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Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa

Published online by Cambridge University Press:  12 February 2013

R. S. Kawuki ,
L. Herselman ,
M. T. Labuschagne ,
I. Nzuki ,
I. Ralimanana ,
M. Bidiaka ,
M. C. Kanyange ,
G. Gashaka ,
E. Masumba  and
G. Mkamilo
...Show all authors
R. S. Kawuki
Affiliation:
National Crops Resources Research Institute (NaCRRI), PO Box 7084, Kampala, Uganda Department of Plant Sciences, University of the Free State, PO Box 339, Bloemfontein9300, South Africa International Institute of Tropical Agriculture (IITA), PO Box 30709, Nairobi, Kenya
L. Herselman
Affiliation:
Department of Plant Sciences, University of the Free State, PO Box 339, Bloemfontein9300, South Africa
M. T. Labuschagne
Affiliation:
Department of Plant Sciences, University of the Free State, PO Box 339, Bloemfontein9300, South Africa
I. Nzuki
Affiliation:
International Institute of Tropical Agriculture (IITA), PO Box 30709, Nairobi, Kenya Bioscience eastern and central Africa, c/o International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
I. Ralimanana
Affiliation:
FOFIFA/DRA, PO Box 1444, Antananarivo, Madagascar
M. Bidiaka
Affiliation:
Institut National pour l'Etude et la Recherche Agronomique (INERA), Kinshasa, Democratic Republic of Congo
M. C. Kanyange
Affiliation:
Institut des Sciences Agronomiques du Rwanda (ISAR), BP 138, Butare, Rwanda
G. Gashaka
Affiliation:
Institut des Sciences Agronomiques du Rwanda (ISAR), BP 138, Butare, Rwanda
E. Masumba
Affiliation:
Root and Tuber Research Program, Naliendele Agricultural Research Institute, PO Box 509, Mtwara, Tanzania
G. Mkamilo
Affiliation:
Root and Tuber Research Program, Naliendele Agricultural Research Institute, PO Box 509, Mtwara, Tanzania
J. Gethi
Affiliation:
Kenya Agricultural Research Institute (KARI), Katumani, PO Box 340, Machakos, Kenya
B. Wanjala
Affiliation:
Kenya Agricultural Research Institute (KARI), Katumani, PO Box 340, Machakos, Kenya
A. Zacarias
Affiliation:
Agricultural Research Institute (IIAM), PO Box 1922, Maputo, Mozambique
F. Madabula
Affiliation:
Agricultural Research Institute (IIAM), PO Box 1922, Maputo, Mozambique
M. E. Ferguson*
Affiliation:
International Institute of Tropical Agriculture (IITA), PO Box 30709, Nairobi, Kenya
*
*Corresponding author. E-mail: [email protected]
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Abstract

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies.

Keywords

Africacassavagenetic differentiationgenetic diversityManihot esculenta Crantzsimple sequence repeats
Type
Research Article
Information
Plant Genetic Resources , Volume 11 , Issue 2 , August 2013 , pp. 170 - 181
Copyright
Copyright © NIAB 2013 

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References

Allem, AC (1994) The origin of Manihot esculenta Crantz (Euphobiaceae). Genetic Resources and Crop Evolution 41: 133–150.CrossRefGoogle Scholar
Asante, IK and Offei, SK (2003) RAPD-based genetic diversity study of fifty cassava (Manihot esculenta Crantz) genotypes. Euphytica 131: 113–119.Google Scholar
Benesi IRM. (2005) Characterisation of Malawian cassava germplasm for diversity, starch extraction and its native and modified properties. PhD Thesis, University of the Free State, Bloemfontein, South Africa, pp. 199.Google Scholar
Balyejusa, Kizito E, Bua, A, Fregene, M, Egwang, T, Gullberg, U and Westerbergh, A (2005) The effect of cassava mosaic disease on the genetic diversity of cassava in Uganda. Euphytica 146: 45–54.Google Scholar
Brookfield, JFY (1996) A simple new method for estimating null frequency from heterozygous deficiency. Molecular Ecology 5: 453–455.Google Scholar
Carter, SE, Fresco, LO, Jones, PG and Fairbairn, JN (1992) An Atlas of Cassava in Africa: Historical, Agroecological and Demographic Aspects of Crop Distribution. Cali: CIAT.Google Scholar
Cours, G (1951) Le manioc à Madagascar. Mémoires de l'Institut Scientifique de Madagascar. Série B Biologie Végétale 3: 203–400.Google Scholar
Cours, G, Fargette, D, Otim-Nape, GW and Thresh, JM (1997) The epidemic of cassava mosaic virus disease in Madagascar in the 1930s–1940s: lessons for the current situation in Uganda. Tropical Science 37: 238–248.Google Scholar
Cours-Darne G. (1968) Improving cassava in Africa. The Abidjan Conference: Agricultural Research Priorities for Economic Development in Africa, vol. 2, pp. 330–339.Google Scholar
Dellaporta, SJ, Wood, J and Hicks, JB (1983) A plant DNA mini preparation. Version II. Plant Molecular Biology Reporter 1: 19–21.CrossRefGoogle Scholar
El Mousadik, A and Petit, RJ (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology 5: 547–555.CrossRefGoogle ScholarPubMed
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.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Fregene, MA, Suarez, M, Mkumbira, J, Kulembeka, H, Ndedya, E, Kulaya, A, Mitchel, S, Gullberg, U, Rosling, H, Dixon, AGO, Dean, R and Kresovich, A (2003) Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop. Theoretical and Applied Genetics 107: 1083–1093.Google Scholar
Ferguson, ME, Hearn, SJ, Close, TJ, Wanamaker, S, Moskal, WA, Town, CD, de Young, F, Marri, PR, Rabbi, IY and de Villiers, EP (2012) Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava. Theoretical and Applied Genetics 124: 685–695.CrossRefGoogle ScholarPubMed
Fregene, M, Bernal, A, Duque, M, Dixon, A and Tohme, J (2000) AFLP analysis of African cassava (Manihot esculenta Crantz) germplasm resistant to the cassava mosaic disease (CMD). Theoretical and Applied Genetics 100: 678–685.Google Scholar
Goudet J. (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available at http://www.unil.ch/izea/softwares/fstat.html.Google Scholar
Hillocks, RJ and Jennings, DL (2003) Cassava brown streak disease: a review of present knowledge and research needs. International Journal of Pest Management 49: 225–234.Google Scholar
Hurtado P, Ospina C, Marin J, Buitrago C, Castelblanco W, Correa A, Alfonso P, Barrera E, Gutierrez I, Fregene M, Hearne S, Ferguson M, Alves A, Fortes-Ferreira C, de Vicente C (2008) Assessment of the diversity in global cassava genetic resources based on simple sequence repeat (SSR) markers. In: Fauquet CM (ed). Cassava: Meeting the challenges of the new millenium. Proceedings of the First Scientific Meeting of the Global Cassava Partnership, 21–25 July 2008, Ghent, Belgium.Google Scholar
Jennings, DL (1959) Manihot melanobasis Muell. Arg. – a useful parent for cassava breeding. Euphytica 8: 157–162.Google Scholar
Jennings, DL (1994) Breeding for resistance to African cassava mosaic geminiviruses in East Africa. Tropical Science 34: 110–122.Google Scholar
Jones, WO (1959) Manioc in Africa. Stanford, CA: Standard University Press, pp. 315.Google Scholar
Kawuki, RS, Ferguson, M, Labuschagne, M, Herselman, L, Orone, J, Ralimanana, I, Bidiaka, M, Lukombo, S, Kanyange, MC, Gashaka, G, Mkamilo, G, Gethi, J and Obiero, H (2011) Variation in qualitative and quantitative traits of cassava germplasm from selected national breeding programmes in sub-Saharan Africa. Field Crops Research 122: 151–156.Google Scholar
Kimura, M and Crow, JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49: 725–738.CrossRefGoogle Scholar
Langlands, BW (1966) Cassava in Uganda 1860–1920. Uganda Journal 30: 211–218.Google Scholar
Legg, JP, Jeremiah, SC, Obiero, HM, Maruthi, MN, Ndyetabula, I, Okao-Okuja, G, Bouwmeester, H, Bigirimana, S, Tata-Hangy, W, Gashaka, G, Mkamilo, G, Alicai, T and Kumar, LP (2011) Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa. Virus Research 159: 161–170.Google Scholar
Lewontin, RC (1972) The apportionment of human diversity. Evolutionary Biology 6: 381–398.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker. Integrated analysis environment for genetic marker data. Bioinformatics 21: 2128–2129.Google Scholar
Lokko, Y, Dixon, A, Offei, S, Danquah, E and Fregene, M (2006) Assessment of genetic diversity among African cassava Manihot esculenta Crantz accessions resistant to the cassava mosaic virus disease using SSR markers. Genetic Resources and Crop Evolution 53: 1441–1453.Google Scholar
Lutaladio, NB and Ezumah, HC (1981) Cassava leaf harvesting in Zaire. In: Tenry, ER, Oduri, KA and Cavaness, F (eds) Tropical Root Crops: Research Strategies for the 1980's. Ohawa: IDRC, pp. 134–136.Google Scholar
Maccaferri, M, Sanguineti, MC, Donini, P and Tuberosa, R (2003) Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theoretical and Applied Genetics 107: 783–797.CrossRefGoogle ScholarPubMed
Masumba E.A. (2006) Genetic diversity and field performance of cassava (Manihot esculenta) landraces commonly grown in eastern, southern and lake zones, Tanzania. A Dissertation submitted in partial fulfilment of the requirements for the degree of Master of Science in Agriculture of Sokoine University of Agriculture, Morogoro, Tanzania.Google Scholar
Mba, REC, Stephenson, P, Edwards, K, Melzer, S, Nkumbira, 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: 21–31.CrossRefGoogle Scholar
Morgante, M and Olivieri, AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant Journal 3: 175–182.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences USA 70: 3321–3323.Google Scholar
Nichols, RFW (1947) Breeding cassava for virus resistance. East African Agricultural Journal 12: 184–194.Google Scholar
Nweke, F, Spencer, D and Lynam, J (2001) The Cassava Transformation: Africa's Best Kept Secret. East Lansing, MI: Michigan State University Press.Google Scholar
Olsen, KM (2004) SNPs, SSRs and inferences on cassava origin. Plant Molecular Biology 56: 517–526.CrossRefGoogle ScholarPubMed
Olsen, KM and Schaal, BA (2001) Microsatellites 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 Scholar
Otim-Nape, GW, Bua, A, Thresh, JM, Baguma, Y, Ogwal, S, Semakula, GN, Acola, G, Byabakama, B and Martin, A (1997) Cassava mosaic virus disease in Uganda: the current pandemic and approaches to control. Chatham: Natural Resources Institute.Google Scholar
Peroni, N, Kageyama, PY and Begossi, A (2007) Molecular differentiation, diversity, and folk classification of “sweet” and “bitter” cassava (Manihot esculenta) in Caicara and Caboclo management systems (Brazil). Genetic Resources and Crop Evolution 54: 1333–1349.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inferences of population structure from multilocus genotypic data. Genetics 155: 945–959.CrossRefGoogle Scholar
R Development Core Team (2010) R: A language and environment for statistical computing. Available at http://www.Rproject.org (verified 3 November 2010).Google Scholar
Silva, R, da 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
Siqueira, MVBM, Queiroz-Silva, JR, Bressan, EA, Borges, A, Pereira, JCK, Pinto, JG and Veasey, AE (2009) Genetic characterisation of cassava (Manihot esculenta) landraces in Brazil assessed with simple sequence repeats. Genetics and Molecular Biology 32: 104–110.Google Scholar
Tautz, D and Renz, M (1984) Simple sequences are ubiquitous components of the eukaryotic genomes. Nucleic Acids Research 12: 4127–4138.Google Scholar
Toro, AA, Fernàndez, J and Caballero, A (2009) Molecular characterization of breeds and its use in conservation. Livestock Science 120: 174–195.Google Scholar
Vellvé, R (1993) The decline of diversity in European agriculture. Ecologist 23: 64–69.Google Scholar
Weir, BS (1990) Genetic Data Analysis: Methods for Discrete Population Genetic Data. Sunderland, MA: Sinauer Associates, Inc.Google Scholar
Zacarias, AM, Botha, AM, Labuschagne, MT and Benesi, IRM (2004) Characterisation and genetic distance analysis of cassava (Manihot eculenta Crantz) germplasm from Mozambique using RAPD fingerprinting. Euphytica 138: 49–53.Google Scholar
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