Skip to main content
SpringerLink
Log in

Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross

  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

To detect QTLs controlling traits of agronomic importance in rice, two elite homozygous lines 9024 and LH422, which represent the indica and japonica subspecies of rice (Oryza sativa), were crossed. Subsequently a modified single-seed-descent procedure was employed to produce 194 recombinant inbred lines (F8). The 194 lines were genotyped at 141 RFLP marker loci and evaluated in a field trial for 13 quantitative traits including grain yield. Transgressive segregants were observed for all traits examined. The number of significant QTLs (LOD ⩾ 2.0) detected affecting each trait ranged from one to six. The percentage of phenotypic variance explained by each QTL ranged from 5.1% to 73.7%. For those traits for which two or more QTLs were detected, increases in the traits were conditioned by indica alleles at some QTLs Japonica alleles at others. No significant evidence was found for epistasis between markers associated with QTLs and all the other markers. Pleitropic effects of single QTLs on different traits are suggested by the observation of clustering of QTLs. No QTL for traits was found to map to the vicinity of major gene loci governing the same traits qualitatively. Evidence for putative orthologous QTLs across rice, maize, oat, and barley is discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Abler BSB, Edwards MD, Stuber CW (1991) Isoenzymatic identification of quantitative trait loci in crosses of elite maize inbreds. Crop Sci 31:267–274

    Google Scholar 

  • Ahn SN, Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90:7980–7984

    Google Scholar 

  • Ahn SN, Anderson JA, Sorrells ME, Tanksley SD (1993a) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241:483–490

    Google Scholar 

  • Ahn SN, Bollich CN, AM McClung, Tanksley SD (1993b) RFLP analysis of genomic regions associated with cooked-kernel elongation in rice. Theor Appl Genet 87:27–32

    Google Scholar 

  • Beavis WD, Grant D, Albertsen M, Fincher R (1991) Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci. Theor Appl Genet 83:141–145

    Google Scholar 

  • Beavis WD, Smith OS, Grant D, Fincher R (1991) Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci 34:882–896

    Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, PC Ronald, 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

    Google Scholar 

  • Champoux MC, Wang G, Sarkarung S, qMackill DJ, O'Toole JC, Huang N, McCouch SR (1995) Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor Appl Genet 90:968–981

    Google Scholar 

  • Cho YG, Eun MY, McCouch SR, Chae YA (1994) The semidwarf gene, sd-1, of rice (Oryza saliva L.). II. Molecular mapping and marker-assisted selection. Theor Appl Genet 89:54–59

    Google Scholar 

  • Data Description, Inc. (1992) Data Desk: Statistics Guide. Data Description, Inc., Ithaca, N.Y.

    Google Scholar 

  • Doebley J, Bacigalupo A, Stec A (1994) Inheritance of kernel weight in two maize-teosinte hybrid populations: implications for crop evolution. J Hered 85:191–195

    Google Scholar 

  • Edwards MD, Helentjaris T, Wright S, Stuber CW (1992) Molecular-marker-facilitated investigations of quantitative trait loci in maize.4. Analysis based on genome saturation with isozyme and restriction fragment length polymorphism markers. Theor Appl Genet 83:765–774

    Google Scholar 

  • Everson EH, Schaller CW (1955) The genetics of yield differences associated with awn barbing in the barley hybrid (Lion x Atlas10) x Atlas. Agron J 47:276–280

    Google Scholar 

  • Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401

    Google Scholar 

  • Koester RP, Sisco PH, Stuber CW (1993) Identification of quantitative trait loci controlling days to flowering and plant height in two near-isogenic lines of maize. Crop Sci 33:1209–1216

    Google Scholar 

  • Kosambi DD (1994) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Google Scholar 

  • Li Z, Pinson SRM, Stansel JW, Park WD (1995) Identification of quantitative trait loci (QTLs) for heading date and plant height in cultivated rice (Oryza sativa L). Theor Appl Genet 91:374–381

    Google Scholar 

  • Lincoln S, Daly M, Lander E (1992a) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 3rd edn.

  • Lincoln S, Daly M, Lander E (1992b) Mapping genes controlling quantitative traits with MAPMAKER/QTL 1.1. Whitehead Institute Technical Report, 2nd edn.

  • Manly KF (1993) A Macintosh program for storage and analysis of experimental genetic mapping data. Mamm Genome 4:303–313

    Google Scholar 

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

    Google Scholar 

  • Olufowote JO (1994) Analysis of chromosomal regions associated with some quantitative traits in barley using restriction fragment length polymorphism (RFLP) markers. PhD dissertation, Cornell University, Ithaca, New York, pp 45–46

    Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete RFLP linkage map. Nature 335:721–726

    Google Scholar 

  • Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197

    Google Scholar 

  • Rasmussen JM (1935) Studies on the inheritance of quantitative characters in Pisun: I.Preliminary note on the genetics of flowering. Hereditas 20:161–180

    Google Scholar 

  • Robertson DS (1985) A possible technique for isolating genic DNA for quantitative traits in plants. J Theor Biol 117:1–10

    Google Scholar 

  • Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Satito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, Yoshimura S, Ideta O, Ohsawa R, Hayano Y, Iwata N, Sugiura M (1991) Linkage map of restriction fragment length polymorphism loci in rice. Japan J Breed 41:665–670

    Google Scholar 

  • Sax K (1923) The association of size differences with seed coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560

    Google Scholar 

  • SAS Institute, Inc (1988) SAS Users Guide: Statistic. SAS Institute, Cary, N.C.

    Google Scholar 

  • Schön CC, Lee M, Melchinger AE, Guthrie WD, Woodman WL (1993) Mapping and characterization of quantitative trait loci affecting resistance against second-generation European corn borer in maize with the aid of RFLPs. Heredity 70: 648–659

    Google Scholar 

  • Schön CC, Melchinger AE, Boppenmaier J, Brunklaus-Jung E, Herrmann RG, Seitzer JF (1994) RFLP mapping in maize: quantitative trait loci affecting testcross performance of elite European flint lines. Crop Sci 34:378–389

    Google Scholar 

  • Siripoonwiwat W (1995) Application of restriction fragment length polymorphism (RFLP) markers in the analysis of chromosomal regions associated with some quantitative traits for hexaploid oat improvement. Msc thesis, Cornell University, Ithaca, New York

    Google Scholar 

  • Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839

    Google Scholar 

  • Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    Google Scholar 

  • Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:247–264

    Google Scholar 

  • Thoday JM (1961) Location of polygenes. Nature 191: 368–370

    Google Scholar 

  • Van Deynze AE, Nelson JC, O'Donoughue LS, Ahn SN, Siripoonwiwat W, Harrington SE, Yglesias ES, Braga DP, McCouch SR, Sorrells ME (1995 a) Comparative mapping in grasses. Oat relationships. Mol Gen Genet (in press)

  • Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995 b) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet (in press)

  • Veldboom LR, Lee M (1994) Molecular-marker-facilitated studies of morphological traits in maize. II. Determination of QTLs for grain yield and yield components. Theor Appl Genet 89: 451–458

    Google Scholar 

  • Veldboom LR, Lee M, Woodman WL (1994) Molecular-marker-facilitated studies in an elite maize population. I. Linkage analysis and determination of QTL for morphological traits. Theor Appl Genet 88:7–16

    Google Scholar 

  • Wang G, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434

    Google Scholar 

  • Xiao J, Yuan L (1988) The heterosis of F1 hybrids between indica and japonica and their relationship with their parents. Hybrid Rice 9:5–9

    Google Scholar 

  • Xiao J, Li J, Yuan L, Tanksley SD (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 140:745–754

    Google Scholar 

  • Xu YB, Shen ZT, Xu JC, Chen Y, Zhu LH (1993) Mapping quantitative trait loci via restriction fragment length polymorphism markers in rice. Rice Genet Newslett 10:135–138

    Google Scholar 

  • Xu YB, Shen ZT, Chen Y, Zhu LH (1995) Molecular mapping for quantitative trait loci controlling yield component characters using a maximum likelihood method in rice (Oryza saliva L.). Acta Genet Sini 22:46–52

    Google Scholar 

  • Young ND, Tanksley SD (1989) Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet 77:95–101

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant Breeding and Biometry, Cornell University, 252 Emerson Hall, 14853-1902, Ithaca, New York, USA

    J. Xiao & S. D. Tanksley

  2. Hunan Hybrid Rice Research Center, 410125, Changsha, Hunan, People's Republic of China

    J. Li & L. Yuan

Authors
  1. J. Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. L. Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. D. Tanksley
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Communicated by F. Salamini

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xiao, J., Li, J., Yuan, L. et al. Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theoret. Appl. Genetics 92, 230–244 (1996). https://doi.org/10.1007/BF00223380

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00223380

Keywords

Search

Navigation