Marker-assisted development of bacterial blight resistant, dwarf, and high yielding versions of two traditional basmati rice cultivars

Crop Science

Volumn 51, Issue 2, 2011, Pages 759-770

  Bhatia, Dharminder ^a   Sharma, Rajiv ^a   Vikal, Yogesh ^a   Mangat, G S ^a   Mahajan, Ritu ^a   Sharma, Neerja ^a   Lore, Jagjeet Singh ^a   Singh, Naveen ^a   Bharaj, Tajinder S ^a   Singh, Kuldeep ^a  

^a PUNJAB AGRICULTURAL UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ORYZA SATIVA;

EID: 79952461692     PISSN: 0011183X     EISSN: 14350653     Source Type: Journal    
DOI: 10.2135/cropsci2010.06.0358     Document Type: Article

References (66)

1. Allard, R.W. 1999. Principles of plant breeding. John Wiley and Sons, Inc., New York, NY.
2. Amarawathi, Y., R. Singh, A.K. Singh, V.P. Singh, T. Mohapatra, T.R. Sharma, and N.K. Singh. 2009. Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol. Breed. 24:185-190.
3. Atwal, S.S., A.K. Singh, and S.N. Sinha. 2009. Maintenance breeding in basmati rice. Indian Farming 59(1):37-41.
4. Ayres, M.H., A.M. McClung, P.D. Larkin, H.F.J. Bligh, C.A. Jones, and W.D. Park. 1997. Microsatellites and single nucleotide polymorphism diff erentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor. Appl. Genet. 94:773-781.
5. Bao, J.S., H. Corke, and M. Sun. 2006. Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor. Appl. Genet. 113:1171-1183.
6. Beharav, A., A. Cahaner, and M.J. Pinthus. 1998. Genetic correlations between culm length, grain yield and seedling elongation within tall (rht1) and semi-dwarf (Rht1) spring wheat (Triticum aestivum L.). Eur. J. Agron. 9:35-40.
7. Berner, D.K., and B.J. Hoff. 1986. Inheritance of scent in American long grain rice. Crop Sci. 26:876-878.
8. Bhatia, D., R. Sharma, V. Gupta, Y. Vikal, and K. Singh. 2007. Rapid method of extraction of ready to use fi ne quality DNA. Indian J. Crop Sci. 2:407-409.
9. Bhattacharjee, P., R.S. Singhal, and P.R. Kulkarni. 2002. Basmati rice: A review. Int. J. Food Sci. Technol. 37:1-12.
10. Bradbury, L.M.T., T.L. Fitzgerald, R.J. Henry, Q. Jin, and D.L.E. Waters. 2005a. The gene for fragrance in rice. Plant Biotechnol. J. 3:363-370.
11. Bradbury, L.M.T., R.J. Henry, Q. Jin, R.F. Reinke, and D.L.E. Waters. 2005b. A perfect marker for fragrance genotyping in rice. Mol. Breed. 16:279-283.
12. Cheema, K.K., N.K. Grewal, Y. Vikal, A. Das, R. Sharma, J.S. Lore, D. Bhatia, R. Mahajan, V. Gupta, and Kuldeep Singh. 2008. A novel bacterial blight resistance gene from Oryza nivara mapped to 38 Kbp region on chromosome 4L and transferred to O. sativa L. Genet. Res. 90:397-407.
13. Chen, S., C.G. Xu, X.H. Lin, and Q. Zhang. 2001. Improving bacterial blight resistance of '6078', an elite restorer line of hybrid rice, by molecular marker-aided selection. Plant Breed. 120:133-137.
14. Chen, S., J. Wu, Y. Yang, W. Shi, and M. Xu. 2006. The fgr gene responsible for rice fragrance was restricted within 69 kb. Plant Sci. 171:505-514.
15. Collard, B.C.Y., C. Vera Cruz, K.L. McNally, P.S. Virk, and D.J. Mackill. 2008. Rice molecular breeding laboratories in the genomics era: current status and future considerations. International Journal of Plant Genomics. doi:10.1155/2008/524847.
16. Cordeiro, G.M., M.J. Christopher, R.J. Henry, and R.F. Reinke. 2002. Identifi cation of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Mol. Breed. 9:245-250.
17. Dela Cruz, N., and G.S. Khush. 2000. Rice grain quality evaluation procedures. p. 26-27. In R. K. Singh, U.S. Singh, and G.S. Khush (ed.) Aromatic rices. Oxford and IBH Publishing Co. Pvt. Ltd., New Delhi, India.
18. Denyer, K., P. Johnson, S. Zeeman, and A.M. Smith. 2001. The control of amylose synthesis. J. Plant Physiol. 158:479-487.
19. Directorate of Rice Research. 2003. Progress report 2002, Vol. 1, Varietal improvement. Directorate of Rice Research, Rajinder Nagar, Hyderabad, India.
20. Directorate of Rice Research. 2010. Progress report 2009, Vol. 1, Varietal improvement. Directorate of Rice Research, Rajinder Nagar, Hyderabad, India.
21. Ellis, M.H., and W. Spielmeyer. 2002. "Perfect" markers for the rice sd-1 semidwarfing gene. IRRI Notes 27:13-14.
22. Garland, S., L. Lewin, A. Blakeney, R. Reinke, and R. Henry. 2000. PCR based molecular markers for the fragrance gene in rice (Oryza sativa L.). Theor. Appl. Genet. 101:364-371.
23. Glaszmann, J.C. 1987. Isozyme and classifi cation of Asian rice varieties. Theor. Appl. Genet. 74:21-30.
24. Huang, N., E.R. Angeles, J. Domingo, G. Magpantay, S. Singh, G. Zhang, N. Kumaravadivel, J. Bennett, and G.S. Khush. 1997. Pyramiding of bacterial blight resistance genes in rice: Marker assisted selection using RFLP and PCR. Theor. Appl. Genet. 95:313-320.
25. IRGSP. 2005. The map-based sequence of the rice genome. Nature 436:793-800.
26. Jena, K.K., and D.J. Mackill. 2008. Molecular markers and their use in marker-assisted selection in rice. Crop Sci. 48:1266-1276.
27. Jin, Q., D. Waters, G.M. Cordeiro, R.J. Henry, and R.F. Reinke. 2003. A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Sci. 165:359-364.
28. Joseph, M., S. Gopalakrishnan, R.K. Sharma, V.P. Singh, A.K. Singh, N.K. Singh, and T. Mohapatra. 2004. Combining bacterial blight resistance and Basmati quality characteristics by phenotypic and molecular marker-assisted selection in rice. Mol. Breed. 13:1-11.
29. Kauffman, H.E., A.P.K. Reddy, S.P.Y. Hsieh, and S.D. Merca. 1973. An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis. Rep. 57:537-541.
30. Kovach, M.J., M.N. Calingacion, M.A. Fitzgerald, and S.R. McCouch. 2009. The origin and evolution of fragrance in rice (Oryza sativa L.). Proc. Natl. Acad. Sci. USA 106:14444-14449.
31. Kumar, I., and G.S. Khush. 1998. Inheritance of amylose content in rice (Oryza sativa L). Euphytica 38:261-269.
32. Leung, H., W. Jianli, B. Liu, M. Bustaman, R. Sridhar, K. Singh, E. Redona, V.D. Quang, K. Zheng, M. Bernardo, G. Wang, J. Leach, R.I. Choi, and C. Vera Cruz. 2004. Sustainable disease resistance in rice: Current and future strategies. In New directions for a diverse planet. Proc. Int. Crop Sci. Cong., 4th, Brisbane, Australia. 26 Sept.-1 Oct. 2004. Available at http://www.cropscience.org.au/icsc2004 (verifi ed 22 Oct. 2010).The Regional Institute Ltd., Gosford, NSW, Australia.
33. Little, R.R., G.B. Hilder, and E.H. Dawson. 1958. Diff erential eff ect of dilute alkali on 25 varieties of milled white rice. Cereal Chem. 35:111-126.
34. Liu, Q., Q. Li, X. Cai, H. Wang, S. Tang, H. Yu, Z. Wang, and M. Gu. 2006. Molecular marker-assisted selection for improved cooking and eating quality of two elite parents of hybrid rice. Crop Sci. 46:2354-2360.
35. Loireux, M., M. Petrov, N. Huang, E. Guiderdoni, and A. Ghesquiere. 1996. Aroma in rice: genetic analysis for a quantitative trait. Theor. Appl. Genet. 93:1145-1151.
36. Mikami, I., N. Uwatoko, Y. Ikeda, J. Yamaguchi, H.Y. Hirano, Y. Suzuki, and Y. Sano. 2008. Allelic diversifi cation at the wx locus in landraces of Asian rice. Theor. Appl. Genet. 116:979-989.
37. Monna, L., R. Yoshino, J. Suzuki, H. Masuda, Y. Maehara, M. Tanji, M. Sato, S. Nasu, and Y. Minobe. 2002. Positional cloning of rice semidwarfi ng gene sd-1: Rice "green revolution gene" encodes a mutant enzyme involved in gibberllin biosynthesis. DNA Res. 9:11-17.
38. Neeraja, C.N., R. Maghirang-Rodriguez, A. Pamplona, S. Heuer, B.C. Collard, E.M. Septiningsih, G. Vergara, D. Sanchez, K. Xu, A.M. Ismail, and D.J. Mackill. 2007. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor. Appl. Genet. 11:5767-5776.
39. Nene, Y.L. 1998. Basmati rice: a distinct variety (cultivar) of Indian sub-continent. Asian Agric. History 2:175-188.
40. Olsen, K.M., and M.D. Purugganan. 2002. Molecular evidence on the origin and evolution of glutinous rice. Genetics 162:941-950.
41. Prigge, V., A.E. Melchinger, B.S. Dhillon, and M. Frisch. 2009. Effi ciency gain of marker-assisted backcrossing by sequentially increasing marker densities over generations. Theor. Appl. Genet. 119:23-32.
42. Randhawa, H.S., J.S. Mutti, K. Kidwell, C.F. Morris, X. Chen, and K.S. Gill. 2009. Rapid and targeted introgression of genes into popular cultivars using marker-assisted background selection. PLoS One 4(6):e5752.
43. Rangi, P.S., M.S. Sidhu, H.P.S. Nagi, and T.S. Bharaj. 2000. Basmati rice in Punjab: production, marketing and export. Monograph. Punjab Agricultural University, Ludhiana, India.
44. Rodell, M., I. Velicogna, and J.S. Famiglietti. 2009. Satellitebased estimates of groundwater depletion in India. Nature 460:999-1003.
45. Rohlf, F.J. 1998. NTCYS-pc (Numerical taxonomy and multivariate analysis system). Version 2.0. Applied Biostatistics Inc., Port Jeff erson, NY.
46. Sanchez, A.C., S. Brar, N. Huang, Z. Li, and G.S. Khush. 2000. Sequence tagged site marker assisted selection for three bacterial blight resistance genes in rice. Crop Sci. 40:792-797.
47. Sasaki, A., M. Ashikari, M.U. Tanaka, H. Itoh, A. Nishimura, D. Swapan, K. Ishiyama, T. Saito, M. Kobayashi, G.S. Khush, H. Kitano, and M. Matsuoka. 2002. A mutant gibberlin-synthesis gene in rice. Nature 416:701-702.
48. Sharma, N., N. Singh, M. Singh, and T.S. Bharaj. 2008. Quality characteristics of aromatic fi ne grained rice (Oryza sativa) genotypes for utilization in basmati improvement. Ind. J. Agric. Sci. 78:42-49.
49. Shi, W., Y. Yang, S. Chen, and M. Xu. 2008. Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol. Breed. 22:185-192.
50. Shobha Rani, N., and R.K. Singh. 2003. Efforts on aromatic rice improvement in India. p. 35-38. In R.K. Singh, and U.S. Singh (ed.). A treatise on the scented rices in India. Kalyani Publishers, New Delhi, India.
51. Singh, R.K., U.S. Singh, and G.S. Khush. 2000. Prologue. p. 1-4. In U.S. Singh, R.K. Singh, and G.S. Khush (ed.). Aromatic rices. Oxford and IBH Publishing Co. Pvt. Ltd., New Delhi, India.
52. Singh, S., D.J. Mackill, and A.M. Ismail. 2009. Responses of SUB1 rice introgression lines to submergence in the field: Yield and grain quality. Field Crops Res. 113:12-23.
53. Singh, S., J.S. Sidhu, N. Huang, Y. Vikal, Z. Li, S. Brar, H.S. Dhaliwal, and G.S. Khush. 2001. Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker assisted selection into indica cultivar PR106. Theor. Appl. Genet. 102:1011-1015.
54. Singh, V.P. 2000. Basmati rices of India. p. 135-154. In U.S. Singh, R.K. Singh, and G.S. Khush (ed.). Aromatic rices. Oxford and IBH Publishing Co. Pvt. Ltd., New Delhi, India.
55. Singh, V.P., A.K. Singh, S.S. Atwal, M. Joseph, and T. Mohapatra. 2002. Pusa 1121: A rice line with exceptionally high cooked kernel elongation and basmati quality. Intl. Rice Res. Notes 27:25-26.
56. Sood, B.C., and E.A. Siddiq. 1978. A rapid technique for scent determinaton in rice. Indian. J. Genet. 38:268-271.
57. Spielmeyer, W., M.E. Ellis, and P.M. Chandler. 2002. Semidwarf (Sd-1), "green revolution" rice contains a defective gibberellin 20-oxidase gene. Proc. Natl. Acad. Sci. USA 99:9043-9048.
58. Steele, K.A., R. Ogden, R. McEwing, H. Briggs, and J. Gorham. 2008. InDel markers distinguish basmati from other fragrant rice varieties. Field Crops Res. 105:81-87.
59. Sundaram, R.M., M.R. Vishnupriya, S.K. Biradar, G.S. Laha, G.A. Reddy, N.S. Rani, N.P. Sharma, and R.V. Sonti. 2008. Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411-422.
60. Tanksley, S.D., N.D. Young, A.H. Paterson, and M.W. Bonierbale. 1989. RFLP mapping in plant breeding: new tools for an old science. Bio-Technology 7:257-264.
61. Temnykh, S., G. De. Clerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S.R. McCouch. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1452.
62. Tian, Z., Q. Qian, Q. Liu, M. Yan, X. Liu, C. Yan, G. Liu, Z. Gao, S. Tang, D. Zeng, Y. Wang, J. Yud, M. Gu, and J. Li. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc. Natl. Acad. Sci. USA 106:21760-21765.
63. Umemoto, T., and N. Aoki. 2005. Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinization and starch association of the enzyme. Funct. Plant Biol. 32:763-768.
64. Wang, L.Q., W.J. Liu, Y. Xu, Y.Q. He, L.J. Luo, Y.Z. Xing, C.G. Xu, and Qifa Zhang. 2007. Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor. Appl. Genet. 115:463-476.
65. Wang, Y., Y. Xu, and J. Li. 2005. Towards molecular breeding and improvement of rice in China. Trends Plant Sci. 10:610-614.
66. Yoshimura, S., A. Yoshimura, R.J. Nelson, T.W. Mew, and N. Iwata. 1995. Tagging Xa-1, the bacterial blight resistance gene in rice, by using RAPD markers. Jpn. J. Breed. 45:81-85.