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Genetic diversity of farmer-preferred cassava landraces in Tanzania based on morphological descriptors and single nucleotide polymorphisms

  • M. K. Mtunguja (a1) (a2), A. Ranjan (a2) (a3), H. S. Laswai (a1), Y. Muzanila (a4), J. Ndunguru (a5) and N. R. Sinha (a2)...


Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.


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Benesi, IRM, Lubuschagne, MT and Mahungu, N (2010) Ethnobotany, morphology and genotyping of cassava germplasm from Malawi. Journal of Biological Sciences 10: 616623.
Ching, A, Caldwell, KS, Jung, M, Dolan, M, Smith, OS, Tingey, S, Morgante, M and Rafalski, AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 114.
Dellaporta, SL, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: Version 2. Plant Molecular Biology Reporter 1: 1922.
Elias, M, Penet, L, Vindry, P, MacKey, 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: 18951907.
FAO Report (2006) Starch market adds value to cassava. Available at: (accessed accessed 10 March 2015).
Fukuda, WMG, Guevara, CL, Kawuki, R and Ferguson, ME (2010) Selected Morphological and Agronomic Descriptors for the Characterization of Cassava. Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA).
Garcia-Lor, A, Curk, F, Snoussi-Trifa, H, Morillon, R, Ancillo, G, Luro, F, Navarro, L and Ollitraut, P (2013) A nuclear phylogenetic analysis; SNPs, indels and SSRs deliver new insight into relationship in the ‘true citrus fruit tree’ group (Citranae, Rutaceae) and the origin of cultivated species. Annals of Botany 111: 119.
Glaubitz, JC, Cassteve, TM, Lu, F, Harriman, J, Elshire, RJ, Sun, Q and Buckler, ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLOS ONE 9: e90346.
Hershey, CH (1993) Manihot esculenta Crantz. In: Kalloo G and Berg BO (eds) Genetic Improvement of Vegetable Crops. New York: Pergamon press, pp. 669–691.
Kawuki, RS, Ferguson, M, Labuschagne, M, Herseliman, L and Kim, D (2009) Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz). Molecular Breeding 23: 669684.
Kizito, EB, Chiwona-Karltun, L, Egwang, T, Fregene, M and Westerbergh, A (2007) Genetic diversity and variety composition of cassava on small scale farms in Uganda: an interdisciplinary study using genetic markers and farmer interviews. Genetica 130: 301318.
Lebot, V (2009) Tropical Root and Tuber Crops: Cassava, Sweet Potato, Yams and Aroids. Wallingford, UK: CABI.
Mammadov, J, Aggarwal, R, Buyyarapu, R and Kumpatla, S (2012) SNP markers and their impact on plant breeding. International Journal of Plant Genomics 2012: 111.
Mezette, FT, Blumer, GC and Veasey, EA (2013) Morphological and molecular diversity among cassava genotypes. Pesquisa Agropecuária Brasileira 48: 510518.
Mkamilo, GS and Jeremiah, SC (2005) Current status of cassava improvement program in Tanzania. African Crop Science Conference Proceedings 7: 13111314.
Mkumbira, J, Chiwona-Karltun, L, Lagercrantz, U, Mahungu, MN, Saka, J, Mhone, A, Bokanga, M, Brimer, L, Gullberg, U and Rosling, H (2003) Classifications of cassava into bitter and cool: from farmers' perception to characterization by molecular markers. Euphytica 132: 722.
Monson-Miller, J, Sanches-Mendez, DC, Fass, J, Henry, IM, Tai, TH and Comal, L (2012) Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. BioMed Central Genomics 13: 72.
Mtunguja, MK, Laswai, HS, Muzanila, YC and Ndunguru, J (2014) Farmer's knowledge on selection and conservation of cassava (Manihot esculenta) genetic resources in Tanzania. Journal of Biology, Agriculture and Healthcare 4: 120129.
Oliveira, EJ, Ferreira, CF, Silva Santos, V, de Juses, ON, Oliveira, GAF and Silva, MS (2014) Potential of SNP markers for the characterization of Brazilian cassava germplasm. Theoretical and Applied Genetics 127: 14231440.
Pujol, B, Renoux, F, Elias, M, Rival, L and Mckey, D (2007) The unappreciated ecology of landrace populations: conservation consequences of soil seed banks in cassava. Biological Conservation 136: 541551.
Rafalski, JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant science 162: 329333.
Raji, AA, Dixon, AGO and Ladeinde, TAO (2007) Agronomic traits and tuber quality attributes of farmer grown cassava (Manihot esculenta) landraces in Nigeria. Journal of Tropical Agriculture 45: 913.
Raman, H, Stodart, BJ, Cavanagh, C, Mackay, M, Matthew, M, Milgate, A and Martin, P (2010) Molecular diversity and genetic structure of modern and traditional landrace cultivars of wheat (Triticum aestivum L.). Crop and Pasture Science 61: 222229.
Rohlf, FJ (2009) NTSYSpc: Numerical Taxonomy System. Ver. 2.21c. Setauket, NY: Exeter Software.
Tairo, F, Mneney, E and Kullaya, A (2008) Morphological and agronomical characterization of sweetpotato [Ipomoea batatas (L.) Lam.] germplasm collection from Tanzania. African Journal of Plant Science 2: 7785.
Varshney, RK, Nayak, SN, May, GD and Jackson, SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trend in Biotechnology 27: 522530.
Vieira, EA, Carvalho, FIF, Bertan, I, Kopp, MM, Zimmer, PD, Benin, G, Silva, JAG, Hartwig, I, Malone, G and Oliveira, AC (2007) Association between genetic distances in wheat (Triticum aestivum L.) as estimated by AFLP and morphological markers. Genetics and Molecular Biology 30: 392399.


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Genetic diversity of farmer-preferred cassava landraces in Tanzania based on morphological descriptors and single nucleotide polymorphisms

  • M. K. Mtunguja (a1) (a2), A. Ranjan (a2) (a3), H. S. Laswai (a1), Y. Muzanila (a4), J. Ndunguru (a5) and N. R. Sinha (a2)...


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