Allelic variation for a candidate gene for GS7, responsible for grain shape in rice

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Theoretical and Applied Genetics (Impact Factor: 3.51). 07/2012; 125(6):1303-12. DOI: 10.1007/s00122-012-1914-7
Source: PubMed

ABSTRACT Grain shape is an important component of end-use quality in rice. The genomic location of the grain shape QTL GS7 was narrowed to lie within a 4.8-kb segment on chromosome 7. The homologous region in cv. Nipponbare contains no annotated genes, while two open reading frames were predicted, one of which (ORF2) represented a likely candidate for GS7 gene on the basis of correlation between sequence variation and phenotype. Semi-quantitative and quantitative RT-PCR analysis of ORF2 transcription showed that the gene was active in both the leaf and panicle when the cv. D50 allele was present, but not in the presence of the cv. HB277 allele. A microsatellite-based phylogeny and a re-sequencing analysis of ORF2 among a set of 52 diverse rice accessions suggested that the cv. D50 GS7 allele may have originated from the tropical japonica genepool. The effect on grain length of the alternative alleles at GS7and GS3 showed that combination type 3/A was associated with longer grains than type 1/A. An Indel marker developed within the ORF2 sequence was informative for predicting grain length.

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    • "In case of grain width MLM analysis (p < 0.0001) detected 130 sites with 73 SNP markers on chromosomes 7 and 4 markers on chromosome 8 (Figure 6c). The significant markers on chromosome 7 (22.7 – 26 Mb) co-localized with the grain breadth QTL identified in the study by Redoña and Mackill (1998) and was near a grain shape QTL GS7 (Shao et al. 2012). The significant markers on chromosome 8 (26.4 -27.2 Mb) co-localized with GW8 OSSPL16 QTL for grain width and yield potential (Wang et al. 2012). "
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    ABSTRACT: Background This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community. Results The indica MAGIC population is the most advanced of the MAGIC populations developed thus far and comprises 1328 lines produced by single seed descent (SSD). At the S4 stage of SSD a subset (200 lines) of this population was genotyped using a genotyping-by-sequencing (GBS) approach and was phenotyped for multiple traits, including: blast and bacterial blight resistance, salinity and submergence tolerance, and grain quality. Genome-wide association mapping identified several known major genes and QTLs including Sub1 associated with submergence tolerance and Xa4 and xa5 associated with resistance to bacterial blight. Moreover, the genome-wide association study (GWAS) results also identified potentially novel loci associated with essential traits for rice improvement. Conclusion The MAGIC populations serve a dual purpose: permanent mapping populations for precise QTL mapping and for direct and indirect use in variety development. Unlike a set of naturally diverse germplasm, this population is tailor-made for breeders with a combination of useful traits derived from multiple elite breeding lines. The MAGIC populations also present opportunities for studying the interactions of genome introgressions and chromosomal recombination.
    Rice 01/2013; 6(1). DOI:10.1186/1939-8433-6-11 · 2.45 Impact Factor
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    • "Recently, this region on chromosome 7 has been fine mapped to a region of 4.8Kb. Candidate gene analyses found no annotated genes in this region while two open reading frames were considered to be more likely candidate for GS7 gene (Shao et al. 2012). "
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    ABSTRACT: Validation of marker-QTL association for genes grain size 3 (GS3), grain weight 2 (GW2), seed width 5 (qSW5) and a QTL qgrl7.1 for grain length was undertaken in a set of 242 diverse rice germplasm. Further, the study was extended to an F2 mapping population derived from cross of Sonasal, a short grain aromatic rice landrace with Pusa Basmati 1121, a variety with extra long slender grains. Seven gene specific markers, namely, SF28, SR17, RGS1and RGS2 based on GS3, W004 for GW2, MS40671 for qSW5 and RM505 for qgrl7.1, were used for validation. Single marker analysis revealed significant association of these markers to grain size and shape. The marker SF28 explained highest phenotypic variance (37 %) while the marker W004 explained lowest variance (2.6 %) for grain length in the germplasm set at the significance level P<0.05. Three markers namely, SF28, MS40671 and RM505 were polymorphic between the parents Sonasal and Pusa Basmati 1121. In the F2 population, the marker SF28 linked to gene GS3 explained highest phenotypic variance (32.5 %), while RM505 linked to qgrl7.1 explained 5.4 % of phenotypic variance for grain length. The marker SF28 was found to be most robust in the validation studies both in germplasm and F2 population. The validated gene specific markers can be utilised in marker assisted selection for improving grain size and shape as these traits have significant contribution towards grain quality and grain yield. This is the first study on validation of gene based markers for grain dimension traits in Indian rice germplasm.
    Journal of Plant Biochemistry and Biotechnology 11/2012; 22(4). DOI:10.1007/s13562-012-0176-4I · 0.81 Impact Factor
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    ABSTRACT: Rice (Oryza sativa) grain shape is a key determinant of grain yield and market values. Facilitated by advancements in genomics and various molecular markers, more than 400 quantitative trait loci (QTLs) associated with rice grain traits have been identified. In this review, we examine the genetic bases of rice grain shape, focusing on the protein products of 13 genes that have been cloned and the chromosome locations of 15 QTLs that have been fine mapped. Although more genes affecting grain traits are likely to be cloned in the near future, characterizing their functions at the biochemical level and applying these molecular data to rice breeding programs will be a more challenging task.
    Trends in Plant Science 12/2012; 18(4). DOI:10.1016/j.tplants.2012.11.001 · 13.48 Impact Factor
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