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Background  The grain number per panicle (GNP), which is one of three grain yield components, is an important trait for the genetic improvement of rice. Although the  NAL1  and  GNP1  genes regulating the rice GNP and grain yield have been cloned, their allelic diversity, functional differences in rice germplasms, and effects of their combination on GNP and grain yield remain unclear.    Results  Based on DNA sequences of these two genes in 198 cultivated rice ( Oryza sativa ) and 8–10 wild rice ( Oryza rufipogon ) germplasms, 16 and 14 haplotypes were identified for  NAL1  and  GNP1 , respectively. The  NAL1  gene had the strongest effects on GNP in  indica  ( xian ) and  japonica  ( geng ) subpopulations. In contrast,  GNP1  had no significant effects in the  geng  subpopulation and was rare in the  xian  background, in which the superior  GNP1  allele ( GNP1 –6) was detected in only 4.0% of the 198 germplasms. Compared with the transgenic lines with  GNP1  or  NAL1 , the transgenic lines with both genes had a higher GNP (15.5%–25.4% and 11.6%–15.9% higher, respectively) and grain yield (5.7%–9.0% and 8.3%–12.3% higher, respectively) across 3 years. The two genes combined in the introgression lines in Lemont background resulted in especially favorable effects on the GNP.    Conclusions  Our results indicated that the  GNP1  and  NAL1  exhibited obvious differentiation and their combinations can significantly increase the grain yield in  geng  rice cultivars. These observations provide insights into the molecular basis of the GNP and may be useful for rice breeding of high yield potential by pyramiding  GNP1  and  NAL1 .

Natural Sequence Variations and Combinations of GNP1 and NAL1 Determine the Grain Number per Panicle in Rice