Abstract
Amylose content (AC), gel consistency (GC) and gelatinazation temperature (GT) are three important traits that influence the cooking and eating quality of rice. The objective of this study was to characterize the genetic components, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs), that are involved in the control of these three traits. A population of doubled haploid (DH) lines derived from a cross between two indica varieties Zhenshan 97 and H94 was used, and data were collected from a field experiment conducted in two different environments. A genetic linkage map consisting of 218 simple sequence repeat (SSR) loci was constructed, and QTL analysis performed using qtlmapper 1.6 resolved the genetic components into main-effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 12 main-effect QTLs for the three traits, with a QTL corresponding to the Wx locus showing a major effect on AC and GC, and a QTL corresponding to the Alk locus having a major effect on GT. Ten digenic interactions involving 19 loci were detected for the three traits, and six main-effect QTLs and two pairs of epistatic QTLs were involved in QEs. While the main-effect QTLs, especially the ones corresponding to known major loci, apparently played predominant roles in the genetic basis of the traits, under certain conditions epistatic effects and QEs also played important roles in controlling the traits. The implications of the findings for rice quality improvement are discussed.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima. Theor Appl Genet 109:630–639
Asaoka M, Okuno K, Sugimoto Y, Kawakami T, Fuwa H (1984) Effect of environmental temperature during development of rice plants on some properties of endosperm starch. Starch/Stärke 36:186–193
Asaoka M, Okuno K, Fuwa H (1985a) Effects of environmental temperatures at the milky stage on amylose content and fine structure of amylopectin of waxy and nonwaxy endosperm starches of rice (Oryza sativa L.). Agric Biol Chem 49:373–379
Asaoka M, Okuno K, Fuwa H (1985b) Developmental changes in the structure of endosperm starch of rice (Oryza sativa L.). Agric Biol Chem 49:1973–1978
Bao JS, He P, Li SG, Xia YW, Chen Y, Zhu LH (2000) Comparative mapping quantitative trait loci controlling the cooking and eating quality of rice. Sci Agric Sin 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
Bollich CN, Webb BD (1973) Inheritance of amylose in two hybrid populations of rice. Cereal Chem 50:631–636
Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality in rice. J Sci Food Agric 24:1589–1594
Chang TT, Li CC (1991) Genetics and breeding. In: Luh BS (ed) Rice production, 2nd edn. Van Nostrand Reinhold, New York, pp 23–101
Chikubu S, Endo I, Tani T (1965) Grain qualities of rice plants grown through the early planting in the early cropping season: cultivar and location differences. 2. Cooking qualities. Rep Natl Food Res Inst 20:13–20
Ebata M (1968) Studies on alkali decomposition in rice kernels. 2. Effects of varieties and some ripening conditions on alkali decomposition of milled white rice. Proc Crop Sci Soc Jpn 37:499–503
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 Ser C 46:661–668
Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2,275 markers using a single F2 population. Genetics 148:479–494
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
Hirano HY, Sano Y (1998) Enhancement of the Wx gene expression and the accumulation of amylose in response to cool temperatures during seed development in rice. Plant Cell Physiol 32:807–812
Jiang GH, He YQ, Xu CG, Li XH, Zhang Q (2004) The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines from an indica by japonica cross. Theor Appl Genet 108:688–698
Juliano BO (1985) Rice chemistry and technology, 2nd edn. American Association of Cereal Chemists, St. Paul
Kudo M (1968) Genetical and thremmatological studies of characters, physiological or ecological, in the hybrids between ecological rice groups. Bull Natl Inst Agric Sci Series D 19:1–84
Kumar I, Khush GS (1988) Inheritance of amylose content in rice (Oryza sativa L.). Euphytica 38:261–269
Lanceras JC, Huang ZL, Naivikul O, 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
Li ZF, Wan JM, Xia JF, Yano M (2003) Mapping of quantitative trait loci controlling physico-chemical properties of rice grains (Oryza sativa L.). Breed Sci 53:209–215
Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with mapmaker/exp 3.0. Whitehead Institute Technical Report, Whitehead Institute, Cambridge, Mass
Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35:111–126
McCouch SR, Teytelman L, Xu Y, Lobos KB, 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 and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207
McKenzie KS, Rutger JN (1983) Genetic analysis of amylose content, alkali spreading score, and grain dimensions in rice. Crop Sci 23:306–319
Resurreccion AP, Hara T, Juliano BO, Yoshida S (1977) Effects of temperatures during ripening on grain quality of rice. Soil Sci Plant Nutr 23:109–112
Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467–473
Sano Y, Hirano HY, Nishimura M (1991) Evolutionary significance of different regulation at the wx locus in rice. In: IRRI (ed) Rice genetics II. IRRI, Manila, pp 11–20
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
Suzuki H, Chikubu S, Tani T (1959) Studies on rice grains produced in the early and late cropping seasons. 1. Physical and chemical properties of non-glutinous rice grains and their starch. J Agric Chem Soc Jpn 37:63–66
Suzuki Y, Sano Y, Hirano HY (2002) Isolation and characterization of a rice mutant insensitive to cool temperatures on amylose synthesis. Euphytica 123:95–100
Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang Q (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
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
Tang SX, Khush GS, Juliano BO (1991) Genetics of gel consistency in rice (Oryza sativa L.). J Genet 70:69–78
Temnykh S, Park WD, Ayres N, Cartihour 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 100:697–712
Temnykh S, Declerck G, Luashova A, Lipovich L, Cartinhour S, 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
Umemoto T, Nakamura Y, Ishikura N (1995) Activity of starch synthase and the amylose content in rice endosperm. Phytochemistry 40:1613–1616
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. Theor Appl Genet 104:1–8
Wang Z, Wu Z, Xing Y, Zheng F, Guo X, Zhang W, Hong M (1990) Nucleotide sequence of rice waxy gene. Nucleic Acids Res 18:5898
Wang DL, Zhu J, Li ZK, Paterson AH (1999) Mapping QTLs with epistatic effects and QTL × environment interactions by mixed linear model approaches. Theor Appl Genet 99:1255–1264
Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Saghai Maroof MA (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231
Zhu J, Weir BS (1998) Mixed model approaches for genetic analysis of quantitative traits. In: Chen LS, Ruan SG, Zhu J (eds) Advanced topics in biomathematics. Proc Int Conf Math Biol. World Scientific Publ, Singapore, pp 321–330
Acknowledgements
This work was supported in part by grants from the National Program on the Development of Basic Research, the National Special Key Project of Functional Genomics and Biochips, and the National Natural Science Foundation of China.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by C. Möllers
Rights and permissions
About this article
Cite this article
Fan, C.C., Yu, X.Q., Xing, Y.Z. et al. The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110, 1445–1452 (2005). https://doi.org/10.1007/s00122-005-1975-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-005-1975-y