There is an urgent need for agricultural systems to intensify sustainably, increasing crop productivity, farmer livelihoods and soil health while using fewer resources. Crop perennialization, the conversion of especially annual grains to perennial forms, has shown such possibility. Here we report the successful breeding of perennial rice and assess its performance and potential. Domesticated, annual Asian rice (Oryza sativa) was hybridized with its perennial African relative Oryza longistaminata. From a single planting, irrigated perennial rice produced grain for eight consecutive harvests over four years, averaging 6.8 Mg ha⁻¹ harvest⁻¹ versus the 6.7 Mg of replanted annual rice, which required additional labour and seed. Four years of cropping with perennial rice resulted in soils accumulating 0.95 Mg ha^–1 yr^–1 organic carbon and 0.11 Mg ha⁻¹ yr⁻¹ nitrogen, along with increases in soil pH (0.3–0.4) and plant-available water capacity (7.2 mm). Perennial cultivars are strongly preferred by farmers; growing them saves 58.1% of labour and 49.2% of input costs in each regrowth cycle. In 2021, perennial rice was grown on 15,333 ha by 44,752 smallholder farmers in southern China. Suited to a broad range of frost-free environments between 40° N and 40° S, perennial rice is a step change with potential to improve livelihoods, enhance soil quality and inspire research on other perennial grains.

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.

Rice (Oryza sativa) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous O. longistaminata genome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 331-Mb telomere-to-telomere (T2T) genome assembly for this species using a hybrid approach combining PacBio HiFi, Hi-C, and CycloneSEQ ultra-long reads, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between O. longistaminata, O. glaberrima, and O. sativa. A total of 2,466 segmentally duplicated genes were enriched in cellular amino acid metabolic processes. We detected slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of O. longistaminata provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.

Significantly increasing crop yield is a major and worldwide challenge for food supply and security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide. Yet, the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery. Here, we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group. We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method, i.e., dynamic cross-tissue (DCT) network analysis. We used one of the candidate genes, OsSPL4, whose function was previously unknown, for gene editing experimental validation of the high yield, and confirmed that OsSPL4 significantly affects panicle branching and increases the rice yield. This study, which included extensive field phenotyping, cross-tissue systems biology analyses, and functional validation, uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice. The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample. DCT can be downloaded from https://github.com/ztpub/DCT.

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.