Skip to main content
SpringerLink
Log in

QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima

Theoretical and Applied Genetics volume 109, pages 630–639 (2004)Cite this article

Abstract

International rice export markets are increasing demands for rapid improvements in grain quality characteristics. The African rice Oryza glaberrima is a new potential source of genes that will enhance the eating, cooking, and milling properties of the rice grain. The objective of this research was to identify and characterize quantitative trait loci (QTLs) among 312 doubled haploid lines derived from the BC3F1 of an interspecific cross of O. sativa × O. glaberrima. Genetic material was planted in replicated plots and evaluated for ten grain quality traits in 2001 in Colombia. A linkage map was constructed with 100 polymorphic microsatellite markers using the mapdisto software program to adjust for segregation distortion. Transgressive segregation was observed for all traits. Interval and composite interval analyses identified 27 QTLs for nine characters located on 11/12 chromosomes. The chromosomal positions of QTLs for percentage amylose, alkali-spreading score, and percentage protein were in agreement with data reported by others, whereas QTL markers for percentage head rice, percentage milled rice, percentage protein, and percentage brown rice were different in our mapping population. Five major QTLs were found to be associated with improved percentage rice bran, percentage amylose, and alkali-spreading score. Seven QTLs for improved percentage rice bran, percentage milled rice, alkali-spreading score, percentage protein, and grain length/width ratio were derived from the O. glaberrima accession. Three new QTLs for percentage rice bran are reported here for the first time. Results from this study suggest that the African rice might be a valuable new source for introgression and improvement of several traits that affect quality traits demanded by the different rice export markets.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  • Anonymous, EMBRAPA (Empresa Brasileira do Pesquisa Agropecuaria) (1997) A producao de sementes no Brasil. Relatorio da Safra 1995–1996

    Google Scholar 

  • Anonymous, EPAMIG (Empresa do Pesquisa Agropecuaria de Minas Gerais) (1994) Caiapo. Nova apcao de arroz de sequeiro, Belo Horizonte, Epamig, Embrapa

  • Bao JS, Sun M, Corke H (2002) Analysis of genetic behavior of some starch properties in indica rice (Oryza sativa L.): thermal properties, gel texture, swelling volume. Theor Appl Genet 104:408–413

    CAS  Google Scholar 

  • Basten CJ, Weir BS, Zeng ZB (1994) zmap—a qtl cartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, Raleigh

  • 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 

  • Chase K, Adler FR, Lark KG (1997) epistat: a computer program for identifying and testing interactions between pairs of quantitative trait loci. Theor Appl Genet 94:724–730

    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 

  • 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 

  • Heuer S, Miezan K (2003) Assessing hybrid sterility in Oryza glaberrima × O. sativa hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties. Theor Appl Genet 107:902–909

    Article  CAS  PubMed  Google Scholar 

  • Heuer S, Miezan KM, Sie M, Gaye S (2003) Increasing biodiversity of irrigated rice in Africa by interspecific crossing of Oryza glaberrima (Steud.) × O. sativa indica (L.). Euphytica 132:31–40

    Article  Google Scholar 

  • Jennings PR, Coffman WR, Kauffman HE (1979) Rice improvement. International Rice Research Institute, Manila

  • Jones MP, Mande S, Aluko K (1997a) Diversity and potential of Oryza glaberrima Steud. in upland rice breeding. Breed Sci 47:395–398

    CAS  Google Scholar 

  • Jones MP, Dingkuhn M, Aluko GK, Mande S (1997b) Interspecific O. sativa L. × O. glaberrima Steud. progenies in upland rice improvement. Euphytica 92:237–246

    Article  Google Scholar 

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

  • Juliano BO, Perez CM, Kaosa-Ard M (1990) Grain quality characteristics of export rice in selected markets. Cereal Chem 67:192–197

    Google Scholar 

  • Kumar I, Khush GS (1988) Inheritance of amylose content in rice (Oryza sativa L.). Euphytica 38:261–269

    CAS  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    CAS  PubMed  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daley M (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 

  • Lark KG, Chase K, Alder F, Mansur LM, Orf J (1995) Interactions between quantitative trait loci in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci USA 92:4656–4660

    CAS  PubMed  Google Scholar 

  • Lentini Z, Reyes P, Martinez CP, Roca WM (1995) Androgenesis of highly recalcitrant rice genotypes with maltose and silver nitrate. Plant Sci 110:127–138

    Article  CAS  Google Scholar 

  • Lincoln S, Daly M, Lander E (1992) Constructing genetic linkage maps with mapmaker/exp. Whitehead Institute Technical Report, Cambridge, Mass. http://www-genome.wi.mit.edu/ftp/distribution/software

  • Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35:111–126

    CAS  Google Scholar 

  • Lorieux M, Ndjiondjop MN, Ghesquiere A (2000) A first interspecific O. sativa × O. glaberrima microsatellite genetic linkage map. Theor Appl Genet 100:593–601

    CAS  Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829

    CAS  Google Scholar 

  • McKenzie KS, Rutger JN (1983) Genetic analysis of amylose content, alkali spreading score, and grain dimensions 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 × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    Article  CAS  Google Scholar 

  • Nakagahra M, Omura T, Iwata N (1972) Gametophyte genes and their loci on the eleventh linkage group of cultivated rice. Jpn J Breed 22:305–312

    Google Scholar 

  • Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    Article  CAS  PubMed  Google Scholar 

  • Redoña E, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor Appl Genet 96:957–963

    Google Scholar 

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

    CAS  Google Scholar 

  • SAS Institute (1998) Users guide to statistics, ver. 8.2. SAS Institute, Cary, N.C.

  • SAS Institute (2003) SAS ver. 9. SAS Institute, Cary, N.C.

  • Second G (1982) Origin of the genetic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jap J Genet 57:25–58

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Takamure I, Kinoshita T (1991) Linkage analysis in chromosomes 3 and 6. Rice Genet Newsl 8:98–100

    Google Scholar 

  • Takeda K, Saito K (1980) Major genes controlling grain size in Japan. Jpn J Breed 30:280–282

    Google Scholar 

  • Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang QF (1999) The three important traits for cooking and eating qualities of rice grain are controlled by a single locus. Theor Appl Genet 99:642–648

    CAS  Google Scholar 

  • Tan YF, Xing YZ, Li JX, Yu SB, Xu CG, Zhang QF (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829

    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 Appl Genet 103:1037–1045

    Article  CAS  Google Scholar 

  • Temnykh S, Park WD, 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 100:698–712

    Article  Google Scholar 

  • Unnevehr LJ, Duff B, Juliano BO (1992) Consumer demand for rice grain quality. International Rice Research Institute, Manila, and International Development Research Center, Ottawa

  • Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTL affecting traits of agronomic importance in a recombinant inbred population derived from sub-specific rice cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Xu Y, Shen ZT (1992) Distorted segregation of waxy gene and its characterization in indica-japonica hybrids. Chin J Rice Sci 6:89–92

    Google Scholar 

  • Xu Y, Shen ZT, Chen Y, Zhu LH (1995) Distorted segregations of RFLP markers and their distribution on chromosomes in an indica-japonica F2 population of rice (Oryza sativa L.). Acta Bot Sin 37:91–96

    Google Scholar 

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch S (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545

    Article  CAS  PubMed  Google Scholar 

  • Xu GG, Yu SB, Zhang Q, Li JX, Xing YZ, Tan YF (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite hybrid. Theor Appl Genet 101:823–829

    CAS  Google Scholar 

  • Yamagishi M, Yano M, Fukui Y, Otani M, Shimada M (1996) Distorted segregation of RFLP markers in regenerated plants derived from anther culture of an F1 hybrid rice. Gene Genet Syst 71:37–41

    Article  CAS  Google Scholar 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    CAS  PubMed  Google Scholar 

  • 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 selection. Theor Appl Genet 106:326–331

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank both the Rockefeller Foundation for the granting of a Postdoctoral Fellowship to G. Aluko and the Ministry of Agriculture of Colombia and CIAT for core funding of this project. We acknowledge the assistance of Z. Lentini, CIAT, for the production of DH lines and A. Almeida and O. Giraldo, CIAT, for assistance in the development of marker data.

Author information

Authors and Affiliations

  1. Department of Agronomy, LSU AgCenter, Louisiana State University, 104 Sturgis Hall, Baton Rouge, LA, 70803, USA

    G. Aluko & J. H. Oard

  2. Centro Internacional de Agricultura Tropical, Apdo aereo 6713, Cali, Columbia

    C. Martinez, J. Tohme & C. Castano

  3. USDA-ARS Rice Research Unit, 1509 Aggie Drive, Beaumont, TX, 77713, USA

    C. Bergman

Authors
  1. G. Aluko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Martinez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Tohme
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. Castano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. Bergman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. J. H. Oard
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J. H. Oard.

Additional information

Communicated by D.J. Mackill

Approved for publication by the Director of the Louisiana Agricultural Experiment Station as paper no. 04-14-0054.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Aluko, G., Martinez, C., Tohme, J. et al. QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima . Theor Appl Genet 109, 630–639 (2004). https://doi.org/10.1007/s00122-004-1668-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1668-y

Keywords

search

Navigation