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.

Rice (Oryza sativa. L) is more sensitive to drought stress than other cereals, and large genotypic variation in drought tolerance (DT) exists within the cultivated rice gene pool and its wild relatives. Selective introgression of DT donor segments into a drought-sensitive (DS) elite recurrent parent by backcrossing is an effective way to improve drought stress tolerance in rice. To dissect the molecular mechanisms underlying DT in rice, deep transcriptome sequencing was used to investigate transcriptome differences among a DT introgression line H471, the DT donor P28, and the drought-sensitive, recurrent parent HHZ under drought stress. The results revealed constitutively differential gene expression before stress and distinct global transcriptome reprogramming among the three genotypes under a time series of drought stress, consistent with their different genotypes and DT phenotypes. A set of genes with higher basal expression in both H471 and P28 compared with HHZ were functionally enriched in oxidoreductase and lyase activities, implying their positive role in intrinsic DT. Gene Ontology analysis indicated that common up-regulated genes in all three genotypes under mild drought stress were enriched in signaling transduction and transcription regulation. Meanwhile, diverse functional categories were characterized for the commonly drought-induced genes in response to severe drought stress. Further comparative transcriptome analysis between H471 and HHZ under drought stress found that introgression caused wide-range gene expression changes; most of the differentially expressed genes (DEGs) in H471 relative to HHZ under drought were beyond the identified introgressed regions, implying that introgression resulted in novel changes in expression. Co-expression analysis of these DEGs represented a complex regulatory network, including the jasmonic acid and gibberellin pathway, involved in drought stress tolerance in H471. Comprehensive gene expression profiles revealed that genotype-specific drought induced genes and genes with higher expression in the DT genotype under normal and drought conditions contribute jointly to DT improvement. The molecular genetic pathways of drought stress tolerance uncovered in this study, as well as the DEGs co-localized with DT-related QTLs and introgressed intervals, will serve as useful resources for further functional dissection of the molecular mechanisms of drought stress response in rice.

Perennial grain crops hold the promise of stabilizing fragile lands, while contributing grain and grazing in mixed farming systems. Recently, perennial rice was reported to successfully survive, regrow, and yield across a diverse range of environments in Southern China and Laos, with perennial rice PR23 being identified as a prime candidate for release to farmers. This paper reports the evaluation of PR23 for release, by (1) comparing its survival, regrowth, performance, and adaptation with preferred annual rices across nine ecological regions in southern Yunnan Province of China; (2) examining the economic costs and benefits of perennial versus annual rice there; and (3) discussing the evidence for the release of PR23 as a broadly adapted and acceptable cultivar for farmers. Overall, the grain yield of PR23 was similar to those of the preferred annual rice cultivars RD23 and HXR7, but the economic analysis indicated substantial labour savings for farmers by growing the perennial instead of the annual. PR23 was comparable to the annuals in phenology, plant height, grain yield, and grain size, and was acceptable in grain and cooking quality. Farmers were keen to grow it because of reduced costs and especially savings in labour. PR23 is proposed for release to farmers because of its comparable grain yields to annual rices, its acceptable grain and milling quality, its cost and labour savings, and the likely benefits to soil stability and ecological sustainability, along with more flexible farming systems.

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.

Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of O. officinalis were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from O. officinalis tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including Desulfomonile and Ruminiclostridium for roots; Lactobacillus, Acinetobacter, Cutibacterium and Dechloromonas for stems; and Stenotrophomonas, Chryseobacterium, Achromobacter and Methylobacterium for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from O. officinalis. Among them, 11 strains identified as Enterobacter mori, E. ludwigii, E. cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae and Kosakonia oryzae were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of O. officinalis and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.