To investigate whether allelic constitution at the DEP1 locus affects grain yield, we compared DEP1 and dep1 NIL line field performance (Fig. 3a–c). The lines did not differ from one another with respect to either the heading date, the length of the grain-filling period or culm number (Fig. 3d). However, grain number per main panicle was significantly higher in the presence of dep1 (Fig. 3c), and there were clear differences in panicle architecture, inflorescence internode and panicle length (Fig. 3b,e), and the number of both primary (Fig. 3b,f) and secondary (Fig. 3g) branches per panicle. Increasing the number of grains can be associated with incomplete grain filling, but there was no evidence for grain-filling failure in the presence of dep1. The 1,000-grain weight of NIL-dep1 plants was slightly less than that of NIL-DEP1 plants (Fig. 3h), but the overall grain yield per plant under field conditions was increased (+40.9%) (Fig. 3i). The vascular system of NIL-dep1 plants appeared rather better developed and their sclerenchyma cell walls were thicker at maturity than those in NIL-DEP1 plants (Supplementary Fig. 6 online). These traits are favorable for both water transport capacity and the mechanical strength of the stem, both of which are important factors for the breeding of high-yielding, lodging-resistant varieties.We tested the effect of dep1 on grain yield in an indica background by backcrossing the dep1 segment present in the japonica variety Wuyunjing 7 into the indica variety Zhefu 802. This NIL, ZF 802 (dep1), produced more grains per panicle and out-yielded its recurrent parent (Supplementary Fig. 7 online). Thus, dep1 is a useful allele for increasing grain yield in rice.