Hostname: page-component-cd9895bd7-8ctnn Total loading time: 0 Render date: 2024-12-27T05:37:37.887Z Has data issue: false hasContentIssue false
  • English
  • Français

Diversity and genetic structure of cassava landraces and their wild relatives (Manihot spp.) in Colombia revealed by simple sequence repeats

Published online by Cambridge University Press:  24 August 2015

E. Tovar ,
J. L. Bocanegra ,
C. Villafañe ,
L. Fory ,
A. Velásquez ,
G. Gallego  and
R. Moreno
E. Tovar*
Affiliation:
The Alexander von Humboldt Biological Resources Research Institute, Bogotá, Colombia
J. L. Bocanegra
Affiliation:
The Alexander von Humboldt Biological Resources Research Institute, Bogotá, Colombia
C. Villafañe
Affiliation:
Ministry of the Environment and Sustainable Development, Bogotá, Colombia
L. Fory
Affiliation:
International Center for Tropical Agriculture (CIAT), Palmira, Colombia
A. Velásquez
Affiliation:
International Center for Tropical Agriculture (CIAT), Palmira, Colombia
G. Gallego
Affiliation:
International Center for Tropical Agriculture (CIAT), Palmira, Colombia
R. Moreno
Affiliation:
The Alexander von Humboldt Biological Resources Research Institute, Bogotá, Colombia
*
*Corresponding author. E-mail: edutovar@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Understanding the genetic composition and population structure of plant species at a molecular level is essential for the development of adequate strategies aimed at enhancing the conservation and use of their genetic resources. In addition, such knowledge can help to plan ahead for a scenario under which wild and cultivated species come into contact with their genetically modified (GM) counterpart(s). Using ten simple sequence repeat markers, we genotyped 409 samples pertaining to the species in the Manihot genus known to occur in Colombia, i.e. cassava (Manihot esculenta) and its wild relatives Manihot brachyloba, Manihot carthaginensis and Manihot tristis. High genetic variation was observed in all the species (HE= 0.212–0.603), with cassava showing highest diversity. Most of the genetic variation was found within species populations. Our results suggest that outcrossing events among populations occur much more frequently in M. tristis and M. esculenta, and particularly so in the latter, where the exchange of varieties among local farmers plays a key role in maintaining and introducing new genetic diversity. The occurrence of gene flow within and among populations of Manihot species in Colombia becomes relevant in a biosafety context, where gene flow from GM cassava, if introduced to the country, might have detrimental effects on the structure and dynamics of populations of wild species. The baseline information on the genetic diversity and structure of the four Colombian species that we have presented here provides a first and indispensable step towards the development of targeted interventions necessary to preserve their genetic resources.

Keywords

cassavacrop wild relativesgenetic diversityGMOManihotsimple sequence repeat
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 3 , September 2016 , pp. 200 - 210
Copyright
Copyright © NIAB 2015 

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

Allem, AC (1994) The origin of Manihot esculenta Crantz (Euphorbiaceae). Genetic Resources and Crop Evolution 41: 133–150.CrossRefGoogle Scholar
Allem, AC, Mendes, RA, Salomão, AN and Burle, ML (2001) The primary gene pool of cassava (Manihot esculenta Crantz subspecies esculenta, Euphorbiaceae). Euphytica 120: 127–132.CrossRefGoogle Scholar
Asiedu, R, Hahn, SK, Bai, KV and Dixon, AGO (1992) Introgression of genes from wild relatives into cassava. In: Akoroda, MO and Arene, OB (eds) Proceedings of the 4th Triennial Symposium of the International Society for Tropical Root Crops – Africa Branch. Nigeria: ISTRC-AB/IDRC/CTA/IITA, pp. 89–91.Google Scholar
Bassam, B, Caetano, G and Gresshoff, P (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry 190: 80–83.CrossRefGoogle Scholar
Blair, MW, Fregene, MA, Beebe, SE and Ceballos, H (2007) Marker assisted selection in common beans and cassava. In: Guimaraes, E (ed) Marker-Assisted Selection. Current Status and Future Perspectives in Crops, Livestock, Forestry and Fish. Italy: Food and Agriculture Organization (FAO), pp. 81–116.Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in the man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Byrne, D (1984) Breeding cassava. Plant Breeding Reviews 2: 73–134.CrossRefGoogle Scholar
Chavarriaga, P, Prieto, S, Herrera, CJ, López, D, Bellotti, A and Tohme, J (2004) Screening transgenics unveils apparent resistance to hornworm (E. ello) in the non-transgenic, African cassava clone 60444. In: Alves, A and Tohme, J (eds) Adding Value to a Small-farmer Crop. Proceedings of the 6th International Scientific Meeting of the Cassava Biotechnology Network. Cali: CIAT, p. 4.Google Scholar
Duputié, A, David, P, Debain, C and McKey, D (2007) Natural hybridization between a clonally propagated crop, cassava (Manihot esculenta ssp. esculenta) and a wild relative in French Guiana. Molecular Ecology 16: 3025–3038.CrossRefGoogle Scholar
Dyer, RJ (2014) gstudio: Analyses and functions related to the spatial analysis of genetic marker data. R package version 1.3. http://CRAN.R-project.org/package = gstudio (accessed accessed July 2014).Google Scholar
Elias, M, Panaud, O and Robert, T (2000) Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers. Heredity 85: 219–230.CrossRefGoogle Scholar
Elias, M, Penet, L, Vindry, P, McKey, D, Panaud, O and Robert, T (2001) Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Molecular Ecology 10: 1895–1907.CrossRefGoogle Scholar
Elias, M, Santos Mühlen, G, McKey, D, Roa, AC and Tohme, J (2004) Genetic diversity of traditional south american landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites. Economic Botany 58: 242–256.CrossRefGoogle Scholar
Ellstrand, NC and Elam, DR (1993) Population genetic consequences of small population size: implications for plant conservation. Annual Review of Ecology, Evolution, and Systematics 24: 217–242.CrossRefGoogle Scholar
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
Food and Agriculture Organization (FAO) (2008) Cassava for food and energy security. http://www.fao.org/newsroom/en/news/2008/1000899/index.html (accessed accessed 14 August 2013).Google Scholar
Fregene, M, Suarez, M, Mkumbira, J, Kulembeka, H, Ndedya, E, Kulaya, A, Mitchel, S, Gullberg, U, Rosling, H, Dixon, A and Kresovich, S (2003) Simple sequence repeat (SSR) diversity of cassava (Manihot esculenta Crantz) landraces: genetic diversity and differentiation in a predominantly asexually propagated crop. Theoretical and Applied Genetics 107: 1083–1093.CrossRefGoogle Scholar
Goudet, J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). http://www.unil.ch/izea/softwares/fstat.html . Updated from Goudet (1995). Google Scholar
Ihemere, U, Arias-Garzon, D, Lawrence, S and Sayre, RT (2006) Genetic modification of cassava for enhanced starch production. Plant Biotechnology Journal 4: 453–465.CrossRefGoogle ScholarPubMed
Kawano, K (1980) Cassava. Chapter 13. In: Fehr, WR and Hadley, HH (eds) Hybridization of Crop Plants. Madison: American Society of Agronomy, pp. 225–233.Google Scholar
Kawuki, RS, Ferguson, M, Labuschagne, M, Herselman, L and Kim, DJ (2009) Identification, characterization and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz). Molecular Breeding 23: 669–684.CrossRefGoogle Scholar
Kawuki, RS, Herselman, L, Labuschagne, MT, Nzuki, I, Ralimanana, I, Bidiaka, M, Kanyange, MC, Gashaka, G, Masumba, E, Mkamilo, G, Gethi, J, Wanjala, B, Zacarias, A, Madabula, F and Ferguson, ME (2013) Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa. Plant Genetic Resources: Characterization and Utilization 11: 170–181.CrossRefGoogle Scholar
Kelley, LA, Gardner, SP and Sutcliffe, MJ (1996) An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally-related subfamilies. Protein Engineering 9: 1063–1065.CrossRefGoogle ScholarPubMed
Lefevre, FA and Charrier, S (1993) Isozyme diversity within African Manihot germplasm. Euphytica 66: 73–80.CrossRefGoogle Scholar
Mba, REC, Stephenson, P, Edwards, K, Melzer, S, Mkumbira, J, Gullberg, U, Apel, K, Gale, M, Tohme, J and Fregene, M (2001) Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theoretical and Applied Genetics 102: 22–31.CrossRefGoogle Scholar
Meireles da Silva, R, Bandel, G and Martins, PS (2003) Mating system in an experimental garden composed of cassava (Manihot esculenta Crantz) ethnovarieties. Euphytica 134: 127–135.CrossRefGoogle Scholar
Milligan, BG, Leebens-Mack, J and Strand, AE (1994) Conservation genetics: beyond the maintenance of marker diversity. Molecular Ecology 12: 844–855.Google Scholar
Montagnac, JA, Davis, CR and Tanumihardio, SA (2009) Nutritional value of cassava for use as a staple food and recent advances for improvement. Comprehensive Reviews in Food Science and Food Safety 8: 181–194.CrossRefGoogle ScholarPubMed
Montero-Rojas, M, Correa, AM and Siritunga, D (2011) Molecular differentiation and diversity of cassava (Manihot esculenta) taken from 162 locations across Puerto Rico and assessed with microsatellite markers. AoB Plants 2011: plr010. doi:10.1093/aobpla/plr010.CrossRefGoogle Scholar
Nassar, N (2003) Gene flow between cassava (Manihot esculenta Crantz), and wild relatives. Genetics and Molecular Research 2: 334–347.Google ScholarPubMed
Olsen, KM (2004) SNPs, SSRs and inferences on cassava's origin. Plant Molecular Biology 56: 517–526.CrossRefGoogle ScholarPubMed
Olsen, KM and Schaal, BA (1999) Evidence on the origin of cassava: phylogeography of Manihot esculenta . Proceedings of the National Academy of Sciences of the United States of America 96: 5586–5591.CrossRefGoogle ScholarPubMed
Olsen, KM and Schaal, BA (2001) Microsatellite variation in cassava (Manihot esculenta . Euphorbiaceae) and its wild relatives: further evidence for a southern Amazonian origin of domestication. American Journal of Botany 88: 131–142.Google ScholarPubMed
Pujol, B, David, P and McKey, D (2005) Microevolution in agricultural environments: how a traditional Amerindian farming practice favours heterozygosity in cassava (Manihot esculenta Crantz. Euphorbiaceae). Ecology Letters 8: 138–147.CrossRefGoogle Scholar
R Core Team(2014) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. http://www.R-project.org (accessed accessed July 2014).Google Scholar
Raji, AAJ, Anderson, JV, Kolade, OA and Ugwu, CD (2009 a) Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biology 9: 118.CrossRefGoogle ScholarPubMed
Raji, AAJ, Fawole, I, Gedil, M and Dixon, AGO (2009 b) Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers. Annals of Applied Biology 155: 187–199.CrossRefGoogle Scholar
Roa, AC, Maya, MM, Duque, MC, Tohme, J, Allem, AC and Bonierbale, MW (1997) AFLP analysis of relationships among cassava and other Manihot species. Theoretical and Applied Genetics 95: 741–750.CrossRefGoogle Scholar
Rogers, DJ and Appan, SG (1973) Manihot and Manihotoides (Euphorbiaceae). A Computer Assisted Study. Flora Neotropica, Monograph No. 13. New York: Hafner Press.Google Scholar
Salick, J, Cellinese, N and Knapp, S (1997) Indigenous diversity of cassava: generation, maintenance, use and loss among the Amuesha, Peruvian upper Amazon. Economic Botany 51: 6–19.CrossRefGoogle Scholar
Sambatti, JBM, Martins, PS and Ando, A (2001) Folk taxonomy and evolutionary dynamics of cassava: a case study in Ubatuba. Brazil. Economic Botany 55: 93–105.CrossRefGoogle Scholar
Sayre, R, Beeching, JR, Cahoon, EB, Egesi, C, Fauquet, C, Fellman, J, Fregene, M, Gruissem, W, Mallowa, S, Manary, M, Maziya-Dixon, B, Mbanaso, A, Schachtman, DP, Siritunga, D, Taylor, N, Vanderschuren, H and Zhang, P (2011) The bio-cassava plus program: biofortification of cassava for sub-saharan Africa. Annual Review of Plant Biology 62: 251–272.CrossRefGoogle ScholarPubMed
Schaal, B, Carvalho, LJCB, Prinzie, T, Olsen, K, Hernandez, M, Cabral, G and Moeller, D (1997) Phylogenetic relationships and genetic diversity in Manihot species. African Journal of Root and Tuber Crops 2: 147–149.Google Scholar
Schaal, BA, Hayworth, DA, Olsen, KM, Rauscher, JT and Smith, WA (1998) Phylogeographic studies in plants: problems and prospects. Molecular Ecology 7: 465–474.CrossRefGoogle Scholar
Siqueira, MVBM, Queiroz-Silva, JR, Bressan, EA, Borges, A, Pereira, KJC, Pinto, JG and Veasey, EA (2009) Genetic characterization of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats. Genetics and Molecular Biology 32: 104–110.CrossRefGoogle ScholarPubMed
Slatkin, M and Barton, NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43: 1349–1368.CrossRefGoogle ScholarPubMed
Turyagyenda, LF, Kizito, EB, Ferguson, ME, Baguma, Y, Harvey, JW, Gibson, P, Wanjala, BW and Osiru, DSO (2012) Genetic diversity among farmer-preferred cassava landraces in Uganda. African Crop Science Journal 20: 15–30.Google Scholar
Wanyera, NMW, Hahn, SK and Aken'ova, ME (1992) Introgression of ceara rubber (Manihot glaziovii Muell-Arg) into cassava (M. esculenta Crantz): a morphological and electrophoretic evidence. In: Akoroda, MO (ed) Proceedings of Root Crops for Food Security in Africa. Ibadan: Africa Branch, pp. 125–130.Google Scholar
White, D and Gramacy, RB (2012) maptree: Mapping, pruning, and graphing tree models. R package version 1.4-7. http://CRAN.R-project.org/package = maptree. (accessed July 2014).Google Scholar
Supplementary material: File

Tovar supplementary material

Table S1

Download Tovar supplementary material(File)
File 34.3 KB