A newly identified QTL, qSW5 (QTL for seed width on chromosome 5) which involved in the determination of grain width in rice, was cloned. Through fine mapping, complementation testing and association analysis, the results showed a deletion in qSW5 causes a significant increase in sink size owing to an increase in cell number in the outer glume (lemma) of the rice flower; the size of the rice glume is one of the determinants of rice endosperm size or grain size. As the Nipponbare allele of qSW5 is recessive, it might have acquired a defect but was selected by ancient human during domestication. NIL (qSW5) in Nipponbare background showed more than 10% reduced grain yield, possibly as a result of reduced grain width due to Kasalath qSW5 introgression.