Abstract
Conventional methods for quantitative trait locus (QTL) mapping require the selection of particular traits to be measured based on assumptions as to their importance. We have tested an alternative approach for the location of QTLs—marker-evaluated selection—that makes no prior assumptions as to which traits are important. The results of phenotype selection were evaluated in the products of modified bulk-population breeding that was replicated across a range of rice ecosystems. Selection was carried out in close collaboration with farmers in bulk populations that were all derived from a cross between an Indian upland variety (Kalinga III) and a high-yielding semi-dwarf variety (IR64). Twenty-seven diverse bulks were produced that were screened with molecular markers in order to determine whether shifts could be detected in marker allele frequency as a result of selection and if such changes varied by genomic region across ecosystems. Marker loci linked to important traits for adaptation to specific environments were identified without making any prior assumptions about which traits might be important. Genomic regions from Kalinga III were strongly selected in the upland environments and regions from IR64 in the lowland ones. However, exceptions occurred where the upland parent contributed positively to lowland adaptation and vice versa. The results can be used as a basis for the development of second-cycle varieties, using marker-assisted selection to produce genotypic ideotypes for specific target environments. The very strong selection for genomic regions from the adapted parents of the wide (upland × lowland) cross indicates that, in non-marker-assisted breeding, where genetically distant parents have been used, modified backcross breeding should be efficient. A single backcross to the adapted parent for a specific ecosystem will result in a higher frequency of segregants with the desired high genetic contribution from the adapted parent.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bajracharya J (2003) Genetic diversity study in landraces of rice (Oryza sativa L.) by agro-morphological characters and microsatellite DNA markers. PhD Thesis, University of Wales
Bao JS, Wu YR, Hu B, Wu P, Cui HR, Shu QY (2002) QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content. Euphytica 128:317–324
Bligh HFR, Till RI, Jones CA (1995) A microsatellite sequence closely linked to the WAXY gene of Oryza sativa. Euphytica 86:83–85
Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin SY, Monna L, Sasaki T, Ohsugi R (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102:793–800
Kumar R, Singh DN, Prasad SC, Gangwar JS, Virk DS, Witcombe JR (2001) Participatory Plant breeding in rice in eastern India. In: An exchange of experiences from South and Southeast Asia: proceedings of the international symposium of participatory plant breeding and participatory plant genetic resources enhancement. CGIAR Programme for Participatory Research and Gender Analysis (PGRA). Cali, Columbia, pp 233–236
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Lebowitz RJ, Soller M, Beckmann JS (1987) Trait-based analyses for the detection of linkage between marker loci and quantitative trait loci in crosses between inbred lines. Theor Appl Genet 73:556–562
Liao CY, Wu P, Hu B, Yi KK (2001) Effects of genetic background and environment on QTLs and epistasis for rice (Oryza sativa L.) panicle number. Theor Appl Genet 103:104–111
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832
Oetting WS, Lee HK, Flanders DJ, Wiesner GL, Sellers GL, King RA (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458
Quarrie SA, Lazi-Janci V, Kovacevi D, Steed A, Peki S (1999) Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize. J Exp Bot 50:1299–1306
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100
Reyna N, Sneller CH (2001) Evaluation of marker-assisted introgression of yield QTL alleles into adapted soybean. Crop Sci 41:1317–1321
Shen L, Courtois B, McNally KL, Robin S, Li Z (2001) Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theor Appl Genet 103:427–437
Sokal RR, Rohlf FJ (1995) Biometry: the principles and practice of statistics in biological research, 3rd edn. Freeman, New York, pp 699–707
Stuber CW, Moll RH, Goodman MM, Schaffer HE, Weir BS (1980) Allozyme frequency changes associated with selection for increased grain yield in maize (Zea mays L.). Genetics 95:225–236
Venuprasad R, Shashidhar HE, Hittalmani S, Hemamalini GS (2002) Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica 128:293–300
Virk DS, Singh DN, Prasad SC, Gangwar JS, Witcombe JR (2003) Collaborative and consultative participatory plant breeding of rice for the rainfed uplands of eastern India. Euphytica 132:95–108
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Witcombe JR, Subedi M, Joshi KD (2001) Towards a practical participatory plant-breeding strategy in predominantly self-pollinated crops. In: An exchange of experiences from South and Southeast Asia: proceedings of the international symposium of participatory plant breeding and participatory plant genetic resources enhancement. CGIAR Programme for Participatory Research and Gender Analysis (PGRA), Cali, Colombia pp 243–248
Yadav R, Courtois B, Huang N, McLaren G (1997) Mapping genes controlling root morphology and root distribution on a double-haploid population of rice. Theor Appl Genet 94:619–632
Zhu JH, Stephenson P, Laurie DA, Li W, Tang D, Gale MD (1999) Towards rice genome scanning by map-based AFLP fingerprinting. Mol Gen Genet 261:184–195
Acknowledgements
Without the genetic material produced from the rice breeding programmes in Nepal and India, the molecular studies reported here would not have been possible. For this work the authors are grateful to the many farmers who participated in the research and, for the PPB in Nepal, to Mr. Madhu Subedi, Ms. Sharmila Sunwar and Mr. Sanjaya Gyawali of LI-BIRD, Pokhara and, for the PPB in India, to Dr. Ravi Kumar and Dr. D.N. Singh, BAU, Ranchi; Mr. J.S. Gangwar and Dr. S.C. Prasad, GVT (East), Ranchi; and Dr. Daljit Virk, CAZS. The authors thank IRRI for the crosses and the supply of IR64, and Mr. Julian Bridges and Ms. Elly Rodriguez for technical assistance in CAZS. This document is an output from a project (Plant Sciences Research Programme R7434) funded by the UK Department for International Development (DFID) for the benefit of developing countries. The views expressed are not necessarily those of DFID.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by D.J. Mackill
Rights and permissions
About this article
Cite this article
Steele, K.A., Edwards, G., Zhu, J. et al. Marker-evaluated selection in rice: shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding. Theor Appl Genet 109, 1247–1260 (2004). https://doi.org/10.1007/s00122-004-1732-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-004-1732-7