Genetic structure of Thai rice and rice accessions obtained from the international rice research institute

Rice

Volumn 5, Issue 1, 2012, Pages

  Chakhonkaen, Sriprapai ^a   Pitnjam, Keasinee ^a   Saisuk, Wachira ^b   Ukoskit, Kittipat ^b   Muangprom, Amorntip ^a  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b THAMMASAT UNIVERSITY   (Thailand)

Author keywords

Genetic diversity; Germplasm evaluation; InDel marker; Oryza sativa; Population structure; Temperature sensitive genetic male sterile

Indexed keywords

EID: 84865141620     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1186/1939-8433-5-19     Document Type: Article

References (41)

1. Ali ML, McClung AM, Jia MH, Kimball JA, McCouch SR, Georgia CE (2011) A Rice Diversity Panel Evaluated for Genetic and Agro-Morphological Diversity between Subpopulations and its Geographic Distribution. Crop Sci 51:2021-2035
2. Baack EJ, Sapir Y, Chapman MA, Burke JM, Rieseberg LH (2008) Selection on domestication traits and quantitative trait loci in crop-wild sunflower hybrids. Mol Ecol 17:666-677
3. Bertin I, Zhu JH, Gale MD (2005) SSCP-SNP in pearl millet-a new marker system for comparative genetics. Theor Appl Genet 110:1467-1472
4. Borchert T, Hohe A (2009) Identification of molecular markers for the flower type in the ornamental crop Calluna vulgaris. Euphytica 170:203-213
5. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
6. Castelblanco W, Fregene M (2006) SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz). Plant Mol Biol Rep 24:229-236
7. Chen H, He H, Zou Y, Chen W, Yu R, Liu X, Yang Y, Gao Y, Xu J, Fan L et al (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theor Appl Genet 123:869-879
8. Chitrakon S, Somrith B (2003) The development of Thai rice varieties. In: Lorlowhakarn S (ed) Science and technology with Thai rice. Thailand's national science and technology development Agency, pp 29-76
9. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47-50
10. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments. Genome Res 14:1812-1819
11. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic Structure and Diversity in Oryza sativa L. Genetics 169:1631-1638
12. Grieu F, Joseph D, Norman P, Iacopetta B (2004) Development of a rapid genotyping method for single nucleotide polymorphisms and its application in cancer studies. Oncol Rep 11:501-504
13. Hashimoto Z, Mori N, Kawamura M, Ishii T, Yoshida S, Ikegami M, Takumi S, Nakamura C (2004) Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers. Theor Appl Genet 109:1586-1596
14. Huff DR (1997) RAPD characterization of heterogeneous perennial ryegrass cultivars. Crop Sci 37:557-564
15. Ishii T, Hiraoka T, Kanzaki T, Akimoto M, Shishido R, Ishikawa R (2011) Evaluation of Genetic Variation Among Wild Populations and Local Varieties of Rice. Rice. doi:10.1007/s12284-011-9067-x
16. Jacquemin J, Laudié M, Cooke R (2009) A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond. BMC Plant Biol 9:146. doi:10.1186/1471-2229-9-146
17. Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar SD (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311-1320
18. Kuhn DN, Motamayor JC, Meerow AW, Borrone JW, Schnell RJ (2008) SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. Electrophoresis 29:4096-4108
19. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129
20. Lopez MT, Toojinda T, Vanavichit A, Tragoonrung S (2003) Microsatellite markers flanking the tms2 gene facilitated tropical TGMS rice line development. Crop Sci 43:2267-2271
21. Lu Y, Curtiss J, Percy RG, Hughs SE, Yu S, Zhang J (2009) DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton. Crop Sci 49:1695-1704
22. Moose SP, Mumm RH (2008) Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol 147:969-977
23. Muangprom A, Thomas SG, Sun TP, Osborn TC (2005) A novel dwarfing mutation in a green revolution gene from Brassica rapa. Plant Physiol 137:931-938
24. Murray MG, Tompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321-4326
25. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonuclease. Proc Natl Acad Sci USA 76:5269-5273
26. Ni J, Colowit PM, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42:601-607
27. Pessoa-Filho M, Beló A, Alcochete AA, Rangel PH, Ferreira ME (2007) A set of multiplex panels of microsatellite markers for rapid molecular characterization of rice accessions. BMC Plant Biol 7:23. doi:10.1186/1471-2229-7-23
28. Pitnjam K, Chakhonkaen S, Toojinda T, Muangprom A (2008) Identification of a deletion in tms2 and development of gene-based markers for selection. Planta 228:813-822
29. Prichard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
30. Provan J, Wolters P, Caldwell KH, Powell W (2004) High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat. Theor Appl Genet 108:1182-1190
31. Ram SG, Thiruvengadam V, Vinod KK (2007) Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers. J Appl Genet 48:337-345
32. Rohlf FJ (1998) NTSYS-pc: Numerical taxonomy and multivariate analysis system, version 2.0,Exeter Software. Setauket, New York
33. Rousseau-Gueutin M, Gaston A, Aïnouche A, Aïnouche ML, Olbricht K, Staudt G, Richard L, Denoyes-Rothan B (2009) Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): New insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 51:515-530
34. Shen Y, Jiang H, Jin JP, Zhang Z-B, Xi B, He Y-Y, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198-1205
35. Sunnucks P, Wilson AC, Beheregaray LB, Zenger K, French J, Taylor AC (2000) SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol Ecol 9:1699-1710
36. Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114:559-568
37. Wen W, Mei H, Feng F, Yu S, Huang Z, Wu J, Chen L, Xu X, Luo L (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet 119:459-470
38. Yeh FC, Yang RC, Boyle T (1999) POPGENE version1.32, Microsoft window-base software for population genetic analysis: a quick user's guide. University of Alberta, Center for International Forestry Research, Alberta, Canada
39. Yu SB, Xu WJ, Vijayakumar CH, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aquino C, Virmani SS, Li ZK (2003) Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theor Appl Genet 108:131-140
40. Zhang P, Li J, Li X, Liu X, Zhao X et al (2011) Population Structure and Genetic Diversity in a Rice Core Collection (Oryza sativa L.) Investigated with SSR Markers. PLoS One 6:e27565
41. Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 24(5):e1078