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Background  Grain size is an extremely important aspect of rice breeding, affecting both grain yield and quality traits. It is controlled by multiple genes and tracking these genes in breeding schemes should expedite selection of lines with superior grain yield and quality, thus it is essential to develop robust, efficient markers.    Result  In this study, 14 genes related to grain size ( GW2 ,  GS2 ,  qLGY3 ,  GS3 ,  GL3.1 ,  TGW3 ,  GS5 ,  GW5 ,  GS6 ,  TGW6 ,  GW6a ,  GLW7 ,  GL7  and  GW8 ) were selected for functional marker development. Twenty-one PCR-gel-based markers were developed to genotype the candidate functional nucleotide polymorphisms (FNPs) of these genes, and all markers can effectively recognize the corresponding allele types. To test the allele effects of different FNPs, a global collection of rice cultivars including 257 accessions from the Rice Diversity Panel 1 was used for allele mining, and four grain-size-related traits were investigated at two planting locations. Three FNPs for  GW2 ,  GS2  and  GL3.1  were genotyped as rare alleles only found in cultivars with notably large grains, and the allele contributions of the remaining FNPs were clarified in both the  indica  and  japonica  subspecies. Significant trait contributions were found for most of the FNPs, especially  GS3 ,  GW5  and  GL7 . Of note,  GW5  could function as a key regulator to coordinate the performance of other grain size genes. The allele effects of several FNPs were also tested by QTL analysis using an F 2  population, and  GW5  was further identified as the major locus with the largest contribution to grain width and length to width ratio.    Conclusions  The functional markers are robust for genotyping different cultivars and may facilitate the rational design of grain size to achieve a balance between grain yield and quality in future rice breeding efforts.

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice