Sequencing of the entire rice genome has made remarkable progress (IRGSP 2005). This sequence information has provided new tools for genetics and has created a new paradigm of plant breeding. Many phenotypic traits of economic interest are controlled by multiple genes and often show complex and quantitative inheritance. Recent progress in rice genomics has had a great impact on the genetic dissection of such traits into single genetic factors, or quantitative trait loci (QTLs) (Tanksley 1993; Yano and Sasaki 1997). Such genetic factors can subsequently be identified at the molecular level by map-based strategies (Yano 2001). Many QTL mapping studies in rice have been conducted during the last decade. Information on individual QTLs is collected and summarized in a cereal genome database, Gramene (http://www.gramene.org/Oryza_sativa/). It is difficult to review all progress due to the tremendous amount of QTL information in this database. Thus, in this chapter, we summarize QTLs with relatively large effects of economic or agronomic interest. Some of them have already been cloned at the molecular level (Table 1). In addition, we describe the platform for use in the systematic exploitation of natural variations and QTLs and in further analyses of QTLs, such as molecular cloning and marker assisted selection (MAS) for the biological study and breeding of rice.
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References
Andaya VC, Mackill DJ (2003) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica and indica cross. Theor Appl Genet 106:1084–1090
Ashikari M, Matsuoka M (2006) Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci 11:344–350
Ashikari M, Sakakibara H, Lin SY, et al. (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745
Cai HW, Morishima H (2000) Genomic regions affecting seed shattering and seed dormancy in rice. Theor Appl Genet 100:840–846
Dai L, Lin X, Ye C, et al. (2004) Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of rice, Kunmingxiaobaigu. Breed Sci 54:253–258
Doi K, Yoshimura A, Iwata N (1998) RFLP mapping and QTL analysis of heading date and pollen sterility using backcross populations between Oryza sativa L. and Oryza glaberrima Steud. Breed Sci 48:395–399
Doi K, Izawa T, Fuse T, et al. (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936
Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of japonica elite cultivar ‘Koshihikari’. Breed Sci 55:65–73
Fujino K, Sekiguchi H, Sato T, et al. (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799
Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:185–190
Gu XY, Kianian SF, Hareland GA, Hoffer BL, Foley ME (2005) Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110:1108–1118
Gu XY, Kianian SF, Foley ME (2006) Isolation of three dormancy QTLs as Mendelian factors in rice. Heredity 96:93–99
IRGSP (International Rice Genome Sequencing Project) (2005) The map-based sequence of the rice genome. Nature 436:793–800
Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes to bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol 6:113–120
Kojima S, Takahashi Y, Kobayashi Y, et al. (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day condition. Plant Cell Physiol 43:1096–1105
Kojima Y, Ebana K, Fukuoka S, Nagamine T, Kawase M (2005) Development of an RFLP-based rice diversity research set of germplasm. Breed Sci 55:431–440
Konishi S, Izawa T, Lin SY, et al. (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Kubo T, Aida Y, Nakamura K, Tsunematsu H, Doi K, Yoshimura A (2002) Reciprocal chromosome segment substitution series derived from japonica and indica cross of rice (Oryza sativa L.). Breed Sci 52:319–325
Li C, Zhou A, Sang T (2006a) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194
Li C, Zhou A, Sang T (2006b) Rice domestication by reducing shattering. Science 311:1936–1939
Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021–1028
Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breed Sci 52:35–41
Lin HX, Liang ZW, Sasaki T, Yano M (2003) Identification and characterization of a quantitative trait locus, Hd4 and Hd5, controlling heading date in rice. Breed Sci 53:51–59
Lin HX, Zhu MZ, Yano M, et al. (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260
Lin SY, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. Theor Appl Genet 96:997–1003
Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299
Miura K, Lin SY, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986
Miyamoto M, Yano M, Hirasawa H (2001) Mapping of quantitative trait loci conferring blast field resistance in the Japanese upland rice variety Kahei. Breed Sci 51:257–261
Miyao A, Iwasaki Y, Kitano H, et al. (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol Biol 63:625–635
Nishimura A, Ashikari M, Lin SY, et al. (2005) Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. Proc Natl Acad Sci USA 102:11940–11944
Raghavan C, Naredo MEB, Wang H, et al. (2007) Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping. Mol Breed 19:87–101
Ren ZH, Gao JP, Li LG, et al. (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146
Saito K, Miura K, Nagano K, et al. (1995) Chromosomal location of quantitative trait loci for cool tolerance at the booting stage in rice variety ‘Norin-PL8’. Breed Sci 45:337–340
Saito K, Miura K, Nagano K, Hayano-Saito Y, Araki H, Kato A (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length. Theor Appl Genet 103:862–868
Saito K, Hayano-Saito Y, Maruyama-Funatsuki W, Sato Y, Kato A (2004) Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice. Theor Appl Genet 109:515–522
Sasaki K, Fukuta Y, Sato T (2005) Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage. Plant Breed 124:361–366
Sato T, Ueda T, Fukuta Y, Kumagai T, Yano M (2003) Mapping of quantitative trait loci associated with ultraviolet-B resistance in rice (Oryza sativa L.). Theor Appl Genet 107:1003–1008
Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927
Takeuchi Y, Hayasaka H, Chiba B, et al. (2001) Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate japonica rice. Breed Sci 51:191–197
Takeuchi Y, Lin SY, Sasaki T, Yano M (2003) Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice. Theor Appl Genet 107:1174–1180
Takeuchi Y, Ebitani T, Yamamoto T, et al. (2006) Development of isogenic lines of rice cultivar Koshihikari with early and late heading by marker-assisted selection. Breed Sci 56:405–413
Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233
Ueda T, Sato T, Numa H, Yano M (2004) Delimitation of chromosomal region for a quantitative trait locus, qUVR-10, conferring resistance to ultraviolet-B radiation in rice (Oryza sativa L.). Theor Appl Genet 108:385–391
Ueda T, Sato T, Hidema J, et al. (2005) qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics 171:1941–1950
Wu JL, Wu C, Lei C, et al. (2005) Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics Plant Mol Biol 59:85–97
Xu, K, Mackill DJ (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol Breed 2:219–224
Xu K, Xu X, Ronald PC, Mackill DJ (2000) A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet 263:681–689
Xu K, Xu X, Fukao T, et al. (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708
Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6, and characterization of its epistatic interaction with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891
Yano M (2001) Genetic and molecular dissection of naturally occurring variations. Curr Opin Plant Biol 4:130–135
Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153
Yano M, Katayose Y, Ashikari M, et al. (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484
Yano M, Kojima S, Takahashi Y, Lin HX, Sasaki T (2001) Genetic control of flowering time in rice, a short-day plant. Plant Physiol 127:1425–1429
Zenbayashi K, Ashikawa T, Tani T, Koizumi S (2002) Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32. Theor Appl Genet 104:547–552
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Yamamoto, T., Yano, M. (2008). Detection and Molecular Cloning of Genes Underlying Quantitative Phenotypic Variations in Rice. In: Hirano, HY., Sano, Y., Hirai, A., Sasaki, T. (eds) Rice Biology in the Genomics Era. Biotechnology in Agriculture and Forestry, vol 62. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74250-0_22
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