and Smouse, PE (2012) Genalex 6.5: genetic analysis in excel. Population genetic software for teaching and research-un update. Bioinformatics (Oxford, England) 28: 2537–2539.10.1093/bioinformatics/bts460CrossRefGoogle Scholar
Tan, H, Tie, M, Luo, Q, Zhu, Y, Lai, J and Li, H (2012) A review of molecular makers applied in cowpea (Vigna unguiculata L. Walp.) breeding. Journal of Life Sciences 6: 1190–1199.Google Scholar
Vekemans, X (2002) AFLP-SURV version 1.0. Distributed by the author. Laboratoire de Génétique et Ecologie Végétale, Université Libre de Bruxelles, Belgium.Google Scholar
Wamalwa, EN, Muoma, J and Wekesa, C (2016) Genetic diversity of cowpea (Vigna unguiculata (L.) Walp.) accession in Kenya gene bank based on simple sequence repeat markers. International Journal of Genomics 2016: 8956412. doi: 10.1155/2016/8956412.CrossRefGoogle ScholarPubMed
Yeh, FC, Yang, R and Boyle, T (1999) POPGENE Version 1.31. Microsoft windows-based freeware for population genetic analysis. University of Alberta and Centre for International Forestry Research, Edmonton, Canada.Google Scholar
Zhivotovsky, LA (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molecular Ecology 8: 907–913.10.1046/j.1365-294x.1999.00620.xCrossRefGoogle ScholarPubMed
Supplementary material: File

dos Santos et al. supplementary material

dos Santos et al. supplementary material

Download dos Santos et al. supplementary material(File)
File 65.5 KB