Association studies of dormancy and cooking quality traits in direct-seeded indica rice

Journal of Genetics

Volumn 93, Issue 1, 2014, Pages 3-12

  Rathi, Sunayana ^a   Pathak, K ^b   Yadav, R N S ^a   Kumar, B ^c   Sarma, R N ^b  

^a DIBRUGARH UNIVERSITY   (India)

^b ASSAM AGRICULTURAL UNIVERSITY   (India)

^c ICAR INDIAN INSTITUTE OF MAIZE RESEARCH   (India)

Author keywords

Assam rice; association mapping; cooking quality; dormancy; amylase

Indexed keywords

MICROSATELLITE DNA;

ALLELE; CHEMISTRY; CLASSIFICATION; DORMANCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; PHYLOGENY; POPULATION GENETICS; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; RICE;

ALLELES; GENETIC ASSOCIATION STUDIES; GENETIC LOCI; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; MICROSATELLITE REPEATS; ORYZA SATIVA; PHYLOGENY; PLANT DORMANCY; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE;

EID: 84903219556     PISSN: 00221333     EISSN: 09737731     Source Type: Journal    
DOI: 10.1007/s12041-014-0319-6     Document Type: Article

References (58)

1. Agrama H. A. and Eizenga G. C. 2008 Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica 160, 339-355.
2. Agrama H. A., Eizenga G. C. and Yan W. 2007 Association mapping of yield and its components in rice cultivars. Mol. Breed. 19, 341-356.
3. Akkaya M. S., Bhagwat A. A. and Cregan P. B. 1992 Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132, 1131-1139.
4. Aluko G., Martinez C., Tohme J., Castano C., Bergman C. and Oard J. H. 2004 QTL mapping of grain quality traits from the interspecific cross Oryza sativa L. and O. Glaberrima. Theor. Appl. Genet. 108, 1445-1452.
5. Bewley J. D. and Black M. 1985 Seeds: physiology of development and germination, pp. 329-347. Plenum Press, New York, USA.
6. Bradbury P. J., Zhang Z., Kroon D. E., Casstevens T. M., Ramdoss Y. and Buckler E. S. 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635.
7. Cagampang G. B., Perez C. M. and Juliano B. O. 1973 A gel consistency test for eating quality of rice. J. Sci. Food Agric. 24, 1589-1594.
8. Cai H. W. and Morishima H. 2000 Genomic regions affecting seed shattering and seed dormancy in rice. Theor. Appl. Genet. 100, 840-846.
9. Chen X., Cho Y. G. and McCouch S. R. 2002 Sequence divergence of rice microsatellites in Oryza and other plant species. Mol. Genet. Genomics 268, 331-343.
10. Cho Y. G., Ishii T., Temnykh S., Chen X., Lipovich L., McCouch S. R. et al. 2000 Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100, 713-722.
11. Clifford H. T. and Stephenson W. 1975 An introduction to numerical classification, pp. 229. Academic Press, London, UK.
12. Cui K. H., Peng S. B., Xing Y. Z., Xu C. G., Yu S. B. and Zhang Q. 2002 Molecular dissection of seedling-vigor and associated physiological traits in rice. Theor. Appl. Genet. 105, 745-753.
13. Donnelly P. 2008 Progress and challenges in genome-wide association studies in humans. Nature 4 56, 728-731.
14. Eaves I. A., Barber R. A. and Merriman T. R. 1998 Comparison of linkage disequilibrium in populations from UK and Finland. Am. J. Hum. Gen. 63, suppl. A1212.
15. Fan R. Z., Spinka C., Jin L. and Jung J. S. 2005 Pedigree linkage disequilibrium mapping of quantitative trait loci. Eur. J. Hum. Genet. 13, 216-231.
16. Farnir F., Coppieters W., Arranz J. J., Berzi P., Cambisano N., Grisart B. et al. 2000 Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10, 220-227.
17. Garris A. J., McCouch S. R. and Kresovich S. 2003 Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5locus of rice (Oryza sativa L.). Genetics 165, 759-769.
18. Garris A. J., Tai T. H., Coburn J., Kresovich S. and McCouch S. R. 2005 Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631-1638.
19. Ge X. J., Xing Y. Z., Xu C. G. and He Y. Q. 2005 QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population. Plant Breed. 124, 121-126.
20. Guei R. G., Sanni K. A., Abamu F. J. and Fawole I. 2005 Genetic diversity of rice (Oryza sativa L.). Agron. Afr. 5, 17-28.
21. He P., Li S. G., Qian Q., Ma Y. Q., Li J. Z., Wang W. M. et al. 1999 Genetic analysis of rice grain quality. Theor. Appl. Genet. 98, 502-508.
22. Hill W. G. and Robertson A. 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226-231.
23. H Ikehashi, Induction and test of dormancy of rice seeds by temperature condition during maturation, Jpn. J. Breed. 22 (1972), 209-216.
24. Jannink J. L., Bink M. C. A. M. and Jansen R. C. 2001 Using complex plant pedigrees to map valuable genes. Trends Plant Sci. 6, 337-342.
25. Jiang W., Lee J., Jin Y. M., Qiao Y., Piao R., Jang S. M. et al. 2011 Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice. Mol. Cell 31, 385-392.
26. Jin L., Lu Y., Xiao P., Sun M., Corke H. and Bao J. 2010 Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor. Appl. Genet. 121, 475-487.
27. Juliano B. O. 1971 A simplified assay for milled rice amylose. Cereal Sci. Today 16, 334-338.
28. Kraakman A. T. W., Niks R. E., van den Berg P. M. M. M., Stam P. and van Eeuwijk F. A. 2004 Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168, 435-446.
29. Kraft T., Hansen M. and Nilsson N. O. 2000 Linkage disequilibrium and fingerprinting in sugar beet. Theor. Appl. Genet. 101, 323-326.
30. Lanceras J. C., Huang Z. L., Naivikul O., Vanavichit A., Ruanjaichon V. and Tragoonrung S. 2000 Mapping of genes for cooking and eating qualities in Thai Jasmine rice (KDML105). DNA Res. 7, 93-101.
31. Li X., Yan W., Agrama H., Jia L., Shen X., Jackson A. et al. 2011 Mapping QTLs for improving grain yield using the USDA rice mini-core collection. Planta 234, 347-361.
32. Little R. R., Hilder G. B. and Dawson E. H. 1958 Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem. 35, 111-126.
33. Mackay I. and Powell W. 2007 Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 12, 57-63.
34. Mather K. A., Caicedo A. L., Polato N. R., Olsen K. M., McCouch S., Purugganan M. D. et al. 2007 The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics177, 2223-2232.
35. Nakamura S., Sameri M., Pourkheirandish M., Matsumoto T., Yano M., Sato K. et al. 2011 Identifying a candidate for the barley grain dormancy QTL SD2. In Proceedings of Plant and Animal Genomes XIX Conference, January 15-19, 2011, San Diego, USA.
36. Nordborg M. and Weigel D. 2008 Next-generation genetics in plants. Nature 456, 720-723.
37. Nordborg M., Hu T. T., Ishino Y., Jhaveri J., Toomajian C., Zheng H. et al. 2005 The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 3, e196.
38. Ogunbodede B. A. 1997 Multivariate analysis of genetic diversity in kenaf, Hibiscus cannabinus (L.). Afr. Crop Sci. J. 5, 127-133.
39. Plaschke J., Ganal M. W. and Rder M. S. 1995 Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor. Appl. Genet. 91, 1001-1007.
40. Pritchard J. K., Stephens M. and Donnelly P. 2000 Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
41. Raji A. A. 2002 Assessment of genetic diversity and heterotic relationships in African improved and local cassava (Manihot esculenta Crantz) germplasm. Ph. D. thesis. University of Ibadan, Nigeria.
42. Rathi S., Baruah A. R., Chowdhury R. K. and Sarma R. N. 2011 QTL Analysis of seed dormancy in indigenous rice of Assam, India. Cereal Res. Commun. 39, 137-146.
43. Remington D. L., Thornsberry J. M., Matsuoka Y., Wilson L. M., Whitt S. R., Doebley J. et al. 2001 Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. 98, 11479-11484.
44. Sabouri A., Rabiei B., Toorchi M., Aharizad S. and Moumeni A. 2012 Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Aust. J. Crop Sci. 6, 808-814.
45. Sadasivam S. and Manickam A. 1996 Biochemical methods. 2nd edition, pp. 179-186. New Age International, New Delhi, India.
46. Sanni K. A., Fawole I., Ogunbayo A., Tia D., Somado E. A., Futakuchi K. et al. 2012. Multivariate analysis of diversity of landrace rice germplasm. Crop Sci. 52, 494-504.
47. Septiningsih E. M., Trijatmiko K. R., Moeljopawiro S. and McCouch S. R. 2003 Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor. Appl. Genet. 107, 1441-1433.
48. Shi C., Navabi A. and Yu K. 2011 Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations. BMC Plant Biol. 11, 52-62.
49. Takeuchi Y., Nonoue Y., Ebitani T., Suzuki K., Aoki N., Sato H. et al. 2007 QTL detection for eating quality including glossiness, stickness, taste and hardness of cooked rice. Breed. Sci. 57, 231-242.
50. Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S. and McCouch S. 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.
51. Ullrich S. E., Lee H., Clancy J. A., del Blanco I. A., Jitkov V. A., Kleinhofs A. et al. 2009. Genetic relationships between preharvest sprouting and dormancy in barley. Euphytica 168, 331-345.
52. Vanniarajan C., Vinod K. K. and Pereira A. 2012 Molecular evaluation of genetic diversity and association studies in rice (Oryza sativa L.) J. Genet. 91, 9-19.
53. Vieira A. R., Vieira M. D. G. G. C., Fraga A. C., Oliviera J. A. and Santos C. D. D. 2002 Action of gibberellic acid (GA3) on dormancy and activity of α-amylase in rice seeds. Rev. Bras. de Sementes 24, 43-48.
54. Wan Y., Cohen J. and Guerra R. 1997 A permutation test for the robust sub-pair linkage method. Ann. Hum. Genet. 61, 79-87.
55. Wang J., McClean P. E., Lee R., Goos R. J. and Helms T. 2008 Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor. Appl. Genet. 116, 777-787.
56. Wen W., Mei H., Feng F., Yu S., Huang Z., Wu J. et al. 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.
57. Zhang D. L., Zhang H. L., Wei X. H., Qi Y. W., Wang M. X., Sun J. L. et al. 2007 Genetic structure and diversity of Oryza sativa L. in Guizhou, China. Chin. Sci. Bull. 52, 343-351.
58. Zhang P., Li J., Li X., Liu X., Zhao X. and Lu Y. 2011 Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One6, e27565.