Increasing effective panicle number per plant (EPN) is one approach to increase yield potential in rice. However, molecular mechanisms underlying EPN remain unclear. In this study, we integrated map-based cloning and genome-wide association analysis to identify the EPN4 gene, which is allelic to NARROW LEAF1 (NAL1). Overexpression lines containing the Teqing allele (TQ) of EPN4 had significantly increased EPN. NIL-EPN4^TQ in japonica (geng) cultivar Lemont (LT) exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT. Haplotype analysis indicated that accessions with EPN4-1 had medium EPN, medium grain number, and medium grain weight, but had the highest grain yield among seven haplotypes, indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield. Furthermore, accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations. Therefore, pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.

The Asian cultivated rice Oryza sativa can be classified into two major subspecies: japonica/geng and indica/xian. There are large physiological and phenotypic differences between the two subspecies, with each having its advantages and disadvantages. Understanding the differences between xian and geng could provide a foundation for cultivar improvement based on hybridization between subspecies in order to synthesize favorable traits. We review the origin and domestication of xian and geng rice, compare their differences in terms of physiological and phenotypical traits, and describe the molecular mechanism differences between the subspecies. Based on this knowledge, we propose an ideal plant architecture of geng rice varieties for northern regions.