Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India

BMC Genetics

Volumn 14, Issue , 2013, Pages

  Das, Basabdatta ^a   Sengupta, Samik ^b   Parida, Swarup K ^d   Roy, Bipasha ^a   Ghosh, Mrityunjay ^c   Prasad, Manoj ^d   Ghose, Tapas K ^a  

^a BOSE INSTITUTE   (India)

^b UNIVERSITY OF CALCUTTA   (India)

^c Bidhan Chandra Krishi Viswavidyala Mohanpur ^*  (India)

^d NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Genetic diversity; Landrace; Oryza sativa; Population structure; SSR polymorphism

Indexed keywords

AMYLOSE;

ARTICLE; GENE AMPLIFICATION; GENE FREQUENCY; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; GERMPLASM; INDIA; LANDRACE; MICROSATELLITE MARKER; MOLECULAR WEIGHT; NONHUMAN; NULL ALLELE; PHYLOGENETIC TREE; PLANT GENETICS; PLANT STRUCTURES; RICE;

ALLELES; CLUSTER ANALYSIS; GENES, PLANT; GENETIC VARIATION; INDIA; ORYZA SATIVA;

ORYZA SATIVA;

EID: 84881535373     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-14-71     Document Type: Article

References (52)

1. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice. Oryza sativa. PNAS 2006, 103(25):9578-9583.
2. Bautista NS, Solis R, Kamijima O, Ishii T. RAPD, RFLP and SSLP analyses of phylogenetic relationships between cultivated and wild species of rice Genes. Genet Syst 2001, 76(2):71-79.
3. Second G. Origin of the genic diversity of cultivated rice (Oryza spp.): Study of the polymorphism scored at 40 isozyme loci Jpn. J Genet 1982, 57:25-57.
4. Khush GS. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 1997, 35:25-34. 10.1023/A:1005810616885, 9291957.
5. Harlan JR. Crops and Man 1975, Madison, Wisconsin: American Society of Agronomy and Crop Science Society of America.
6. Hore DK. Rice diversity collection, conservation and management in northeastern India. Genet Resour Crop Evol 2005, 52:1129-1140.
7. Mackill DJ. Plant genetic resources. Classifying japonica rice cultivars with RAPD markers. Crop. Sci. 1995, 35:889-894.
8. Glaszmann JC. Isozymes and classification of Asian rice varieties. Theor Appl Genet 1987, 74:21-30.
9. Nei M, Li W. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 1979, 76:5269-5273. 10.1073/pnas.76.10.5269, 413122, 291943.
10. Wu KS, Tanksley SD. Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 1993, 241:225-235.
11. Panaud O, McCouch SR, Chen X. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 1996, 252:597-607.
12. Xiao J, Li J, Yuan L, McCouch SR, Tanksley SD. Genetic diversity and its relationship to hybrid performance and heterosis in rice as revealed by PCR based markers. Theor Appl Genet 1996, 92:637-643.
13. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Goto M, McCouch SR. Comparative evaluation of within cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 1997, 40:370-378. 10.1139/g97-050, 9202415.
14. Thanh ND, Zheng HG, Dong NV, Trinh LN, Ali ML, Nguyen HT. Genetic variation in root morphology and microsatellite DNA loci in upland rice (Oryza sativa L.) from Vietnam. Euphytica 1999, 105:43-51.
15. Yang GP, Maroof MAS, Xu CG, Zang Q, Baiyashev RM. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 1994, 245:187-194.
16. Akagi K, Sandig V, Vooijs M, Van der Valk M, Giovannini M, Strauss M, Berns A. Pre-mediated somatic site-specific recombination in mice. Nucl Acids Res 1997, 25:1766-1773. 10.1093/nar/25.9.1766, 146656, 9108159.
17. Blair MW, Panaud O, McCouch SR. Inter simple sequence repeat (ISSR) amplification for microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 1999, 98:780-792.
18. Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS. Genetioc diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 2000, 100:1311-1320.
19. Bobba S, Siddiq EA. ISSR and SSR markers based on AG and GA repeats delineate geographically diverse (Oryza nivara L.) accessions and reveal rare alleles. Curr Sci 2003, 84:683-689.
20. Herrera TG, Duque DP, Almeida IP, Núñez GT, Pieters AJ, Martinez CP, Tohme JM. Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Electron J Biotechnol 2008, 11(5):1-14.
21. Pervaiz ZH, Rabbani MA, Khaliq I, Pearce SR, Malik SA. Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces. Electron J Biotechnol 2010, 13(3):1-14.
22. Maytinee Kladmook M, Kumchoo T, Hongtrakul V. Genetic diversity analysis and subspecies classification of Thailand rice landraces using DNA markers. Afr J Biotechnol 2012, 11(76):14044-14053.
23. Behera L, Patra BC, Sahu RK, Nanda A, Sahu SC, Patnaik A, Rao GJN, Singh ON. Assessment of genetic diversity in medicinal rices using microsatellite markers. Australian Journal of Crop Science 2012, 6(9):1369-1376.
24. Ge XJ, Xing YZ, Xu CG, He YQ. QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population. Plant Breeding 2005, 124:121-126.
25. Bai X, Luo L, Yan W, Rao MK, Zhan W, Xing Y. Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genetics: 2010, 11:16.
26. Ahmadi J, Fotokian MH. Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza Sativa) using SSR markers. Iranian Journal of Biotechnology 2011, 9:1.
27. Lin MH, Lin CW, Chen JC, Lin YC, Cheng SY, Liu TH, Jan FJ, Wu ST, Thseng FS, Ku HM. Tagging Rice Drought-related QTL with SSR DNA Markers. Crop, Environment & Bioinformatics 2007, 4:65-76.
28. Sudharshan I, Prasad GSV, Manish K Pandey, Shobha Rani N. Historical significance, grain quality features and precision breeding for improvement of export quality basmati varieties in India. Indian. J Crop Science 2006, 1(1-2):29-41.
29. Biswas S, Dey N, Ray Chaudhury T, Dey SR, De M, Prasad M, Ghose TK. Indentification of major QTL for cooked kernel elongation on chromosome 8 of rice (O.sativa L) 2004, 31. Hyderabad, India: Proceedings of Symposium on Comparative and Functional Genomics.
30. Eizenga GC, Agrama HA, Lee FN, Yan W, Jia Y. Identifying Novel Resistance Genes in Newly Introduced Blast Resistant Rice Germplasm. Crop Sci 2006, 46:1870-1878.
31. Breusegem FV, Dekeyser R, Garcia AB, Claes B, Gielen J, Van Montagu M, Caplan AB. Heat-inducible rice hsp82 and hsp70 are not always co-regulated. Planta 1994, 193(1):57-66.
32. Standard Evaluation Systems for rice International Rice Testing Program 1996, Manila, Philippines: IRRI, 4, Standard Evaluation Systems for rice.
33. Das B. Genetic diversity analysis of a set of rice landraces using dna markers. PhD thesis 2012, Jadavpur University: LIfe Science Department.
34. Walbot V. Preparation of DNA from single rice seedling. Rice Genet Newsl 1988, 5:149-151.
35. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: A laboratory manual 1989, New York: Cold Spring Harbour Laboratory Press, 2.
36. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, Park WD, Ayres N, Cartinhour S, McCouch SR. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 2000, 100:713.
37. Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR. Incidence and origin of " null" alleles in the (AC) n microsatellite markers. Am J Hum Genet 1993, 52:922-927. 1682051, 8488841.
38. Jain S, Jain RK, McCouch SR. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 2004, 109:965-977. 10.1007/s00122-004-1700-2, 15309297.
39. Jaccard P. Nouvelle recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 1908, 44:223-270.
40. Rohlf FJ. NTSYS-pc. Numerical taxonomy and multivariance analysis system version 2.02e 1997, New York, USA: Exeter Software, http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html.
41. Yap IP, Nelson R, Boot W. A programm for performing boot strap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms 1995, IPRI Discussion Paper series.
42. Anderson PA, Lawrence GJ, Morrish BC, Ayliffe MA, Finnegan EJ, Ellis JG. Inactivation of the Flax rust resistance gene M associated with loss of a repeated unit within the leucine rich repeat coding region. Plant Cell 1997, 9:641-651. 156945, 9144966.
43. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959. 1461096, 10835412.
44. Excoffier L, Lischer HEL. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 2010, 10:564-567. 10.1111/j.1755-0998.2010.02847.x, 21565059.
45. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xinfg Y, Zhang Q, Kono I, Yano M, Fjellstorm R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 2002, 9:199-207. 10.1093/dnares/9.6.199, 12597276.
46. Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aquino C, Virmani SS, Li ZK. Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Theoretical and Applied Genetics 2003, 108:131-140. 10.1007/s00122-003-1400-3, 13679990.
47. Jain N, Jain S, Saini N, Jain RK. SSR analysis of chromosome 8 regions associated with aroma and cooked kernel elongation in Basmati rice. Euphytica 2006, 152:259-273.
48. Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE. Genetic analysis of traditional and evolved Basmati and non Basmati rice varieties by using fluorescence based ISSR PCR and SSR markers. Proc Natl Acad Sci, USA 2002, 99:5836-5841. 10.1073/pnas.042099099, 122863, 11959900.
49. Archak S, Lakshminarayanareddy V, Nagaraju J. High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis 2007, 28:2396-2405. 10.1002/elps.200600646, 17577195.
50. Rashid M, Ren-hu L, Wei J, Yong-han X, Fu-lin W, Yue-zhi T, Jun-mei W, Cheema AA, Jin-qing C, He G. Genomic diversity among Basmati rice (Oryza sativa L) mutants obtained through 60Co gamma radiations using AFLP markers. Afr J Biotechnol 2009, 8(24):6777-6783.
51. Singh D, Kumar A, Sirohi A, Kumar P, Singh J, Kumar V, Jindal A, Kumar S, Kumar N, Kumar V, Sharma V, Gupta S, Gupta S. Improvement of Basmati rice (Oryza sativa L.) using traditional breeding technology supplemented with molecular markers. Afr J Biotechnol 2011, 10(4):499-506.
52. Deb D. Folk Rice varieties of West Bengal: agronomic and morphological characteristics 2000, New Delhi: Research Foundation for Science, Technology and Ecology.