Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers

• Autorzy: Ram S G , Thiruvengadam V , Vinod K K
• Języki publikacji: EN

Abstrakty

EN

Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.

• Wydawca: -
• Czasopismo: Journal of Applied Genetics
• Rocznik: 2007
• Tom: 48
• Numer: 4
• Opis fizyczny: p.337-345,fig.,ref.

Twórcy

autor

Ram S G

• Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India

autor

Thiruvengadam V

• Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India

autor

Vinod K K

• Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India

Bibliografia

• Akagi H, Inagaki YA, Fujimura T, 1997. Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94: 61-67.
• Bautista SN, Vaughan D, Jayasuriya AHM, Liyanage ASU, Kaga A, Tomooka N, 2006. Genetic diversity in AA and CC genome Oryza species in southern South Asia. Genet Res Crop Evol 53: 631-640.
• Botstein D, White RL, Skolnick M, Davis RW, 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32: 314-331.
• Cai HW, Morishima H, 2002. QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104: 1217-1228. Chakravarthy KB, Rambabu N, 2006. SSR marker based DNA fingerprinting and diversity study in rice (Oryza sativaL.). Afr J Biotechnol 5: 684-688.
• Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR, 1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95: 553-567.
• Dale MFB, Ford-Loyd BV, Arnold MH, 1985. Variation in some agronomically important characters in a germplasm collection of beet. Euphytica 34: 449-455.
• De Woody JA, Honeycutt RL, Skow LC, 1995. Microsatellite markers in white-tailed deer. J Hered 86: 317-319.
• Felsenstein J, 1985. Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39: 783-791.
• Ferreira ME, Grattapaglia D, 1998. Introduçăo ao Uso de Marcadores Moleculares em Análise Genética. 3. ed. Embrapa, Brasilia: 220.
• Ford-Lloyd BV, Jackson MT, Newbury HJ, 1997. Molecular markers and the management of genetic resources in seed genebanks: a case study of rice. In: Callow JA, Ford-Lloyd BV, Newbury HJ, eds. Biotechnology and plant genetic resources: conservation and use. Wallingford, CAB International.
• Frey KJ, Cox TS, Rodgers DM, Barmel-Cox P, 1984. Increasing cereal yields with genes from wild and weedy species. In: Chopra VL, Joshi BC, Sharma RP, Bansal HC, eds. Genetics: new frontiers. Proc 15th Int Genet Congr, Oxford & IBH Publishing Co., New Delhi.
• Ganesh SK, Vivekanandan P, Nadarajan N, Chandra Babu R, Shanmugasundaram P, Priya PA, Manickavelu A, 2004. Genetic improvement for drought tolerance in rice (Oryza sativa L.). In: III. Germplasm Characterization and Improvement. Rockefeller Foundation Workshop on Drought: CIMMYT, Mexico: 98-99.
• Ishikawa R, Yamanaka S, Fukuta Y, Chitrakon S, Bounphanousay C, Kanyavong K, et al. 2006. Genetic erosion from modern varieties into traditional upland rice cultivars (Oryza sativa L.) in northern Thailand. Genet Res Crop Evol 53: 245-252.
• McCouch SR, Temnykh S, Lukashova A, Coburn J, Declerck G, Cartinhour S, et al. 2001. Microsatellite markers in rice: Abundance, diversity and applications. In: Rice genetics IV. IRRI, Manila, Philippines: 117-135.
• Murray MG, Thompson WF, 1980. Rapid isolation of high-molecular weight plant DNA. Nucleic Acids Res 8: 4321-4327.
• Panaud O, Chen XL, McCouch SR, 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252: 597-607.
• Ravi M, Geethanjali S, Sameeyafarheen F, Maheswaran M, 2003. Molecular marker based genetic diversity analysis in rice (Oryza sativa L.) using RAPD and SSR markers. Euphytica 133: 243-252.
• Rezai A, Frey KJ, 1990. Multivariate analysis of variation among wild oat accessions-seed traits. Euphytica 49: 111-119.
• Rohlf FJ, 2000. NTSYS-pc: Numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Publications, New York, USA.
• Siddiq EA, Saxena S, Malik SS, 2005. Plant genetic resources: food grain crops. In: Dhillon BS, Saxena S, Agrawal A, Tyagi RK, eds. Indian Society of Plant Genetic Resources, New Delhi, Narosa Publishing House, New Delhi, India: 27-57.
• Sneath PHA, Sokal RR, 1973. Numerical taxonomy. Freeman, San Francisco: 573.
• Song ZP, Xu X, Wang B, Chen JK, Lu BR, 2003. Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers. Theor Appl Genet 107: 1492-1499.
• Song WY, Wang GL, Chen L, Kim HS, Pi LY, Garner J, et al. 1995. A receptor kinase-like protein encoded by the rice disease resistance gene Xa21. Science 270: 1804-1806.
• Tautz D, 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17: 6463-6471.
• Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovtiesich L, et al. 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 697-712.
• Vaughan DA, 1991. Choosing rice germplasm for evaluation. Euphytica 54: 147-154.
• Vaughan DA, 1994. The wild relatives of rice. IRRI, Manila.
• Virk PS, Newbury JH, Bryan GJ, Jackson MT, Ford-Lloyd BV, 2000. Are mapped or anonymous markers more useful for assessing genetic diversity? Theor Appl Genet 100: 607-613.
• Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Homes M, et al. 1995. AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414.
• Weir BS, 1996. Genetic data analysis II, 2nd ed. Sunderland, Massachusetts, Sinauer Associates: 377.
• Welsh J, McClelland M, 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18: 7213-7218.
• Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV, 1990. DNA polymorphism amplified by arbitrary primers are usefiil as genetic markers. Nucleic Acids Res 18: 6531-653.
• Wu KS, Tanksley SD, 1993. Genetic and physical mapping of telomeres and microsatellites of rice. Plant Mol Biol 22: 861-872.
• Yang GP, Maroof MAS, Xu CG, Zhang Q, Biyashev RM, 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245: 187-194.
• Yap IV, Nelson RJ, 1996. WinBoot: A program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI Discussion Paper Series 14. International Rice Research Institute, Manila, the Philippines.
• Yuan LP, 1993. Advantages and constraints to the use of hybrid rice varieties. In: Wilson KJ, ed. Proceedings of the International Workshop on Apomixis in Rice. The Rockefeller Foundation and China National Center for Biotechnology Development, New York and Beijing: 1-4.
• Zhai WX, Li W, Tian Y, Pan S, Zhao X, Zhao B, Zhang Q, Zhu L, 2000. Introduction of a blight resistance gene, Xa21, into five Chinese rice varieties through an Agrobacterium mediated system. Sci China 43: 361-368.