The rice orthologue of maize domestication geneTeosinte branched 1(Tb1) affects tillering. But, unlike maizeTb1gene, it was not selected during domestication. Here, we report that anOsTb1duplicate gene (OsTb2) has been artificially selected during upland rice adaptation and that natural variation inOsTb2is associated with tiller number. Interestingly, transgenic rice overexpressing this gene shows increased rather than decreased tillering, suggesting thatOsTb2gains a regulatory effect opposite to that ofOsTb1following duplication. Functional analyses suggest that the OsTb2 protein positively regulates tillering by interacting with the homologous OsTb1 protein and counteracts the inhibitory effect of OsTb1 on tillering. We further characterize two functional variations withinOsTb2that regulate protein function and gene expression, respectively. These results not only present an example of neo-functionalization that generates an opposite function following duplication but also suggest that theTb1homologue has been selected in upland rice.

The genetic control of plant architecture in crops is critical for agriculture and understanding morphological evolution. This study showed that an open reading frame (ORF) of the rice domestication gene PROG1 appeared 3.4–3.9 million years ago (Mya). Subsequently, it acquired a novel protein-coding gene function in the genome of O. rufipogon (~0.3–0.4 Mya). This extremely young gene and its paralogous C2H2 genes located nearby define the prostrate architecture of O. rufipogon and, thus, are of adaptive significance for wild rice in swamp and water areas. However, selection for dense planting and high yield during rice domestication silenced the PROG1 gene and caused the loss of the RPAD locus containing functional C2H2 paralogs; hence, domesticated lines exhibit an erect plant architecture. Analysis of the stepwise origination process of PROG1 and its evolutionary genetics revealed that this zinc-finger coding gene may have rapidly evolved under positive selection and promoted the transition from non- or semi-prostrate growth to prostrate growth. A transgenic assay showed that PROG1 from O. rufipogon exerts a stronger function compared with PROG1 sequences from other Oryza species. However, the analysis of the expression levels of PROG1 in different Oryza species suggests that the transcriptional regulation of PROG1 has played an important role in its evolution. This study provides the first strong case showing how a fundamental morphological trait evolved in Oryza species driven by a gene locus.

There are two ecotypes, upland rice and irrigate rice, during its evolution in rice. Upland rice exhibits aerobic adaptive phenotype via its stronger root system and more rapid drought responses compared with its counterpart, irrigated rice. We assessed the functional variation and applications of the aerobic adaptive allele OsNCED2 ^T cloned from IRAT104 which is a cultivar of upland rice. OsNCED2 -overexpressing transgenic rice and OsNCED2 ^T -NILs exhibited significantly higher ABA contents at the seedling and reproductive stages, which can improve root development (RD) and drought tolerance (DT) to promote aerobic adaptation in upland rice. RNA-Seq-based expression profiling of transgenic versus wild-type rice identified OsNCED2- mediated pathways that regulate RD and DT. Meanwhile, OsNCED2 -overexpressing rice exhibited significantly increased reactive oxygen species (ROS)-scavenging abilities and transcription levels of many stress- and development-related genes, which regulate RD and DT. A SNP mutation (C to T) from irrigated rice to upland rice, caused the functional variation of OsNCED2 , and the enhanced RD and DT mediated by this site under aerobic conditions could promote higher yield of upland rice. These results show that OsNCED2 ^T , through ABA synthesis, positively modulates RD and DT which confers aerobic adaptation in upland rice and might serve as a novel gene for breeding aerobic adaptive or water-saving rice.