Grain shape is one of the most important influencing factor to rice grain yield. Among all of the cloned grain shape genes, GW2 is an important one controlling grain width. We obtained the sequences of the important grain shape gene GW2 using cDNA cloning strategy from rice variety TD70 and Kasalath and design its functional marker based on gene sequence difference to analyze genotype and phenotype of recombinant inbred lines(RILs) from TD70/Kasalath cross, some indica restorer lines and japonica rice cultivars in Jiangsu Province. GW2TD70 shared 100% identity to GW2WY3 and 99.77% identity to GW2 sequence（GenBank: EF447275）and there exist a single nucleotide mutation at site 114 without changing amino acid, a single nucleotide deletion at site 316 which generate termination codon at site 346, 347 and 348,thus the expression of GW2 protein stopped in advance. The sequence of GW2Kasalath showed 99.92% identity to GW2 which is known, and there exists a single nucleotide change at site 114 without the variation in amino acid. Comparing with GW2 in TD70, the gene in Kasalath express the intact protein without advanced stop. For GW2 gene, the dCAPS marker was designed according to a base deletion of A in the 316 site of sequence. Digested by Apo I, TD70 showed 21 bp and 30 bp fragments and Kasalath showed 51 bp fragment. Among the 240 RILs, 82 contained GW2TD70 and 158 contain GW2Kasalath , there are significant differences between their phenotypic value. No GW2TD70 gene exit in 10 japonica rice cultivars from Jiangsu Province and 8 indica restorer lines. GW2 gene derived from TD70 may have regulatory effects on grain width，and we can use it to improve grain weight in rice breeding.
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