OsPPG encodes a pseudouridine-5'-phosphate glycosidase and regulates rice spikelet development

Florets are the basic structural units of spikelets,and their morphogenesis determines the yield and quality of rice grains.However,whether and how pseudouridine-5’-phosphate glycosidase participates in rice spikelet development remains an open question.In this study,we identified a novel gene,OsPPG,which encodes a peroxisome-localized pseudouridine-5’-phosphate glycosidase and regulates the development of rice spikelets.osppg mutants exhibited abnormal sterile lemma,lemma,palea,lodicule,stamens,and pistils;male sterility;shorter panicles;and reduced plant height.OsPPG was found to regulate several OsMADS genes,thereby affecting the morphogenesis of rice spikelets.Furthermore,metabolomics revealed that the OsPPG gene was involved in the decomposition of pseudouridine via the pyrimidine metabolism pathway and may affect the jasmonic acid signaling pathway.These results suggest that OsPPG is a key regulator of rice spikelet development.

Two novel gene-specific markers at the Pik locus facilitate the application of rice blast resistant alleles in breeding

Blast,a disease caused by Magnaporthe oryzae,is a major constraint for rice production worldwide.Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to control the disease.The blast resistance Pik locus,located on chromosome 11,contains at least six important resistance genes,but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs due to their limited scope of application.In this study,two PCR-based markers,Pikp-Del and Pi1-In,were developed to target the specific In Del(insertion/deletion)of the Pik-p and Pi-1 genes,respectively.The two markers precisely distinguished Pik-p,Pi-1,and the K-type alleles at the Pik locus,which is a necessary element for functional genes from rice varieties.Results also revealed that only several old varieties contain the two genes,of which nearly half carry the K-type alleles.Therefore,these identified varieties can serve as new gene sources for developing blast resistant rice.The two newly developed markers will be highly useful for the use of Pik-p,Pi-1 and other resistance genes at the Pik locus in markerassisted selection(MAS)breeding programs.

Changes in bacterial community and abundance of functional genes in paddy soil with cry1Ab transgenic rice

A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16 S rRNAbased Illumina Mi Seq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted Uni Frac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted Uni Frac distance, indicated that the above separations between line GM and cultivar M were statistically significant(P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina Mi Seq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amo A gene, archaeal amo A gene and denitrifying bacterial nir K gene significantly increased(P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.

Rice sl-MH-1 mutant induces cell death and confers blast resistance via the synergistic roles of signaling systems

Serotonin is ubiquitous across all forms of life and functions in responses to biotic and abiotic stresses.In rice,the conversion of tryptamine to serotonin is catalyzed by Sekiguchi lesion(SL).Previous studies have identified an sl mutation(a null mutation of SL)in several rice varieties and confirmed its increase of resistance and cell death.However,a systematic understanding of the reprogrammed cellular processes causing cell death and resistance is lacking.We performed a multi-omics analysis to clarify the fundamental mechanisms at the protein,gene transcript,and metabolite levels.We found that cell death and Magnaporthe oryzae(M.oryzae)infection of the sl-MH-1 mutant activated plant hormone signal transduction involving salicylic acid(SA),jasmonic acid(JA),and abscisic acid(ABA)in multiple regulatory layers.We characterized the dynamic changes of several key hormone levels during disease progression and under the cell death conditions and showed that SA and JA positively regulated rice cell death and disease resistance.SL-overexpressing lines confirmed that the sl-MH-1 mutant positively regulated rice resistance to M.oryzae.Our studies shed light on cell death and facilitate further mechanistic dissection of programmed cell death in rice.

Efficacy of insect-resistance Bt/Cp TI transgenes in F5–F7generations of rice crop–weed hybrid progeny: implications for assessing ecological impact of transgene flow

Ecological impact of transgene flow into populations of wild/weedy relatives is associated with fitness effects in hybrid progeny. Most studies assessing fitness effects focus essentially on early-generation hybrid progeny. However, whether the transgenes remain effective and durable in advanced generations of hybrid progeny remains unclear. We conducted a common garden experiment with F5–F7hybrid progeny derived from crosses between insect-resistant transgenic(Bt/Cp TI) rice and weedy rice, to examine their insect resistance and fitness effects of transgenes on progeny. Hybrid progeny were grown under different insect pressures and cultivation modes where insect damage and fitness-related traits were measured in the same growth season. Plants with transgenes showed significantly lower insect damage(10 % vs.32 %) and higher fecundity(551 vs. 392 seeds/plant) than those without transgenes in F5–F7populations, suggesting the efficacy of transgenes for insect resistance. Fitness benefits of the transgenes were similar among the F5–F7populations, indicating the stability of transgenic effects. A positive correlation between insect index and fecundity change was detected, stressing the important role of ambient insect pressures in assessing fitness effects caused by insect-resistance transgenes. Our results have importantimplications for assessing ecological impacts caused by transgene flow to wild/weedy relatives. For cost-effectiveness, the experimental estimation of fitness effects is probably sufficient based on data from hybrids in early generations. Given that fitness effects of insect-resistance transgenes are associated with ambient insect pressure,ecological risk assessment on transgene flow should consider this variable in experimental design, reasonably reflecting actual situations in wild/weedy populations.

Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome∞

Continuously increasing global temperatures present great challenges to food security.Grain size,one of the critical components determining grain yield in rice(Oryza sativa L.),is a prime target for genetic breeding.Thus,there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress.However,quantitative trait loci(QTLs)endowing heat stress tolerance and grain size in rice are extremely rare.Here,we identified a novel negative regulator with pleiotropic effects,Thermo‐Tolerance and grain Length 1(TTL1),from the super pan‐genomic and transcriptomic data.Loss‐of‐function mutations in TTL1 enhanced heat tolerance,and caused an increase in grain size by coordinating cell expansion and proliferation.TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane.Furthermore,haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars.Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies,but still had much breeding potential for increasing grain length and thermotolerance.These findings provide insights into TTL1 as a novel potential target for the development of high‐yield and thermotolerant rice varieties.

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression （SAGE） revealed 1183 differentially expressed genes （DGs）, among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F1 hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F1 hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci （QTL）, a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

Limited ecological risk of insect-resistance transgene flow from cultivated rice to its wild ancestor based on life-cycle fitness assessment

Ecological impact caused by transgene flow from genetically engineered(GE) crops to their wild relatives is largely determined by the fitness effect brought by a transgene. To estimate such impact is critical for the ecological risk assessment prior to the commercialization of GE crops. We produced F1 and F2hybrid descendants from crosses of two insect-resistant GE rice lines(Bt, Bt/Cp TI)and their non-GE rice parent with a wild rice(Oryza rufipogon) population to estimate the transgenic fitness. Insect damages and life-cycle fitness of GE and non-GE crop–wild hybrid descendants as well as their wild parent were examined in a common-garden experiment. No significant differences in insect damages were observed between the wild rice parent and GE hybrid descendants under highinsect pressure. The wild parent showed significantly greater relative survival-regeneration ratios than its GE and non-GE hybrid descendants under both high- and low-insect pressure. However, more seeds were produced in GE hybrid descendants than their non-GE counterparts under high-insect pressure. Given that the introduction of Bt and Bt/Cp TI transgenes did not provide greater insect resistance to crop–wild hybrid descendants than their wild parent, we predict that transgene flow from GE insect-resistant rice to wild rice populations may not cause considerable ecological risks.