Euphytica

, Volume 152, Issue 2, pp 259–273 | Cite as

SSR analysis of chromosome 8 regions associated with aroma and cooked kernel elongation in Basmati rice

  • Neelu Jain
  • Sunita Jain
  • Navinder Saini
  • Rajinder K. Jain
Article

Abstract

Aroma and cooked kernel elongation (CKE) are the two most important quality traits, which differentiate the highly valued Basmati rice from other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked and present on chromosome number 8. We have evaluated the genetic diversity in 33 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati derived from indica × Basmati rice crosses and non-Basmati (indica and japonica) rice varieties for chromosome number 8 using 26 SSR markers including a specific marker (SCU-SSR1) for RG28 locus; the results have been compared with whole genome based SSR allelic data. The 26 SSR markers (24 polymorphic and 2 monomorphic) amplified a total of 106 alleles; 21 of these alleles were detected to be unique, present in only one genotype. The number and size of the alleles, and polymorphism information content (PIC) values ranged between 1–8, 87–312 and 0–0.736 bp, respectively. SCU-SSR1 marker amplified a total of three alleles (128, 129 and 130 bp). All the TB varieties except Basmati 217 (129 bp) and 7/13 cross-bred Basmati varieties had the 130 bp allele. Alleles of 129 and 128 bp were present in majority of the indica and japonica varieties, respectively. The average pair-wise Jaccard similarity coefficients for TB, indica and japonica varieties were 0.512, 0.483 and 0.251, respectively. Average similarity coefficient between TB and japonica was higher (0.236) compared to that between TB and indicas (0.150). Genetic relationships as determined by Principal Component Analysis (PCA, NTSYS-pc), PowerMarker tree, and Structure analyses, clearly showed high-level differentiation between TB and indica rice varieties, which formed two distinct clusters. The cross-bred Basmati and japonica rice genotypes were placed between these two clusters. Basmati 217 and Ranbir Basmati were quite divergent from rest of the TB varieties. Some of cross-bred Basmati varieties including Super, CSR30 and kernel were closer to TB. Indica rice varieties, CSR10 (salt tolerant variety) and Pokkali (salt tolerant landrace) formed a separate distinct cluster. The Pritchard structure analysis divided the rice genotypes in four major sub-populations of TB, cross-bred Basmati, indica and japonica (including Ranbir Basmati and Basmati 217) rice varieties. Chromosome 8 data-set showed a positive correlation (Mantel test, r = 0.739) with the allelic data-set for 30 SSR markers well-distributed on 12 rice chromosomes indicating a higher level of similarity between the two. The study demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides several novel markers for differentiation between TB rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.

Keywords

Aroma Basmati rice Chromosome 8 Genetic diversity Kernel elongation Oryza sativa SSR 

Abbreviations

PCR

Polymerase chain reaction

PCA

Principal Component Analysis

PIC

Polymorphism information content

SSR

Simple sequence repeat

TB

Traditional Basmati

UPGMA

Un-weighted pair-group method with an arithmetic average

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Notes

Acknowledgements

This research was supported by grants from the Rockefeller Foundation, New York, USA (RF2000FS(023) and Indian Council of Agricultural Research, New Delhi (NATP, CGPII-314).

References

  1. Aggarwal RK, Shenoy VV, Ramadevi J, Rajkumar R, Singh L (2002) Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP. Theor Appl Genet 105:680–690PubMedCrossRefGoogle Scholar
  2. Ahn SN, Bollich CN, Tanksley SD (1992) RFLP tagging of a gene for aroma in rice. Theor Appl Genet 84:825–828CrossRefGoogle Scholar
  3. Ahn SN, Bollich CN, McClung AM, Tanksley SD (1993) RFLP analysis of genomic regions associated with cooked kernel elongation in rice. Theor Appl Genet 87:27–32CrossRefGoogle Scholar
  4. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186PubMedGoogle Scholar
  5. Bhasin VK (2000) India and the emerging global rice trade. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford, IBH Pub., New Delhi, India, pp 252–276Google Scholar
  6. Blair MW, Hedetale V, McCouch SR (2002) Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theor Appl Genet 105:449–457PubMedCrossRefGoogle Scholar
  7. Bligh HFJ (2000) Detection of adulteration of Basmati rice with non-premium long grain rice. Int J Food Sci Technol 35:257–265CrossRefGoogle Scholar
  8. Bligh HFJ, Blackhall NW, Edwards KJ, McClung AM (1999) Using amplified fragment length polymorphism and simple sequence length polymorphisms to identify cultivars of brown and white milled rice. Crop Sci 39:1715–1721CrossRefGoogle Scholar
  9. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The gene for fragrance in rice. Plant Biotechnol J 3:363–370PubMedCrossRefGoogle Scholar
  10. 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 95:553–567CrossRefGoogle Scholar
  11. Cordeiro GM, Christopher MJ, Henry RJ, Reinke RF (2002) Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Mol Breed 9:245–250CrossRefGoogle Scholar
  12. Garland S, Lewin L, Blakeney A, Reinke R, Henry R (2000) PCR-based molecular markers for the fragrance gene in rice (Oryza sativa L.). Theor Appl Genet 101:364–371CrossRefGoogle Scholar
  13. Garris A, McCouch S, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769PubMedGoogle Scholar
  14. Ghosh S, Karanjawala ZE, Hauser ER, Ally D, Knapp JI, Rayman JB, Musick A, Tannenbaum J, Te C, Shapiro S, Eldridge W, Musick T, Martin C, Smith JR, Carpten JD, Brownstein MJ, Powell JI, Whiten R, Chines P, Nylund SJ, Magnuson VL, Boehnke M, Collins FS (1997) Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. Genome Res 7:165–178PubMedGoogle Scholar
  15. Glaszmann JC (1987) Isozyme and classification of Asian rice varieties. Theor Appl Genet 74:21–30CrossRefGoogle Scholar
  16. Glaszmann JC (1988) Geographic pattern of variation among Asian native cultivars (Oryza sativa L.) based on fifteen isozyme loci. Genome 30:782–792Google Scholar
  17. Grosch W, Schieberle P (1997) Flavor of cereal products—a review. Cereal Chem 74:91–97Google Scholar
  18. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  19. Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109:965–977PubMedCrossRefGoogle Scholar
  20. Jin Q, Waters D, Cordeiro GM, Henry RJ, Reinke RF (2003) A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Sci 165:359–364CrossRefGoogle Scholar
  21. Juliano BO (1998) Rice quality for the future. Cashiers options Mediterraneennes 24: Rice quality. A pluridisciplinary approach. (CD ROM computer file) CIHEAM, ParisGoogle Scholar
  22. Juliano BO, Duff B (1991) Rice grain quality as an emerging priority in national rice breeding programmes. In: Rice grain marketing and quality issues. Selected papers from Intl. Rice Research Conf. held in Seoul, the Korea Republic, from 27–31 August 1990. International Rice Research Institute, Los Baños, Philippines, pp 55–64Google Scholar
  23. Khush GS (2000) Taxonomy and origin of rice. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford, IBH Pub., New Delhi, India, pp 5–13Google Scholar
  24. Khush GS, dela Cruz N (2002) Developing Basmati rices with high yield potential. In: Duffy R (ed) Speciality rices of the world: breeding, production and marketing. Science Pub, Inc, Enfield, USA, pp 15–18Google Scholar
  25. Khush GS, Juliano BO (1991) Research priorities for improving rice grain quality. In: Rice grain marketing and quality issues. IRRI, Manila, Philippines, pp 65–66Google Scholar
  26. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquiere A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93:1145–1151CrossRefGoogle Scholar
  27. Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  28. McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P, Li J (2001) Microsatellite markers in rice: abundance, diversity, and applications. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV, IRRI, Los Baños, Philippines. Science Publishers, Inc., New Delhi, India, pp 117–135Google Scholar
  29. McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207PubMedCrossRefGoogle Scholar
  30. Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Sci Acad USA 99:5836–5841CrossRefGoogle Scholar
  31. Nene YL (2003) Basmati rice: a distinct variety (cultivar) of the Indian subcontinent. In: Singh RK, Singh US (eds) A treatise on the scented rices of India. Kalyani Publishers, Inc., New Delhi, India, pp 7–21Google Scholar
  32. Ni J, Colowit PM, Mackill DJ (2002) Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci 42:601–607CrossRefGoogle Scholar
  33. Pal S, Jain S, Saini N, Jain RK (2001) DNA isolation from milled rice samples for PCR-based molecular marker analysis. Rice Genet Newslett 18:94–97Google Scholar
  34. Pal S, Jain S, Saini N, Aarti, Jain RK (2004) Identification of microsatellite markers for differentiating various grades of milled Basmati rice. Ind J Biotechnol 3:519–526Google Scholar
  35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  36. Rohlf FJ (1993) NTSYS-PC: numerical taxonomy and multivariate analysis system. Version 1.8. Exeter Software, New YorkGoogle Scholar
  37. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8019PubMedCrossRefGoogle Scholar
  38. Saini N, Jain N, Jain S, Jain RK (2004) Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP, ISSR and SSR markers. Euphytica 140:133–146CrossRefGoogle Scholar
  39. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  40. Singh RK, Singh US, Khush GS (2000a) Aromatic rices. Oxford, IBH Pub. Co. Pvt. Ltd., New Delhi, IndiaGoogle Scholar
  41. Singh RK, Khush GS, Singh US, Singh AK, Singh S, (2000b). Breeding aromatic rice for high yield, improved aroma and grain quality. In: Singh RK, Singh US, Khush GS (eds) Aromatic rices. Oxford, IBH Pub., New Delhi, India, pp 71–105Google Scholar
  42. Shobha-Rani N, Singh RK (2003) Efforts on aromatic rice improvement in India. In: Singh RK, Singh US (eds) A treatise on the Scented Rices of India. Kalyani Publishers, Inc., New Delhi, India, pp 23–72Google Scholar
  43. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712CrossRefGoogle Scholar
  44. Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.):frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Neelu Jain
    • 1
  • Sunita Jain
    • 2
  • Navinder Saini
    • 1
  • Rajinder K. Jain
    • 1
  1. 1.Department of Biotechnology and Molecular BiologyCCS Haryana Agricultural UniversityHisarIndia
  2. 2.Department of BiochemistryCCS Haryana Agricultural UniversityHisarIndia

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