Abstract
To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment substitution lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.
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Asano K, Takashi T, Miura, Qian Q, Kitano H, Matsuoka M, Ashikari M (2007) Genetic and molecular analysis of utility of sd1 alleles in rice breeding. Breed Sci 57:53–58
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745
Basten CJ, Weir BS, Zeng ZB (2004) QTL cartographer, ver. 1.17. Department of Statistics, North Carolina State University, Raleigh
Doi K, Iwata N, Yoshimura A (1997) The construction of chromosome introgression lines of African rice (Oryza glaberrima Steud.) in the background of japonica rice (O. sativa L.). Rice Genet Newsl 14:39–41
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (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
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171
INTERNATIONAL RICE GENOME SEQUENCING PROJECT (2005) The map-based sequence of the rice genome. Nature 436:793–800
Kobayashi S, Fukuta Y, Sato T, Osaki M, Khush GS (2003) Molecular marker dissection of rice (Oryza sativa L.) plant architecture under temperate and tropical climates. Theor Appl Genet 107:1350–1356
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Kroymann J, Mitchell-Olds T (2005) Epistasis and balanced polymorphism influencing complex trait variation. Nature 435:95–98
Li ZK, Pinson SR, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465
Lu C, Shen L, Tan Z, Xu Y, He P, Chen Y, Zhu L (1996) Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population. Theor Appl Genet 93:1211–1217
Matsubara K, Ando T, Mizubayashi T, Ito S, Yano M (2007) Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross. Theor Appl Genet 115:179–186
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 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207
Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB, Paterson AH, Li ZK (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107:89–101
Mei HW, Xu JL, Li ZK, Yu XQ, Guo LB, Wang YP, Ying CS, Luo LJ (2006) QTLs influencing panicle size detected in two reciprocal introgressive line (IL) populations in rice (Oryza sativa L.). Theor Appl Genet 112:648–656
Nagata K, Fukuta Y, Shimizu H, Yagi T, Terao T (2002) Quantitative trait loci or sink size and ripening traits in rice (Oryza sativa L.). Breed Sci 52:259–276
Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963
Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146
Sasahara H, Fukuta Y, Fukuyama T (1999) Mapping of QTLs for vascular bundle system and spike morphology in rice, Oryza sativa L. Breed Sci 49:75–81
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630
Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927
Takeuchi Y, Ebitahi T, Yamamoto T, Sato H, Ohta H, Hirabayashi H, Kato H, Ando I, Nemoto H, Imbe T, Yano M (2006) Development of isogenic lines of rice cultivar Koshihikari with early and late heading by marker-assisted selection. Breed Sci 56:405–413
Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580
Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49:476–484
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (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
Yoshida S, Parao FT (1976) Climatic influence on yield and yield components of lowland rice in the tropics. In: Climate and Rice, International Rice Research Institute, Los Baños, The Philippines, pp 471–494
You A, Lu X, Jin H, Ren X, Liu K, Yang G, Yang H, Zhu L, He G (2006) Identification of quantitative trait loci across recombinant inbred lines and testcross populations for traits of agronomic importance in rice. Genetics 172:1287–1300
Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, 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
Acknowledgments
The seeds and genotype information of the CSSLs are available from the Rice Genome Resource Center (http://www.rgrc.dna.affrc.go.jp/index.html) of NIAS. This work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Green Technology Project DM-1003 and QT-1005).
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Communicated by Q. Zhang.
T. Ando and T. Yamamoto contributed equally to this work.
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Ando, T., Yamamoto, T., Shimizu, T. et al. Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116, 881–890 (2008). https://doi.org/10.1007/s00122-008-0722-6
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DOI: https://doi.org/10.1007/s00122-008-0722-6