No abstract

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 .

A total of 420 individuals belonged to 18 native teak (Tectona grandis L.f.) provenances from all four distributed countries and 10 introduced provenances were analyzed to for genetic variation, structure and genetic origin using SSR markers. The unbiased gene diversity for each provenance ranged from 0.4692 to 0.8523 with a mean value 0.6612, showing high variation within teak provenances and variation in India provenances was highest than in other countries’ provenances.AMOVA analysis showed that the majority of variation existed within provenances (84.760%) and also substantial variation among countries (10.586%). As more as possible plus trees from large population should be selected or conserved in order to keep genetic variability for future improvement. Different countries populations should be preserved in the natural habitat or collected for ex site conservation with cooperation and region-wise strategies.A Mantel test revealed significant correlation between genetic distances and geographic distances of teak provenances (R=0.7355, P<0.001). The cluster analyses by UPGMA, PCA and STRUCTURE methods gave very similar results, showing India provenances were firstly differentiated, and Laos provenances clustered with Thailand provenances, then introduced provenances and Myanmar provenances successively joined in the clusters. The introduced provenances no. 19, 20, 22, 23, 25, 27 and 28 appeared to be very closely linked to Laos provenances (especially no. 17) and Thailand provenances (especially no. 5 and 6), while provenances no. 21, 24, 26 may be originated from Myanmar provenance (especially no. 16).

To tackle food insecurity faced by an ever-growing population, there is an urgent need to develop new forms of highly productive and ecologically-secure agricultural systems. Crop perennialization provides a novel and promising solution to both food security and environmental challenges. Compared with annual grain production systems, which often undermine basic ecosystem services, perennial crops could maintain important ecosystem functions and reduce agricultural inputs. Here, we report our successful breeding of perennial rice (PR) taking over 20 years. We introduced perennial growth into domesticated Asian rice by interspecific hybridization and subsequently developed several perennial cultivars that have been commercialized recently in China and successfully trialed in multiple countries. The perennial cultivars produce yields comparable to commercialized annual rice (AR) varieties and maintain them for 4-5 consecutive years from a single planting. They exhibit robust regrowth, acceptable grain and milling quality, and are strongly preferred by farmers. We also quantified the social-economic, ecological and soil benefits attributable to perennial rice cultivation. Finally, we estimated the geographical areas potentially suitable for perennial rice cultivation worldwide, based on the correlation between regrowth rate and over-winter temperatures. Our innovation would help maintain food security and ecological integrity, and also inspire research on other perennial grains.

Oryza longistaminata is the only AA-genome Oryza species that is perennial via rhizome production. This undomesticated rice species, which is native to Africa, is hypothesized to be a good candidate for expanding the cultivated rice gene pool. However, its phylogenetic relationships with other Oryza members are still unresolved, and it is underutilized as a genetic resource in the breeding of cultivated rice (Oryza sativa L.). This study therefore genotyped 361 O. longistaminata, 35 cultivated rice, 1 Japonica weedy-type, 25 AA genome and 8 CC genome wild rice accessions by using 67 SSR markers. Genotypic grouping confirmed the distinctness of O. longistaminata from other rice accessions and the sub-differentiation of this population influenced by eco-geographical conditions. The higher genetic diversity within the O. longistaminata population also implies its candidacy as a donor of diverse traits of interest.