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 genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication. We generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Intriguingly, although the number of expressed genes varied little, the domestic species generally exhibited lower gene expression diversity than did the wild species, and this lower diversity was observed for both domestic plants and different kinds of domestic animals including insect, bird and mammal in the whole-genome gene set (WGGS), candidate selected gene set (CSGS) and non-CSGS, with CSGS exhibiting a higher degree of decreased expression diversity. Moreover, different from previous reports which found 2 to 4% of genes were selected by human, we identified 6892 candidate selected genes accounting for 7.57% of the whole-genome genes in rice and revealed that fewer than 8% of the whole-genome genes had been affected by domestication. Our results showed that domestication affected the pattern of variation in gene expression throughout the genome and generally decreased the expression diversity across species, and this decrease may have been associated with decreased genetic diversity. This pattern might have profound effects on the phenotypic and physiological changes of domestic animals and plants and provide insights into the genetic mechanisms at the transcriptome level other than decreased genetic diversity and increased linkage disequilibrium underpinning artificial selection.

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.

Grain weight and grain number, the two important yield traits, are mainly determined by grain size and panicle architecture in rice. Herein, we report the identification and functional analysis of OsSPL4 in panicle and grain development of rice. Using CRISPR/Cas9 system, two elite alleles of OsSPL4 were obtained, which exhibited an increasing number of grains per panicle and grain size, resulting in increase of rice yield. Cytological analysis showed that OsSPL4 could regulate spikelet development by promoting cell division. The results of RNA-seq and qRT-PCR validations also demonstrated that several MADS-box and cell-cycle genes were up-regulated in the mutation lines. Co-expression network revealed that many yield-related genes were involved in the regulation network of OsSPL4. In addition, OsSPL4 could be cleaved by the osa-miR156 in vivo, and the OsmiR156-OsSPL4 module might regulate the grain size in rice. Further analysis indicated that the large-grain allele of OsSPL4 in indica rice might introgress from aus varieties under artificial selection. Taken together, our findings suggested that OsSPL4 could be as a key regulator of grain size by acting on cell division control and provided a strategy for panicle architecture and grain size modification for yield improvement in rice.

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.