Skip to main content

Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars

Journal of Genetics volume 90, pages 209–215 (2011)Cite this article

Abstract

The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.

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

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

References

  • Ashikari M., Sakakibara H., Lin S. Y., Yamamoto T., Takashi T., Nishimura A. et al. 2005 Cytokinin oxidase regulates rice grain production. Science 309, 741–745.

    PubMed  Article  CAS  Google Scholar 

  • Bai X. F., Luo L. J., Yan W. H., Kovi M. R., Zhan W. and Xing Y. Z. 2010 Genetic dissection of rice grain shape using a recombinant inbred line population derived from two very contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genet. 11, 16.

    PubMed  Article  Google Scholar 

  • Cho Y. G., Blair M. W., Panaud O. and McCouch S. R. 1996 Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver stained polyacrylamide gels. Genome 39, 373–378.

    PubMed  Article  CAS  Google Scholar 

  • Cho Y. C., Suh J. P., Choi I. S., Hong H. C., Baek M. K., Kang K. H. et al. 2003 QTLs analysis of yield and its related trait in wild rice relative Oryza rufipogon. Treat. Crop Res. 4, 19–29.

    Google Scholar 

  • Doi K., Izawa T., Fuse T., Yamanouchi, U., Kubo T., Shimatani Z. 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.

    PubMed  Article  CAS  Google Scholar 

  • Fan C. C., Xing Y. Z., Mao H. L., Lu T. T., Han B., Xu C. G. et al. 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.

    PubMed  Article  CAS  Google Scholar 

  • Huang X. Z., Qian Q., Liu Z. B., Sun H. Y., He S. Y., Luo D. et al. 2009 Natural variation at the DEP1 locus enhances grain yield in rice. Nat. Genet. 41, 494–497.

    PubMed  Article  CAS  Google Scholar 

  • Kojima S., Takahashi Y., Kobayashi Y., Monna L., Sasaki T., Araki T. and Yano M. 2002 Hd3a, a Rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol. 43, 1096–1105.

    PubMed  Article  CAS  Google Scholar 

  • Lin L. H. and Wu W. R. 2003 Mapping of QTLs underlying grain shape and grain weight in rice. Mol. Plant Breed. 1, 337–342.

    CAS  Google Scholar 

  • Liu T. M., Mao D. H., Zhang S. P. and Xing Y. Z. 2009 Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa). Theor. Appl. Genet. 118, 1509–1517.

    PubMed  Article  CAS  Google Scholar 

  • Liu T. M., Shao D., Kovi M. R. and Xing Y. Z. 2010 Mapping and validation of quantitative trait loci for spikelets per panicle and 1,000-grain weight in rice (Oryza sativa L.). Theor. Appl. Genet. 120, 933–942.

    PubMed  Article  CAS  Google Scholar 

  • Ma D. P., Luo L. J., Wang Z. Y. and He Y. Q. 2004 Mapping QTLs for yield and its component trait f rice using a recombinant inbred line population. Mol. Plant Breed. 2, 507–512 (in Chinese).

    CAS  Google Scholar 

  • Matsubara K., Kono I., Hori K., Nonoue Y., Ono N, Shomura A. et al. 2008 Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars. Theor. Appl. Genet. 117, 935–945.

    PubMed  Article  CAS  Google Scholar 

  • Monna L., Lin H. X., Kojima S., Sasaki T. and Yano M. 2002 Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice. Theor. Appl. Genet. 104, 772–778.

    PubMed  Article  CAS  Google Scholar 

  • Nonoue Y., Fujino K., Hirayama Y., Yamanouchi U., Lin S.Y. and Yano M. 2008 Detection of quantitative trait loci controlling extremely early heading in rice. Theor. Appl. Genet. 116, 715–722.

    PubMed  Article  CAS  Google Scholar 

  • Rahman M. L., Chu S. H., Choi M. S., Qiao Y. L., Jiang W. Z., Piao R. et al. 2007 Identification of QTLs for some agronomic traits in rice using an introgression line from Oryza minuta. Mol. Cell 24, 16–26.

    CAS  Google Scholar 

  • Septiningsih E. M., Prasetiyono J., Lubis E., Tai T. H., Tjubaryat T., Moeljopawiro S. and McCouch S. R. 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. 107, 1419–1432.

    PubMed  Article  CAS  Google Scholar 

  • Shomura A., Izawa T., Ebana K., Ebitani T., Kanegae H., Konishi S. and Yano M. 2008 Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40, 1023–1028.

    PubMed  Article  CAS  Google Scholar 

  • Song X. J., Huang W., Shi M., Zhu M. Z. and Lin H. X. 2007 A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39, 623–630.

    PubMed  Article  CAS  Google Scholar 

  • Spielmeyer W., Ellis M. H. and Chandler P. M. 2002 Semidwarf (sd-1), ‘green revolution’ rice, contains a defective gibberellin 20-oxidase gene. PNAS 99, 9043–9048.

    PubMed  Article  CAS  Google Scholar 

  • Thomson M. J., Tai T. H., McClung A. M., Hinga M. E., Lobos K. B., Xu Y. et al. 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.

    PubMed  Article  CAS  Google Scholar 

  • Tian F., Zhu Z. F., Zhang B. S., Tan L. B., Fu Y. C., Wang X. K. and Sun C. Q. 2006 Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza ruWpogon GriV.). Theor. Appl. Genet. 113, 619–629.

    PubMed  Article  CAS  Google Scholar 

  • Vanooijen J. W. 1999 LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83, 613–624.

    Article  Google Scholar 

  • Wang S., Basten C. J. and Zeng Z. B. 2007 Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, USA. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm).

  • Weng J. F., Gu S. H., Wan X. Y., Gao H., Guo T., Su N. et al. 2008 Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res. 18, 1199–1209.

    PubMed  Article  CAS  Google Scholar 

  • Xiao J., Li J., Yuan L. and Tanksley S. D. 1996 Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor. Appl. Genet. 92, 230–244.

    Article  CAS  Google Scholar 

  • Xie X. B., Song M. H., Jin F. X., Ahn S. N., Suh J. P., Hwang H. G. and McCouch S. R. 2006 Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon. Theor. Appl. Genet. 113, 885–894.

    PubMed  Article  CAS  Google Scholar 

  • Xie X. B., Jin F. X., Song M. H., Suh J. P., Hwang H. G., Kim Y. G. et al. 2008 Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa × O. rufipogon cross. Theor. Appl. Genet. 116, 613–622.

    PubMed  Article  Google Scholar 

  • Xing Y. Z., Tan Y. F., Hua J. P., Sun X. L., Xu C. G. and Zhang Q. F. 2002 Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield trait in rice. Theor. Appl. Genet. 105, 248–257.

    PubMed  Article  CAS  Google Scholar 

  • Xue W. Y., Xing Y. Z., Weng X. Y., Zhao Y., Tang W. J., Wang L. et al. 2008 Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat. Genet. 40, 761–767.

    PubMed  Article  CAS  Google Scholar 

  • Yamamoto T., Kuboki Y., Lin S. Y., Sasaki T. and Yano M. 1998 Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor. Appl. Genet. 97, 37–44.

    Article  CAS  Google Scholar 

  • Yamamoto T., Lin H. X., Sasaki T. and Yano M. 2000 Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154, 885–891.

    PubMed  CAS  Google Scholar 

  • Yan C. J., Liang G. H., Chen F., Li X., Tang S. Z., Yi C. D. et al. 2003 Mapping Quantitative Trait Loci Associated with Rice Grain Shape Based on an indica/japonica Backcross Population. Acta Genet. Sin. 30, 711–716.

    PubMed  CAS  Google Scholar 

  • Yan W. H., Wang P., Chen H. X., Zhou H. J., Li Q. P., Wang C. R. et al. 2011 A major QTL, Ghd8, plays pleiotrophic roles in regulating grain productivity, plant height, and heading date in rice. Mol. Plant 4, 319–330.

    PubMed  Article  CAS  Google Scholar 

  • Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T. 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, 2473–2483.

    PubMed  CAS  Google Scholar 

  • Yano M., Kojima S., Takahashi Y., Lin H. X. and Sasaki T. 2001 Genetic control of flowering time in rice, a short-day plant. Plant Physiol. 127, 1425–1429.

    PubMed  Article  CAS  Google Scholar 

  • Zhang Q. F. 2007 Strategies for developing green super rice. Proc. Natl. Acad. Sci. USA 104, 16402–16409.

    PubMed  Article  CAS  Google Scholar 

  • Zhang Y. S., Luo L. J., Xu C. G., Zhang Q. F. and Xing Y. Z. 2006 Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor. Appl. Genet. 113, 361–368.

    PubMed  Article  CAS  Google Scholar 

Download references

Author information

Affiliations

  1. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    XU FENG BAI, WEN HAO YAN, MALLIKARJUNA RAO KOVI & YONG ZHONG XING

  2. Shanghai Agrobiological Gene Center, 2901 Beidi Road, Shanghai, 201106, People’s Republic of China

    LI JUN LUO

Authors
  1. XU FENG BAI
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. LI JUN LUO
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. WEN HAO YAN
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. MALLIKARJUNA RAO KOVI
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. YONG ZHONG XING
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to YONG ZHONG XING.

Additional information

[Bai X. F., Luo L. J., Yan W. H., Kovi M. R. and Xing Y. Z. 2011 Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars. J. Genet. 90, 209–215]

Rights and permissions

Reprints and Permissions

About this article

Cite this article

BAI, X.F., LUO, L.J., YAN, W.H. et al. Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars. J Genet 90, 209–215 (2011). https://doi.org/10.1007/s12041-011-0057-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-011-0057-y

Keywords

  • rice
  • correlation
  • QTL cluster
  • yield