Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa)

New Phytologist

Volumn 189, Issue 2, 2011, Pages 593-601

  Yu, Guoqin ^a,b   Olsen, Kenneth M ^a   Schaal, Barbara A ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

Author keywords

Amylopectin; Crop domestication; Genotype phenotype association; Nonsynonymous mutation; Oryza sativa (rice); Starch quality; Starch synthase IIa

Indexed keywords

NUCLEOTIDE; STARCH; STARCH SYNTHASE; STARCH SYNTHASE II; VEGETABLE PROTEIN;

AGRONOMY; COLIFORM BACTERIUM; DOMESTICATION; ENZYME ACTIVITY; GENOTYPE; MUTATION; PHENOTYPE; RICE; STARCH;

ARTICLE; ENZYMOLOGY; EXON; GENETIC ASSOCIATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HAPLOTYPE; MUTATION; PHENOTYPE; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD; STATISTICAL MODEL;

EXONS; GENETIC ASSOCIATION STUDIES; HAPLOTYPES; LINEAR MODELS; MUTATION; NUCLEOTIDES; ORYZA SATIVA; PHENOTYPE; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; STARCH; STARCH SYNTHASE;

ESCHERICHIA COLI; JAPONICA; ORYZA RUFIPOGON; ORYZA SATIVA;

EID: 78650355706     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2010.03495.x     Document Type: Article

References (36)

1. Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
2. Bhattacharya KR. 1979. Gelatinization temperature of rice starch and its determination. Laguna, Los Banos, Philippines: International Rice Research Institute.
3. Bligh HFJ, Larkin PD, Roach PS, Jones CA, Fu HY, Park WD. 1998. Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Molecular Biology 38: 407-415.
4. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
5. Buléon A, Colonna P, Planchot V, Ball S. 1998. Starch granules: structure and biosynthesis. International Journal of Biological Macromolecules 23: 85-112.
6. Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
7. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
8. Gao Z, Keeling P, Shibles R, Guan HP. 2004. Involvement of lysine-193 of the conserved 'K-T-G-G' motif in the catalysis of maize starch synthase IIa. Archives of Biochemistry and Biophysics 427: 1-7.
9. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638.
10. He Y, Han Y, Jiang L, Xu C, Lu J, Xu M. 2006. Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities. Molecular Breeding 18: 277-290.
11. Khush GS. 1997. Origin, dispersal, cultivation and variation of rice. Plant Molecular Biology 35: 25-34.
12. Kudo M. 1968. Genetical and thremmatological studies of characters, physiological or ecological, in the hybrids between ecological rice groups. Bulletin of the National Institute of Agricultural Sciences Series D 19: 1-8.
13. Li C, Sang T. 2006. Rice domestication by reducing shattering. Science 311: 1936-1939.
14. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
15. Little R, Hilder G, Dawson E. 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chemistry 35: 111-126.
16. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA. 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences, USA 103: 9578-9583.
17. Marchini J, Cardon LR, Phillips MS, Donnelly P. 2004. The effects of human population structure on large genetic association studies. Nature Genetics 36: 512-517.
18. Myers AM, Morell MK, James MG, Ball SG. 2000. Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiology 122: 989-997.
19. Nakamura Y, Francisco PB, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N. 2005. Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Molecular Biology 58: 213-227.
20. Nichols DJ, Keeling PL, Spalding M, Guan HP. 2000. Involvement of conserved aspartate and glutamate residues in the catalysis and substrate binding of maize starch synthase. Biochemistry 39: 7820-7825.
21. Rozas J, Sànchez-DelBarrio JC, Messequer X, Rozas R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
22. Sang T, Ge S. 2007. The puzzle of rice domestication. Journal of Integrative Plant Biology 49: 760-768.
23. Sweeney M, McCouch S. 2007. The complex history of the domestication of rice. Annals of Botany 100: 951-957.
24. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR. 2007. Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genetics 3: e133.
25. Tajima F. 1983. Evolutionary relationship of DNA-sequences in finite populations. Genetics 105: 437-460.
26. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
27. Templeton AR, Boerwinkle E, Sing CF. 1987. A cladistic-analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. 1. Basic theory and an analysis of alcohol-dehydrogenase activity in Drosophila. Genetics 117: 343-351.
28. Tian ZX, Qian Q, Liu QQ, Yan MX, Liu XF, Yan CJ, Liu GF, Gao ZY, Tang SZ, Zeng DL et al. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proceedings of the National Academy of Sciences, USA 106: 21760-21765.
29. Umemoto T, Aoki N. 2005. Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme. Functional Plant Biology 32: 763-768.
30. Umemoto T, Aoki N, Lin HX, Nakamura Y, Inouchi N, Sato Y, Yano M, Hirabayashi H, Maruyama S. 2004. Natural variation in rice starch synthase IIa affects enzyme and starch properties. Functional Plant Biology 31: 671-684.
31. Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y. 2002. Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics 104: 1-8.
32. Wang ZY, Zheng FQ, Shen GZ, Gao JP, Snustad DP, Li MG, Zhang JL, Hong MM. 1995. The amylose content in rice endosperm is related to the posttranscriptional regulation of the waxy gene. Plant Journal 7: 613-622.
33. Warth F, Darabsett D. 1914. Disintegration of rice grains by means of alkali. Bulletin of Agricultural Research Institute 38: 1-9.
34. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7: 256-276.
35. Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES. 2002. Genetic diversity and selection in the maize starch pathway. Proceedings of the National Academy of Sciences, USA 99: 12959-12962.
36. Yu G. 2009. Evolution of endosperm starch synthesis pathway genes in the context of rice (Oryza sativa) domestication. PhD thesis, Washington University in St. Louis, St. Louis, MO, USA.