AJPS  Vol.4 No.8 , August 2013
Identification of Genetically Distinct Cassava Clones from On-Farm Plantations to Widen the Thai Cassava Breeding Gene Pool
Abstract: Cassava (Manihot esculenta Crantz) is one of the most important economic crops in Thailand. However, the Thai cassava breeding gene pool was genetically narrow with only 11 distinct landraces. An attempt was made here to characterize 266 cassava clones collected from 80 farms in eight provinces using 35 SSR markers. A total of 365 polymorphic alleles were detected in the assayed samples. The molecular analysis of variance revealed that a large SSR variance (19.8%) was present among the farm samples. The genetic relationships of the 266 farm samples revealed by the principal coordinate analysis confirmed the large SSR variation observed among the collected cassava samples. The average dissimilarity (AD) of a cassava sample against the other 265 samples was calculated and the AD values obtained ranged from 0.256 to 0.502 with a mean of 0.319. Based on these AD values, a set of 50 unique cassava samples with AD values of 0.346 or higher was assembled from the on-farm samples to widen the genetic base of the Thai cassava breeding gene pool.
Cite this paper: P. Wangsomnuk, B. Ruttawat and P. Wongtiem, "Identification of Genetically Distinct Cassava Clones from On-Farm Plantations to Widen the Thai Cassava Breeding Gene Pool," American Journal of Plant Sciences, Vol. 4 No. 8, 2013, pp. 1574-1583. doi: 10.4236/ajps.2013.48190.

[1]   J. H. Cock, “Cassava: New Potential for a Neglected Crop,” Westview Press, Boulder, 1985.

[2]   D. Debouck, D. Dominique, J. Alexandra, C. Hershey and R. Llerme, “Conservation of Cassava Genetic Resource,” 2011.

[3]   C. Ratanawaraha, N. Senanarong and P. Suriyapan, “Status of Cassava in Thailand: Implications for Future Research and Development: A Review of Cassava in Asia with Country Case Studies on Thailand and Vietnam,” Proceedings of the Validation Forum on the Global Cassava Development Strategy, Rome, 26-28 April 2000.

[4]   C. H. Hershey and D. Debouck, “A Global Conservation Strategy for Cassava and Wild Manihot Species,” A Summary of Stakeholder Deliberations and Recommendations Prepared for the Global Crop Diversity Trust, 2010.

[5]   Office of Agricultural Economics, “Cassava Production Statistics,” 2013.

[6]   ASEAN Economic Community, “Thailand Tapioca Strategic Framework under the AEC,” Bangkok, 2013.

[7]   C. Rojanaridpiched, V. Vichukit, E. Sarobol and P. Changlek, “Breeding and Dissemination of New Cassava Varieties in Thailand,” Proceedings of the 7th Regional Cassava Workshop, Bangkok, 1 November-28 October 2002.

[8]   S. Sarakarn, A. Limsila, D. Suparhan, P. Wongtiem, J. Hansetasuk and W. Watananonta, “Cassava Germplasm Conservation and Crop Improvement in Thailand,” Proceedings of the 7th Regional Cassava Workshop, Bangkok, 1 November-28 October 2002.

[9]   M. Fregene, M. Suarez, J. Mkumbira, H. Kulembeka, E. Ndedya, A. Kulaya, S. Mitchel, U. Gullberg, H. Rosling, A. Dixon, R. Dean and S. Kresovich, “Simple Sequence Repeat Marker Diversity in Cassava Landraces: Genetic Diversity and Differentiation in an Asexually Propagated Crop,” Theoretical and Applied Genetics, Vol. 107, 2003, pp. 1083-1093. doi:10.1007/s00122-003-1348-3

[10]   A. A. Raji, I. Fawole, M. Gedil and A. G. O. Dixon, “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, Vol. 155, 2009, pp. 187-199.

[11]   M. Montero-Rojas, A. M. Correa and D. Siritunga, “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

[12]   P. Chavarriaga-Aguirre, M. Maya, M. Bonierbale, S. Kresovich, M. Fregene, J. Tohme and G. Kochert, “Microsatellites in Cassava (Manihot esculenta Crantz): Discovery, Inheritance and Variability,” Theoretical and Applied Genetics, Vol. 97, No. 3, 1998, pp. 493-501. doi:10.1007/s001220050922

[13]   O. Rocha, M. Zaldimar, L. Castro, E. Castro and R. Barrantes, “Microsatellite Variation of Cassava (Manihot esculenta Crantz) in Home Gardens of Chibchan Amerindians from Costa Rica,” Conservation Genetics, Vol. 9, No. 1, 2008, pp. 107-118. doi:10.1007/s10592-007-9312-4

[14]   S. Sakuanrungsirikul, P. Sarawat, P. Wongtiem, S. Sarakarn, V. Khonsantear and R. Khantahad, “Molecular Characterization of the CIAT Cassava Core Collection and the Thai and Lao Germplasm Collection Using ISSR-Touchdown PCR,” Proceedings of the 8th Regional Workshop, Vientiane, 20-24 October 2008.

[15]   B. Ruttawat, P. P. Wangsomnuk and P. Wangsomnuk, “Genetic Studies of Selected Thai Cassava by SSR Markers,” Proceedings of the 12th Graduate Research Conference, KhonKaen University, 28 January 2011.

[16]   O. H. Frankel, “Genetic Perspectives of Germplasm Conservation,” In: W. K. Arber, K. Llimensee, W. J. Peacock, and P. Starlinger, Eds., Genetic Manipulation: Impact on Man and Society, Cambridge University Press, Cambridge, 1984, pp. 161-170.

[17]   O. H. Frankel and A. H. D. Brown, “Plant Genetic Resources Today: A Critical Appraisal,” In: J. H. W. Holden and J. T. Williams, Eds., Crop Genetic Resources: Conservation & Evaluation, George Allen & Unwin, London, 1984, pp. 249-257.

[18]   Y. B. Fu, “Redundancy and Distinctness in Flax Germplasm as Revealed by RAPD Dissimilarity,” Plant Genetic Resources, Vol. 4, 2006, pp. 117-124. doi:10.1079/PGR2005106

[19]   T. H. Tai and S. D. Tanksley, “A Rapid and Inexpensive Method for Isolation of Total DNA from Dehydrated Plant Tissue,” Plant Molecular Biology Reporter, Vol. 8, No. 4, 1990, pp. 297-303. doi:10.1007/BF02668766

[20]   R. E. C. Mba, P. Stephenson, K. Edwards, S. Melzer, J. Nkumbira, U. Gullberg, K. Apel, M. Gale, J. Tohme and M. Fregene, “Simple Sequence Repeat (SSR) Marker Survey of the Cassava (Manihot esculenta Crantz) Genome: Towards an SSR-Based Molecular Genetic Map of Cassava,” Theoretical and Applied Genetics, Vol. 102, No. 1, 2001, pp. 21-31. doi:10.1007/s001220051614

[21]   A. A. Raji, J. V. Anderson, O. A. Kolade, C. D. Ugwu, A. G. Dixon and I. L. Ingelbrecht, “Gene-Based Microsatellites for Cassava (Manihot esculenta Crantz): Prevalence, Polymorphisms, and Cross-Taxa Utility,” BMC Plant Biology, Vol. 9, 2009, p. 118. doi:10.1186/1471-2229-9-118

[22]   S. Kunkeaw, T. Yoocha, S. Sraphet, A. Boonchanawiwat, O. Boonseng, D. A. Lightfoot, K. Triwitayakorn and S. Tangphatsornruang, “Construction of a Genetic Linkage Map Using Simple Sequence Repeat Markers from Expressed Sequence Tags for Cassava (Manihot esculenta Crantz),” Molecular Breeding, Vol. 27, No. 1, 2010, pp. 67-75. doi:10.1007/s11032-010-9414-4

[23]   B. J. Bassam, G. Caetano-Anollés and P. M. Gresshoff, “Fast and Sensitive Silver Staining of DNA in Polyacrylamide Gels,” Analytical Biochemistry, Vol. 196, No. 1, 1991, pp. 80-83. doi:10.1016/0003-2697(91)90120-I

[24]   F. Awoleye, M. van Duren, J. Dolezel and F. J. Novak, “Nuclear DNA Content and in Vitro Induced Somatic Polyploidization Cassava (Manihot esculenta Crantz) Breeding,” Euphytica, Vol. 76, No. 3, 1994, pp. 195-202. doi:10.1007/BF00022164

[25]   D. L. Jennings, “Manihot esculenta (Euphorbiaceae),” In: J. Smartt and N. W. Simmonds, Eds., Evolution of Crop Plants, Wiley, New York, 1995, pp. 128-132.

[26]   M. H. Reyes-Valdes and C. G. Williams, “An EntropyBased Measure of Founder Informativeness,” Genetics Research, Vol. 85, No. 1, 2005, pp. 81-88.

[27]   R. Peakall and P. E. Smouse, “GENALEX 6: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research,” Molecular Ecology Notes, Vol. 6, No. 1, 2006, pp. 288-295. doi:10.1111/j.1471-8286.2005.01155.x

[28]   F. J. Rohlf, “NTSYS-pc 2.1. Numerical Taxonomy and Multivariate Analysis System,” Exeter Software, Setauket, 1997.

[29]   R. Silva, G. Bandel and P. Martins, “Mating System in an Experimental Garden Composed of Cassava (Manihot esculenta Crantz) Ethnovarieties,” Euphytica, Vol. 134, No. 2, 2003, pp. 127-135. doi:10.1023/B:EUPH.0000003644.60126.4a

[30]   L. F. Turyagyenda, E. B. Kizito, M. E. Ferguson, Y. Baguma, J. W. Harvey, P. Gibson, B. W. Wanjala and D. S. O. Osiru, “Genetic Diversity among Farmer-Preferred Cassava Landraces in Uganda,” African Crop Science Journal, Vol. 20, No. S1, 2012, pp. 15-30.

[31]   M. Elias, L. Penet, P. Vindry, D. Mckey, O. Panaud and T. Robert, “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, Vol. 10, No. 8, 2001, pp. 1895-1907. doi:10.1046/j.0962-1083.2001.01331.x

[32]   J. Sardos, E. Mackey, M. F. Duval, R. Malapa, J. L. Noyer and V. Lebot, “Evolution of Cassava (Manihot esculenta Crantz) after Recent Introduction into a South Pacific Island System: The Contribution of Sex to the Diversification of a Clonally Propagated Crop,” Genome, Vol. 51, No. 11, 2008, pp. 912-921. doi:10.1139/G08-080

[33]   A. El Bakkali, H. Haouane, A. Moukhli, E. Costes, P. V. Damme and B. Khadar, “Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Oleaeuropaea L.) Genetic Resources,” PLoS ONE, Vol. 8, No. 5, 2013, Article ID: e61265. doi:10.1371/journal.pone.0061265

[34]   A. Diederichsen, P. M. Kusters, D. Kessler, Z. Bainas and R. K. Gugel, “Assembling a Core Collection from the Flax World Collection Maintained by Plant Gene Resources of Canada,” Genetic Resources and Crop Evolution, Vol. 60, No. 4, 2013, pp. 1479-1485. doi:10.1007/s10722-012-9936-1