Conservation recommendations for Oryza rufipogon Griff. in China based on genetic diversity analysis

Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India

Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O. nivara (H' = 1.09) and O. rufipogon (H' = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (- 0.58) and panicle bearing tillers (- 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon's information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.

Red Rice Seed Coat Targeting SPHK2 Ameliorated Alcoholic Liver Disease via Restored Intestinal Barrier and Improved Gut Microbiota in Mice

Alcoholic liver disease (ALD), leading to the most common chronic liver diseases, is increasingly emerging as a global health problem, which is intensifying the need to develop novel treatments. Herein, our work aimed to estimate the therapeutic efficacy of red rice (Oryza sativa L.) seed coat on ALD and further uncover the underlying mechanisms. Red rice seed coat extract (RRA) was obtained with citric acid-ethanol and analyzed via a widely targeted components approach. The potential targets of RRA to ALD were predicted by bioinformatics analysis. Drunken behavior, histopathological examination, liver function, gut microbiota composition and intestinal barrier integrity were used to assess the effects of RRA (RRAH, 600 mg/kg·body weight; RRAL, 200 mg/kg·body weight) on ALD. Oxidative stress, inflammation, apoptosis associated factors and signaling pathways were measured by corresponding kits, Western blot and immunofluorescence staining. In ALD model mice, RRA treatment increased sphingosine kinase 2 (SPHK2) and sphingosine-1-phosphate (S1P) levels, improved gut microbiota composition, restored intestinal barrier, decreased lipopolysaccharide (LPS) levels in plasma and the liver, cut down Toll-like receptor 4 (TLR4)/Nuclear factor kappa B (NF-κB) pathways, alleviated liver pathological injury and oxidative stress, attenuated inflammation and apoptosis and enhanced liver function. To sum up, RRA targeting SPHK2 can ameliorate ALD by repairing intestinal barrier damage and reducing liver LPS level via the TLR4/NF-κB pathway and intestinal microbiota, revealing that red rice seed coat holds potential as a functional food for the prevention and treatment of ALD.

Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974

Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.

Agrobacterium-Mediated High-Efficiency Genetic Transformation and Genome Editing of Chaling Common Wild Rice (Oryza rufipogon Griff.) Using Scutellum Tissue of Embryos in Mature Seeds

Genetic transformation is an important strategy for revealing gene function, and it is used extensively in both functional genomics study and molecular breeding of rice. Demand for its application in wild Oryza species is rising for their extensive genetic diversity. However, genetic transformation of wild Oryza accessions with AA genome using calli induced from scutellum tissue of embryos in mature seeds has not been successfully established. In the present study, we used Chaling common wild rice (CLCWR) (Oryza rufipogon Griff.) with AA genome to successfully establish an Agrobacterium-mediated genetic transformation system based on scutellum tissue of embryos in mature seeds. The calli from embryos in mature seeds of CLCWR were easy to be induced and regenerated. The callus induction rate and texture were optimum under 2.5 mg/L 2,4-D. The optimal hormone combination used for regeneration was 2 mg/L ZT + 0.1 mg/L NAA. Studies on genetic transformation and genome editing showed that the transformation efficiency was 87-94%, the efficiency of single genome editing and multiplex genome editing were about 60-70% and 20-40%, respectively. Compared with Nipponbare (Nip), CLCWR had higher Hygromycin-resistant callus frequency and transformation efficiency. Taken together, our study establishes a highly efficient transformation system for common wild rice with AA genome and provides a good rice material for de novo domestication by genome editing in the future.

Dynamics of photosynthetic induction and relaxation within the canopy of rice and two wild relatives

Wild rice species are a source of genetic material for improving cultivated rice (Oryza sativa) and a means to understand its evolutionary history. Renewed interest in non-steady-state photosynthesis in crops has taken place due its potential in improving sustainable productivity. Variation was characterized for photosynthetic induction and relaxation at two leaf canopy levels in three rice species. The wild rice accessions had 16%-40% higher rates of leaf CO2 uptake (A) during photosynthetic induction relative to the O. sativa accession. However, O. sativa had an overall higher photosynthetic capacity when compared to accessions of its wild progenitors. Additionally, O. sativa had a faster stomatal closing response, resulting in higher intrinsic water-use efficiency during high-to-low light transitions. Leaf position in the canopy had a significant effect on non-steady-state photosynthesis, but not steady-state photosynthesis. The results show potential to utilize wild material to refine plant models and improve non-steady-state photosynthesis in cultivated rice for increased productivity.

Genetic Variation of Typical Plant Species in Hay Meadows: The Effect of Land Use History, Landscape Structure, and Habitat Quality

Global changes in land use are threatening the diversity of many ecosystems on both the intra- and interspecific levels. Among these ecosystems are the species-rich hay meadows, which have drastically declined in quality and quantity, due to land use intensification or abandonment in recent decades. The remaining genetic resources of their plant species must therefore be protected. To determine the driving forces impacting genetic variation in common hay meadow species (Dactylis glomerata, Heracleum sphondylium, andTrifolium pratense), we used data on the land use history, historic and present landscape structure and habitat quality. Our results showed average genetic diversity within the study sites, with low differentiation levels and a high gene flow among grasslands. Land use history, landscape structure and habitat quality were found to be related to the distribution of genetic diversity in the studied species, highlighting the complex forces acting in these ecosystems and showing the specific impact of litter accumulation on genetic diversity. Both historic and current environmental variables influence genetic diversity, demonstrating the importance of the land use history of a habitat. The most important group of variables impacting genetic variation in all three species was the landscape structure (e.g., distance to the nearest-located urban area or grassland). Also important was the influence of litter cover on genetic diversity inD. glomerata, which provides an interesting starting point for further research.