Abstract
Apparent amylose content (AAC), gel consistency (GC), and gelatinization temperature (GT) are recognized as the most important determinants of rice eating and cooking qualities. The contributions of major starch-synthesis genes to these three traits have been investigated in the three consecutive experiments. In an initial QTL mapping with 130 doubled haploid (DH) lines, derived from an inter-subspecific cross of ‘Nanjing11’/‘Balilla’, the major QTLs responsible for AAC, GC, and GT coincided with the Wx (granule-bound starch synthase gene), Wx, and Sss IIa (soluble starch synthase gene) loci, respectively. In the second experiment, contributions of the major starch-synthesis genes to AAC, GC, and GT variations were estimated by using a multiple linear regression analysis. As shown, the Wx locus was a principal determinant for both AAC and GC, and could account for 58.5% and 38.9% of the phenotypic variations, respectively; while the Sss IIa locus was associated with GT, and could explain 25.5% of the observed variation. Eventually, a F2 population consisting of 501 individuals, derived from an inter-subspecific cross of the two sticky rice varieties ‘Suyunuo’ and ‘Yangfunuo 4’, was examined with gene-tagged markers. In the absence of the Wx gene, none of the starch-synthesis genes investigated could dominate the GC variation, however, the Sss IIa locus could also explain 25.1% of the GT variation. In summary, the Wx locus dominates the AAC variation, and meanwhile plays a major role in the GC variation. The Sss IIa locus is a major factor in explaining the GT variation. Apart from the major genes, other genetic factors may also contribute to the GC/GT variations.
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References
Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773–781
Baba T, Nishihara M, Mizuno K, Kawasaki T, Shimada H, Kobayashi E, Ohnishi S, Tanaka K, Arai Y (1993) Identification, cDNA cloning, and gene expression of soluble starch synthase in rice (Oryza sativa L.) immature seeds. Plant Physiol 103:565–573
Ball S, Guan HP, James M, Myers A, Keeling P, Mouille G, Buleon A, Colonna P, Preiss J (1996) From glycogen to amylopectin: a model explaining the biogenesis of the plant starch granule. Cell 86:349–352
Bao JS, Xia YW (1999) Genetic control of the paste viscosity characteristics in indica rice (Oryza sativa L.). Theor Appl Genet 98:1120–1124
Bao JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH (2000a) QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.). Theor Appl Genet 100:280–284
Bao JS, He P, Li SG, Xia YW, Chen Y, Zhu LH (2000b). Comparative mapping quantitative trait loci controlling the cooking and eating quality of rice (Oryza sativa L.). Scientia Agricultura Sinica 33:8–13
Bao JS, Wu YR, Hu B, Wu P, Cui HR, Shu QY (2002) QTL for rice grain quality based on a DH population derived from parents with similar apparent amylase content. Euphytica 128:317–324
Blakeney AB (1996) Rice. In: Henry RJ, Kettlewell PS (eds) Cereal grain quality. Chapman & Hall, London, pp 55–76
Bligh HFJ, Till RI, Jones CA (1995) A microsatellite sequence closely linked to the wx gene of Oryza sativa. Euphytica 86:83–85
Bligh HFJ, Larkin PD, Roach PS, Jones CA, Fu YH, Park WD (1998) Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol Biol 38:407–415
Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for the eating quality of rice. J Sci Food Agric 24:1589–1594
Cai XL, Wang ZY, Xing Y, Zhang JL, Hong MM (1998) Aberrant splicing of intron leads to the heterogeneous 5′UTR and decreased expression of the waxy gene in rice cultivars of intermediate amylose content. Plant J 14:459–465
Denyer K, Clarke B, Hylton C, Tatge H, Smith AM (1996) The elongation of amylose and amylopectin chains in isolated starch granules. Plant J 10:1135–1143
Denyer K, Johnson P, Zeeman S, Smith AM (2001) The control of amylase synthesis. J Plant Physiol 158:479–487
Dian WM, Jiang HW, Chen QS, Liu FY, Wu P (2003) Cloning and characterization of the granule-bound starch synthase II gene in rice: gene expression is regulated by the nitrogen level, sugar and circadian rhythm. Planta 218:261–268
Erlander S (1958) Proposed mechanism for the synthesis of starch by glycogen. Enyzymologia 19:273–283
Francisco PB, Zhang Y, Park S, Ogata N, Yamanouchi H, Nakamura Y (1998) Genomic DNA sequence of a rice gene coding for a pullulanase-type of starch debranching enzyme. Biochim Biophys Acta 1387:469–577
Fujita N, Kubo A, Francisco PB, Nakakita M, Harada K, Minaka N, Nakamura Y (1999) Purification, characterization, and cDNA structure of isoamylase from developing endosperm of rice. Planta 208:283–293
Gao ZY, Zeng DL, Cui X, Zhou YH, Yan MX, Huang DN, Li JY, Qian Q (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China (Series C) 46:661–668
Gidley MJ, Bulpin PV (1987) Crystallisation of malto-oligosaccharides as models of the crystalline forms of starch: minimum chain-length requirement for the formation of double helices. Carbohydr Res 161:291–300
He P, Li SG, Qian Q, Ma YQ, Li JZ, Wang WM, Chen Y, Zhu LH (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502–508
Huang FS, Sun ZX, Hu PS, Tang SQ (1998) Analysis of quantitative trait loci which contribute to anther culturability in rice (Oryza sativa L.). Mol Breeding 4:165–172
Isshiki M, Morino K, Nakajima M, Okagaki RO, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the waxy locus has a GT to TT mutation at the 5′splice site of the first intron. Plant J 15:133–138
Isshiki M, Nakajima M, Satoh H, Shimamoto K (2000) dull: rice mutants with tissue-specific effects on the splicing of the waxy pre-mRNA. Plant J 23:451–460
James MG, Denyer K, Myers AM (2003) Starch synthesis in the cereal endosperm. Curr Opin Plant Biol 6:1–8
Jenkins PJ, Cameron RE, Donald AM (1993) A universal feature in the structure of starch granules from different botanical source. Starch 45:417–420
Jiang HW, Dian WM, Liu FY, Wu P (2004) Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta 218:1062–1070
Juliano BO (1985) Criteria and tests for rice grain quality. In: Juliano BO (ed). Rice chemistry and technology. America Association of Cereal Chemists, Incorporated, Saint Paul, Minnesota, USA, pp 443–513
Lanceras JC, Hun ZL, Naivikul Q, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai Jasmine rice (KDML105). DNA Res 7:93–101
Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkalia on 25 varieties of milled white rice. Cereal Chem 35:111–126
Liu XY, Gu MH, Han YP, Ji Q, Lu JF, Gu SL, Zhang R, Li X, Chen JM, Korban SS, Xu ML (2004) Developing gene-tagged molecular markers for functional analysis of starch-synthesizing genes in rice (Oryza sativa L.). Euphytica 135:345–353
McKenzie KS, Rutger JN (1983) Genetic analysis of amylose content, alkali spreading score, and grain dimensions in rice. Crop Sci 23:306–311
Mikami I, Aikawa M, Hirano HY, Sano Y (1999) Altered tissue-specific expression at the Wx gene of the opaque mutants in rice. Euphytica 105:91–97
Mikami L, Dung LV, Hirano HY, Sano Y (2000) Effects of the two most common Wx alleles on different genetic background in rice. Plant Breed. 119:505–508
Mizuno K, Kawasaki T, Shimada H, Satoh H, Kobayashi E, Okumura S, Arai Y, Baba T (1993) Alteration of the structural properties of starch component by the lack of an isoform of starch branching enzyme in rice seeds. J Biol Chem 286:19084–19091
Mizuno K, Kobayashi E, Tachibana M, Kawasaki T, Fujimura T, Funane K, Kobayashi M, Baba T (2001) Characterization of an isoform of rice starch branching enzyme, RBEIV, in developing seeds. Plant Cell Physiol 42:349–357
Moates GK, Noel TR, Parker R, Ring SG (1997) The effect of chain length and solvent interactions on the dissolution of the B-type crystalline polymorph of amylose in water. Carbohydr Res 298:327–333
Myers AM, Morell MK, James MG, Bill SG (2000) Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol 122:989–998
Nakamura Y, Umemoto T, Takahata Y, Amano E (1992) Characteristics and roles of key enzymes associated with starch biosynthesis in rice endosperm. Gamma Fiele Symp 31:25–44
Nakamura Y (1996) Some properties of starch debranching enzymes and their possible roles in amylopectin biosynthesis. Plant Sci 121:1–18
Nakamura Y (2002) Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell Physiol 43:718–725
Noda T, Takahata Y, Sato T, Suda I, Morishita T, Ishiguro K, Yamakawa O (1998) Relationships between chain length distribution of amylopectin and gelatinization properties within the same botanical origin for sweet potato and buckwheat. Carbohydr Polym 37:153– 158
Patrick DL, Anna MM, Ayres NM, Park WD (2003). The effect of the waxy locus on pasting curve characteristics in specialty rice. Euphytica 131:243–253
Safford R, Jobling SA, Sidebottom CM, Westcott RJ, Cooke D, Tober KJ, Strongitharm BH, Russel AL, Gidley MJ (1998) Consequences of antisense RNA inhibition of starch branching enzyme activity on properties of potato starch. Carbohydr Polym 35:155–168
Sano Y, Katsumata M, Omura K (1986) Genetic studies of speciation in cultivated rice. Inter and intraspecific differentiation in the waxy gene expression of rice. Euphytica 35:1–9
SAS Institute Inc (2000). SAS/STAT User’s Guide. Cary, NC USA
Satoh H, Nishi A, Fujita N, Kubo A, Nakamura Y, Kawasaki T, Okita TW (2003) Isolation and characterization of starch mutants in rice. J Appl Glycosci 50:225–230
Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (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 107:1433–1441
Smith AM, Denyer K, Martin C (1997) The synthesis of the starch granule. Annu Rev Plant Physiol Plant Mol Biol 48:67–87
Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang QF (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648
Tan YF, Zhang QF (2001) Correlation of simple sequence repeat (SSR) variants in the leader sequence of the wx gene with amylose content of the grain in rice. Acta botanica sinica 43:146–150
Tanaka K, Ohnishi S, Kishimoto N, Kawasaki T, Baba T (1995) Structure, organization, and chromosomal location of the gene encoding a form of rice soluble starch synthase. Plant Physiol 108:677–683
Tian R, Jiang GH, Shen LH, Wang LQ, He YQ (2004) Mapping quantitative trait loci underlying the cooking and eating quality of rice using a DH population. Mol Breeding 15:117–124
Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y (2002) Mapping of a gene responsible for the difference in rice varieties. Theor Appl Genet 104:1–8
Unnevehr LJ, Duff B, Juliano BO (1992) Consumer demand for rice grain quality. International Rice Research Institue, Manila, The Philippines and International Development Research Center, Ottawa, Canada
Van de Wal M, D’Hulst C, Vincken JP, Buleon A, Visser R, Ball S (1998) Amylose is synthesized in vitro by extension of and cleavage from amylopectin. J Biol Chem 273:22232–22240
Wang ZY, Zhang FQ, Shen GZ, Gao JP, Snustad DP, Li MG, Zhang JL, Hong MM (1995) The amylase content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613–622
Webb BD (1980) Rice quality and grades. In: Luh BS (ed). Rice: production and utilization, Avi Publication Company. Incorporated. Westport, Connecticut USA, pp 543–565
Williams VR, Wu WT, Tsai HY, Bates HG (1958) Varietal differences in amylose content of rice starch. J Agric Food Chem 6:47–48
Zeeman SC, Umemoto T, Lue WL, Yeung PA, Martin C, Smith AM, Chen J (1998) A mutant of Arabidopsis lacking a chloroplastic isoamylase accumulates both starch and phytoglycogen. Plant Cell 10:1699–1712
Zhou PH, Tan YF, He YQ, Xu CG, Zhang Q (2003) Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted election. Theor Appl Genet 106:326–331
Zhou ZK, Robards K, Helliwell S, Blanchard C (2002) Composition and functional properties of rice. Int J of Food Sci Tech 37:849–868
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He, Y., Han, Y., Jiang, L. et al. Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities. Mol Breeding 18, 277–290 (2006). https://doi.org/10.1007/s11032-006-5505-7
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DOI: https://doi.org/10.1007/s11032-006-5505-7