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Starch deposited in the endosperm of cereal seeds serves as a source of food and animal feed, and as a substrate for bioethanol production. To gain insights into the molecular mechanisms underlying genetic variation in seed size and seed starch content, this study investigated transcriptional regulation of starch biosynthesis genes during seed filling in two wheat genotypes that exhibit contrasting phenotype in seed size. Our data showed that variation in starch accumulation during seed filling is closely associated with modulations in the expression patterns of specific starch biosynthesis genes including TaAGPL1, TaAGPS2, TaGBSSI, TaSSI, TaSSIV, TaSBEIIa, TaISA1, and TaISA3, as well as alterations in the activity of AGPase, GBSS, and SS enzymes. Consistently, the genotype that produces larger seeds that are characterized by a higher seed starch content generated higher amounts of fermentable sugars and bioethanol before and after fermentation, respectively. Since the amount of phenol per seed dry weight is higher in the genotype that produces smaller seeds, the prevalence of lower starch to bioethanol conversion efficiency in this genotype, despite the higher amount of glucose generated per bioavailable starch, suggests that the phenolic compounds interfere with the fermentation process and thereby affecting the bioethanol yield. [ABSTRACT FROM AUTHOR]