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

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.