Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement

The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus

One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.

Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications

The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.

Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice

Partial root-zone drying (PRD) is an effective water-saving irrigation strategy that improves stress tolerance and facilitates efficient water use in several crops. It has long been considered that abscisic acid (ABA)-dependent drought resistance may be involved during partial root-zone drying. However, the molecular mechanisms underlying PRD-mediated stress tolerance remain unclear. It's hypothesized that other mechanisms might contribute to PRD-mediated drought tolerance. Here, rice seedlings were used as a research model and the complex transcriptomic and metabolic reprogramming processes were revealed during PRD, with several key genes involved in osmotic stress tolerance identified by using a combination of physiological, transcriptome, and metabolome analyses. Our results demonstrated that PRD induces transcriptomic alteration mainly in the roots but not in the leaves and adjusts several amino-acid and phytohormone metabolic pathways to maintain the balance between growth and stress response compared to the polyethylene glycol (PEG)-treated roots. Integrated analysis of the transcriptome and metabolome associated the co-expression modules with PRD-induced metabolic reprogramming. Several genes encoding the key transcription factors (TFs) were identified in these co-expression modules, highlighting several key TFs, including TCP19, WRI1a, ABF1, ABF2, DERF1, and TZF7, involved in nitrogen metabolism, lipid metabolism, ABA signaling, ethylene signaling, and stress regulation. Thus, our work presents the first evidence that molecular mechanisms other than ABA-mediated drought resistance are involved in PRD-mediated stress tolerance. Overall, our results provide new insights into PRD-mediated osmotic stress tolerance, clarify the molecular regulation induced by PRD, and identify genes useful for further improving water-use efficiency and/or stress tolerance in rice.

Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data

Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N⁶-methyladenosine (m⁶A) modification, suggesting a clear indication between alternative 3′UTR and m⁶A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.

Correction to: Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement

[This corrects the article DOI: 10.1186/s13068-019-1612-7.].