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      Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

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          Abstract

          Mapping chromosome regions responsible for quantitative phenotypic variation in recombinant populations provides an effective means to characterize the genetic basis of complex traits. We conducted a quantitative trait loci (QTL) analysis of 150 rice recombinant inbred lines (RILs) derived from a cross between two cultivars, Oryza sativa ssp. indica cv. 93-11 and Oryza sativa ssp. japonica cv. Nipponbare. The RILs were genotyped through next-generation sequencing, which accurately determined the recombination breakpoints and provided a new type of genetic markers, recombination bins, for QTL analysis. We detected 49 QTL with phenotypic effect ranging from 3.2 to 46.0% for 14 agronomics traits. Five QTL of relatively large effect (14.6–46.0%) were located on small genomic regions, where strong candidate genes were found. The analysis using sequencing-based genotyping thus offers a powerful solution to map QTL with high resolution. Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice.

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          The online version of this article (doi:10.1007/s00122-010-1449-8) contains supplementary material, which is available to authorized users.

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          A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

          J. Yu (2002)
          We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
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            Cytokinin oxidase regulates rice grain production.

            Motoyuki Ashikari, Hitoshi Sakakibara, Shaoyang Lin … (2005)
            Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.
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              A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.

              Xian-Jun Song, Wei Huang, Min Shi … (2007)
              Grain weight is one of the most important components of grain yield and is controlled by quantitative trait loci (QTLs) derived from natural variations in crops. However, the molecular roles of QTLs in the regulation of grain weight have not been fully elucidated. Here, we report the cloning and characterization of GW2, a new QTL that controls rice grain width and weight. Our data show that GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity, which is known to function in the degradation by the ubiquitin-proteasome pathway. Loss of GW2 function increased cell numbers, resulting in a larger (wider) spikelet hull, and it accelerated the grain milk filling rate, resulting in enhanced grain width, weight and yield. Our results suggest that GW2 negatively regulates cell division by targeting its substrate(s) to proteasomes for regulated proteolysis. The functional characterization of GW2 provides insight into the mechanism of seed development and is a potential tool for improving grain yield in crops.
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                Author and article information

                Contributors
                : +86-21-64845260 , bhan@ncgr.ac.cn
                Journal
                Journal ID (nlm-ta): Theor Appl Genet
                Title: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
                Publisher: Springer-Verlag (Berlin/Heidelberg )
                ISSN (Print): 0040-5752
                ISSN (Electronic): 1432-2242
                Publication date (Electronic): 28 September 2010
                Publication date PMC-release: 28 September 2010
                Publication date (Print): February 2011
                Volume: 122
                Issue: 2
                Pages: 327-340
                Affiliations
                [1 ]National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233 China
                [2 ]State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006 China
                [3 ]Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
                [4 ]Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
                Author notes

                Communicated by T. Sasaki.

                Article
                Publisher ID: 1449
                DOI: 10.1007/s00122-010-1449-8
                PMC ID: 3021254
                PubMed ID: 20878143
                SO-VID: a83c6e4e-72a3-42ef-8129-1be6f0d89e30
                Copyright © © The Author(s) 2010
                History
                Date received : 22 November 2009
                Date accepted : 8 September 2010
                Categories
                Subject: Original Paper
                Custom metadata
                issue-copyright-statement © Springer-Verlag 2011

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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