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

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.