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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

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Abstract

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC2F2 families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.

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References

  • Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773–781

    CAS  Google Scholar 

  • Basten CJ, Weir BS, Zeng Z-B (1997) QTL Cartographer: A reference manual and tutorial for QTL mapping. Raleigh, NC, Department of Statistics, North Carolina State University

    Google Scholar 

  • Bernacchi D, Beck BT, Eshed Y, Lopez Y, Petiard V, Uhlig J, Zamir D, Tanksley SD (1998a) Advanced backcross QTL analysis in tomato. I. Identification of QTL for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet 97:381–397

    Article  CAS  Google Scholar 

  • Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D, Tanksley S (1998b) Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97:170–180

    CAS  Google Scholar 

  • Bres-Patry C, Lorieux M, Clement G, Bangratz M, Ghesquiere A (2001) Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theor Appl Genet 102:118–126

    Article  CAS  Google Scholar 

  • Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality in rice. J Sci Food Agr 24:1589–1594

    CAS  PubMed  Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    CAS  PubMed  Google Scholar 

  • Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) Theor Appl Genet 95:553–567

    Google Scholar 

  • Damardjati DG and Oka M (1991) Evaluation of rice grain characteristics preferred by Indonesian urban consumers. In: Naewbanji JO (ed) Grain postharvest research and development: priorities for the nineties. Proceedings of the 12th ASEAN Seminar on Grain Postharvest Technology, Surabaya, Indonesia, 29–31 August 1989. ASEAN Grain Postharvest Programme, Bangkok, Thailand, pp 268–292

  • Del Rosario AR, Briones VP, Vidal AJ, Juliano BO (1968) Composition and endosperm structure of developing and mature rice kernel. Cereal Chem 45:225–235

    Google Scholar 

  • Foolad MR, Chen FQ (1999) RFLP mapping of QTLs conferring salt tolerance during the vegetative stage in tomato. Theor Appl Genet 99:235–243

    CAS  Google Scholar 

  • Fulton TM, Beck BT, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894

    Article  CAS  Google Scholar 

  • Fulton TM, Grandillo S, Beck BT, Fridman E, Frampton A, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (2000) Advanced backcross QTL analysis of a Lycopersicon esculentum X Lycopersicon parviflorum cross. Theor Appl Genet 100:1025–1042

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Hsieh SC (1991) Studies of physicochemical aspect of eating quality and grading of rice. Bull Taichung Dist Agr Improv Stat 31:1–11

    Google Scholar 

  • Hwang CD, Shin DK, Lee KY, Park ST, Kim SC, Kim KU (1998) The critical seeding date of corrugated furrow seeding rice in eastern coastal area. RDA J Crop Sci 40:62–69

    Google Scholar 

  • Juliano BO (1971) A simplified assay for milled-rice amylose. Cereal Sci Today 16:334–360

    Google Scholar 

  • Juliano BO (1972) Physiochemical properties of starch and protein in relation to grain quality and nutritional value of rice. In: Rice Breeding. International Rice Research Institute, Los Banos, Philippines, pp 389–405

  • Juliano BO (1979) Amylose analysis in rice — a review. In: Proceedings of the Workshop on Chemical Aspects of Rice Grain Quality. International Rice Research Institute, Manila, Philippines, pp 251–260

  • Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. International Rice Research Institute, Manila, Philippines, p 205

  • Kinoshita T (1995) Report of committee on gene symbolization, nomenclature, and linkage groups. Rice Genet Newsl 12:9–93

    Google Scholar 

  • Lander R, Green P, Abrahamson L, Barlow A, Daley M, Lincoln S, Newburg L (1987) Mapmaker: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Google Scholar 

  • Li, T, Takano T, Nagamura Y, Takeda G (1994) Linkage analysis of rice lactate dehydrogenase gene. Rice Genet Newsl 11:109–111

    Google Scholar 

  • McCouch SR, Thomson MJ, Septiningsih EM, Moncada P, Li J, Xiao J, Martinez C, Tohme J, Moelpojawiro S, Yuan LP, McClung A, Tai T, Guimaraes E, Moon HP, Ahn SN (2001) Wild QTLs for rice improvement. In: Rice research and production in the 21st century: a symposium honoring Robert F. Chandler, Jr., 15–17 June 2000, Ithaca, NY, pp 151–169

  • McKenzie KS and Rutger JN (1983) Genetic analysis of amylose content, alkali spreding score, and grain dimension in rice. Crop Sci 23:306–311

    CAS  Google Scholar 

  • Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa x Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    Article  CAS  Google Scholar 

  • Nelson JC (1997) QGENE: software for marker-based genomic analysis and breeding. Mol Breeding 3:239–245

    Article  CAS  Google Scholar 

  • Perez CM (1979) Gel Consistency and Viscosity of Rice. In: Proceedings of the Workshop on Chemical Aspects of Rice Grain Quality. International Rice Research Institute, Manila, Philippines, pp 293–302

  • Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68:467–473

    CAS  Google Scholar 

  • Sano Y, Katsumata M, Okuno K (1986) Genetic studies of speciation in cultivated rice.5. inter- and intra-specific differentiation in the waxy gene expression in rice. Euphytica 35:1–9

    Google Scholar 

  • Sarkar RK, Nanda BB, Dash AB, Lodh SB (1994) Grain characteristic and cooking quality of aromatic and non-aromatic, long and slender varieties of rice (Oryza sativa). Indian J Agr Sci 64:305–309

    Google Scholar 

  • Septiningsih EM, PrasetiyonoJ, LubisE, TaiTH, TjubaryatT, MoeljopawiroS, McCouchSR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet DOI 10.1007/s00122-003-1373-2

  • Tan YF, Li JX, Yu SB, Xing YZ, Xu CG (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

    CAS  Google Scholar 

  • Tan YF, Sun M, Xing YZ, Hua JP, Sun XL, Zhang QF, Corke H (2001) Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor App Genet 103:1037–1045

    CAS  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: A method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224

    Article  CAS  Google Scholar 

  • Temnykh S, Park W, Ayres N, Cartinhour 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

    CAS  Google Scholar 

  • Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computations and experimental analysis of microsatellites of rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    CAS  PubMed  Google Scholar 

  • Thomson MJ, Tai TH, McClung AM, Hinga ME, Lobos KB, Xu Y, Martinez C, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components, and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Google Scholar 

  • Venkateswarlu B, Vergara BS, Visperas RM (1987) Influence of photosynthetically active radiation of grain density of rice. Crop Sci 27:1210–1214

    Google Scholar 

  • Williams VR, Wu WT, Tsai HY, Bates HG (1958) Varietal differences in amylose content of rice starch. J Agric Food Chem 8:47–48

    Google Scholar 

  • Xiao J, J Li, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR (1998) Identification of trait-improving QTL alleles from a wild rice relative, Oryza rufipogon. Genetics 150:899–909

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank Suismono at the Sukamandi Research Institute for Rice for the grain quality data, F. Onishi for technical assistance in the greenhouse, M.J. Thomson for editing the manuscript, and L. Swales for the formatting. A PhD fellowship to E. Septiningsih and much of the grain quality evaluation in Indonesia were funded by the Rockefeller Foundation, and a Postdoctoral fellowship to E.S. was funded through NSF Plant Genome Award DBI-0110004.

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Authors and Affiliations

  1. Department of Plant Breeding, Cornell University, 240 Emerson Hall, Ithaca, NY 14853–1901, USA

    E. M. Septiningsih & S. R. McCouch

  2. Research Institute for Food Crop Biotechnology, 16111, Bogor, Indonesia

    K. R. Trijatmiko & S. Moeljopawiro

Authors
  1. E. M. Septiningsih
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  2. K. R. Trijatmiko
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  3. S. Moeljopawiro
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  4. S. R. McCouch
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Correspondence to S. R. McCouch.

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Communicated by D. Mackill

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Septiningsih, E.M., Trijatmiko, K.R., Moeljopawiro, S. et al. 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 (2003). https://doi.org/10.1007/s00122-003-1376-z

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