Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice.

Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development. We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full-length OsXRNL and regulate miRNA abundance. We found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development. Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.

Engineering a New Chloroplastic Photorespiratory Bypass to Increase Photosynthetic Efficiency and Productivity in Rice.

Over the past few years, three photorespiratory bypasses have been introduced into plants, two of which led to observable increases in photosynthesis and biomass yield. However, most of the experiments were carried out using Arabidopsis under controlled environmental conditions, and the increases were only observed under low-light and short-day conditions. In this study, we designed a new photorespiratory bypass (called GOC bypass), characterized by no reducing equivalents being produced during a complete oxidation of glycolate into CO2 catalyzed by three rice-self-originating enzymes, i.e., glycolate oxidase, oxalate oxidase, and catalase. We successfully established this bypass in rice chloroplasts using a multi-gene assembly and transformation system. Transgenic rice plants carrying GOC bypass (GOC plants) showed significant increases in photosynthesis efficiency, biomass yield, and nitrogen content, as well as several other CO2-enriched phenotypes under both greenhouse and field conditions. Grain yield of GOC plants varied depending on seeding season and was increased significantly in the spring. We further demonstrated that GOC plants had significant advantages under high-light conditions and that the improvements in GOC plants resulted primarily from a photosynthetic CO2-concentrating effect rather than from improved energy balance. Taken together, our results reveal that engineering a newly designed chloroplastic photorespiratory bypass could increase photosynthetic efficiency and yield of rice plants grown in field conditions, particularly under high light.

De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.

Oxalate accumulation and regulation is independent of glycolate oxidase in rice leaves.

Cellular oxalate, widely distributed in many plants, is implicated to play important roles in various functions and is also known to affect food qualities adversely in fruits and vegetables. How oxalate is regulated in plants is currently not well understood. Glycolate oxidase (GLO) has long been considered as an important player in oxalate accumulation in plants. To gain further insight into the biochemical and molecular mechanisms, the possible roles of GLO in the process were studied. Drastically different levels of oxalate could be achieved by treating rice with various nitrogen forms (nitrate versus ammonium). While nitrate stimulated oxalate accumulation, ammonium reduced its level. Such treatments resulted in similar pattern changes for some other related organic acids, such as glycolate, oxaloacetate, and malate. By feeding plants with exogenous glycolate it was possible almost completely to restore the ammonium-decreased oxalate level. Under the two treatments few differences were observed for GLO mRNA levels, protein levels, and in vitro activities. Both K(m) for glycolate/glyoxylate and K(i) for oxalate remained almost the same for GLO purified from either nitrate- or ammonium-fed leaves. A further in vivo study, with transgenic plants carrying an estradiol-inducible GLO antisense gene, showed that, while the estradiol-induced antisense expression remarkably reduced both GLO protein levels and activities, oxalate levels were not significantly altered in the estradiol-treated transgenic plants. Taken together, it is suggested that oxalate accumulation and regulation is independent of GLO in rice leaves.