Skip to main content
Log in

Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara

  • RESEARCH ARTICLE
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1, and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1, showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of more than 15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1, and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488–RM431 and RM6–RM535 on chromosomes 1 and 2, respectively. The co-location of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2, and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification.

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

Access this article

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

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2

Similar content being viewed by others

References

  • Ali M. L., Sanchez P. L., Yu S., Lorieux M. and Eizenga G. C. 2010 Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa). Rice 3, 218–234.

    Article  Google Scholar 

  • Arcade A., Labourdette A., Falque M., Mangin B., Chardon F., Charcosset A. et al. 2004 BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 14, 2324–2326.

    Article  Google Scholar 

  • Brar D. S. and Khush G. S. 2004 Alien introgression in rice. Plant Mol. Biol. 35, 35–47.

    Article  Google Scholar 

  • Brondani C., Rangel P. H. N., Brondani R. P. V. and Ferreira M. E. 2001 QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor. Appl. Genet. 104, 1192– 1203.

    Google Scholar 

  • Chen L. J., Lee D. S., Song Z. P., Suh H. S. and Lu B. R. 2004 Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Ann. Bot. 93, 67–73.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cho Y. G., Eun M. Y., McCouch S. R. and Chae Y. A. 1994 The semi dwarf gene sd-1 of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection. Theor. Appl. Genet. 89, 54–59.

  • . Y., Wang Y. M., Zhang Z. J., Shen Y., Lin X. Y., Ou X. F. et al. 2006 Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor. Appl. Genet. 113, 196–205.

  • Gur A. and Zamir D. 2004 Unused natural variation can lift yield barriers in plant breeding. PLOS Biol. 2, e245.

    Article  PubMed Central  PubMed  Google Scholar 

  • Hoan N. T., Sarma N. P. and Siddiq E. A. 1998 Wide hybridization for diversification of CMS in rice. Int. Rice Res. Notes 23, 5–6.

  • Joshi S. P., Gupta V. S., Aggarwal R. K., Ranjekar P. K. and Brar D. S. 2000 Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor. Appl. Genet. 100, 1311–1320.

    Article  CAS  Google Scholar 

  • Das A., Joshi S. V., Sharma S., Yogesh V. Y., Patra B. C. et al. 2006 Oryza nivara (Sharma et Shastry), the progenitor of O. sativa (L.) subspecies indica harbors rich genetic diversity as measured by SSR markers. Curr. Sci. 91, 1079–1085.

  • Khush G. S. 2000 Rice germplasm enhancement at IRRI. Phillipp. J. Crop Sci. 25, 45–51.

    Google Scholar 

  • Kosambi D. D. 1944 The estimation of map distances from recombination values. Ann. Eugen. 12, 172–175.

    Article  Google Scholar 

  • Li X., Qian Q., Fu Z., Wang Y., Xiong G., Zeng D. et al. 2003 Control of tillering in rice. Nature 422, 618–621.

    Article  CAS  PubMed  Google Scholar 

  • Li C., Zhou A. and Sang T. 2006 Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol. 170, 185–194.

    Article  CAS  PubMed  Google Scholar 

  • Liu T., Li L., Zhang Y., Xui C., Li X. and Xing Y. 2011 Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. J. Genet. 90, 377–382.

    Article  PubMed  Google Scholar 

  • Lu B. R., Naredo M. E. B., Juliano A. B. and Jackson M. T. 1998 Taxonomic status of Oryza glumaepatula Steud. III. Assessment of genomic affinity among AA genome species from the New World, Asia and Australia. Genet. Res. Crop Evol. 45, 215– 223.

    Article  Google Scholar 

  • Marri P. R., Sarla N., Reddy V. L. N. and Siddiq E. A. 2005 Identification and mapping of yield-related QTL from an Indian accession of Oryza rufipogon. BMC Genet. 6, 33.

  • McCouch S. R., Sweeney M., Li J., Jiang H., Thomson M., Septiningsih E. et al. 2007 Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154, 317–339.

    Article  CAS  Google Scholar 

  • Mijalski T., Mijalski A., Harder T., Halder M., Kersten M., Horsch T. et al. 2005 Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc. Natl. Acad. Sci. USA 102, 8621–8626.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Niroula R. K., Subedi L. P. and Upadhyay M. P. 2009 Cytogenetic analyses of intragenomic rice hybrids derived from Oryza sativa L. and O. nivara Sharma et Shastry. Bot. Res. Int. 4, 277–283.

    Google Scholar 

  • Price A. H. 2006 Believe it or not QTL are accurate. Trends Plant Sci. 11, 213–216.

    Article  CAS  PubMed  Google Scholar 

  • Quan C. Z., You Y. F., Qing L. D., Qiong Y. T., Jian F., Jun Y. H. et al. 2012 Genetic diversity of wild rice species in Yunnan province of China. Rice Sci. 19, 21–28.

    Article  Google Scholar 

  • Rahman M. L., Chu S. H., Choi M., Qiao Y. L., Jiang W., Piao R. et al. 2008 Identification of QTL for some agronomic traits in rice using an introgression line from Oryza minuta. Mol. Cells 24, 16–26.

    Google Scholar 

  • Ram T., Majumder N. D., Krishnaveni D. and Ansari M. M. 2007 Rice variety, Dhanrasi, an example of improving yield potential Rice variety, Dhanrasi, an example of improving yield potential (Oryza rufipogon). Curr. Sci. 92, 987–992.

  • Sarla N., Bobba S. and Siddiq E. A. 2003 ISSR and SSR markers based on AG and GA repeats delineate geographically diverse Oryza nivara accessions and reveal rare alleles. Curr. Sci. 84, 683–690.

    Google Scholar 

  • Septiningsih E. M., Prasetiyono J., Lubis E., Tai T. H., Tjubaryat T., Moeljopawiro S. et al. 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.

    Article  CAS  PubMed  Google Scholar 

  • Steele K. A., Virk D. S., Kumar R., Prasad S. C. and Witcombe J. R. 2007 Field evaluation of upland rice lines selected for QTL controlling root traits. Field Crops Res. 101, 180–186.

    Article  Google Scholar 

  • Swamy B. P. M. and Sarla N. 2008 Yield enhancing quantitative trait loci (QTL) from wild species. Biotechnol. Adv. 26, 106– 120.

    Article  CAS  PubMed  Google Scholar 

  • Swamy B. P. M. and Sarla N. 2011 Meta-analysis of yield QTL derived from inter-specific crosses of rice reveals consensus regions and candidate genes. Plant. Mol. Biol. Rep. (doi: 10.1007/s11105-010-0274-1).

  • Tanksley S. D. and Nelson J. C. 1996 Advanced backcross QTL analysis; a method for simultaneous discovery and transfer of valuable QTL from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92, 191–203.

    Article  CAS  PubMed  Google Scholar 

  • Tanksley S. D. and McCouch S. R. 1997 Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063–1066.

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Thanh P. T., Sripichitt P., Chanprame S. and Peyachoknagu S. 2006 Transfer of drought resistant character from wild rice (Oryza meridionalis and Oryza nivara) to cultivated rice (Oryza sativa L.) by backcrossing and immature embryo culture. Kasetsart J. 40, 582–594.

    Google Scholar 

  • Thomson M. J., Tai T. H., McClung A. M., Lai X. H., Hinga M. E., Lobos K. B. 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.

  • Tian F., Li D. J., Fu Q., Zhu Z. F., Fu Y. C., Wang X. K. et al. 2005 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.

    Article  PubMed  Google Scholar 

  • Van Ooijen J. W. and Voorrips R. E. 2001 JoinMap 3.0 software for the calculation of genetic linkage maps. Plant Research International, Wageningen, the Netherlands.

  • Wang Y. M., Dong Z. Y., Zhang Z. J., Lin X. Y., Shen Y., Zhou D. et al. 2005 Extensive de novo variation in rice induced by introgression from wild rice (Zizania latifolia). Genetics 170, 1945–1956.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang S., Basten C. J. and Zen Z. B. 2011 Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC.

    Google Scholar 

  • Wickneswari R., Bhuiyan M. A. R., Kalluvettankuzhy S., Lim L. S., Thomson M. J., Narimah M. K. et al. 2012 Identification and validation of quantitative trait loci for agronomic traits in advanced backcross breeding lines derived from Oryza rufipogon × Oryza sativa cultivar MR219. Plant Mol. Biol. Rep. (doi: 10.1007/s11105-011-0404-4).

  • Xiao J, Li J., Grandillo S., Ahn S. N., Yuan L., Steven D. et al. 1998 Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150, 899–909.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Xie X., Song H. M., Jin F., Ahn S., Suh J., Hwang H. G. et al. 2008 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.

    Article  Google Scholar 

  • Xing Y. Z., Tang W. J., Xue W. Y., Xu C. G. and Zhang Q. 2008 Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice. Theor. Appl. Genet. 116, 789–796.

    Article  CAS  PubMed  Google Scholar 

  • Xiong L. Z., Liu K. D., Dai X. K., Xu C. G. and Zhang Q. 1999 Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon. Theor. Appl. Genet. 98, 243– 251.

    Article  CAS  Google Scholar 

  • Yano M. 2001 Genetic and molecular dissection of naturally occurring variation. Curr. Opin. Plant Biol. 4, 130–135.

    Article  CAS  PubMed  Google Scholar 

  • Yoon D. B., Kang K. H., Kim H. J., Ju H. G., Kwon S. J. and Suh J. P. 2006 Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor. Appl. Genet. 12, 1052–1062.

    Article  Google Scholar 

  • Zheng K., Subudhi P. K., Domingo J., Magpantay G and Huang N. 1995 Rapid DNA isolation for marker assisted selection in rice breeding. Rice Genet. News Lett. 12, 255–258.

Download references

Acknowledgements

BPMS thank the University Grants Commission–Council of Scientific and Industrial Research (UGC-CSIR) for providing fellowship; KK thank the Indian Council of Agricultural Research (ICAR), Government of India, for fellowship. This project was also supported by the Department of Biotechnology, Government of India.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to B. P. MALLIKARJUNA SWAMY.

Additional information

Swamy B. P. M., Kaladhar K., Reddy G. A., Viraktamath B. C. and Sarla N. 2014 Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara. J. Genet. 93, xx–xx

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

MALLIKARJUNA SWAMY, B.P., KALADHAR, K., REDDY, G.A. et al. Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara . J Genet 93, 643–654 (2014). https://doi.org/10.1007/s12041-014-0420-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12041-014-0420-x

Keywords

Navigation