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Multi-omics analysis of small RNA, transcriptome and degradome in T. turgidum – regulatory networks of grain development and abiotic stress response

ABSTRACT: Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. turgidum developing grains, under single and combined water-deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNA (DEMs) specific to genotypes, stress types and different reproductive time-points are provided. The first degradome-seq report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome-seq profiled 53,146 T. turgidum genes, with differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development and hormone transduction pathways. miRNA-mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed, based on integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.

ORGANISM(S): Triticum turgidum subsp. durum

PROVIDER: GSE153932 | GEO | 2020/10/19

REPOSITORIES: GEO

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Project description:Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. Yield loss in durum wheat can be exacerbated due to minimal rainfall in the early reproductive stages of development during Spring in Australia. This study describes genotypic differences in the miRNAome between water deficit tolerant/sensitive durum, using flag leaf and developing head tissue, and more specifically identifies miRNAs associated with water deficit stress. Results: Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes (Tamaroi, Yawa, EGA Bellaroi, Tjilkuri), with or without water deficit stress. Illumina sequencing and subsequent analysis detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of the abundance of sequencing reads revealed 66 conserved miRNAs and five novel miRNA hairpins showing differential expression under water deficit stress. During stress, several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes studied. Several miRNAs were also identified to have different abundance in the flag leaf compared to the developing head regardless of treatment. Predicted mRNA targets from four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development. Conclusion: For the first time, we present a comprehensive study of the miRNA transcriptome of flag leaf and developing head tissues in different durum genotypes under water deficit stress. The identification of differentially expressed miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotype-specific physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs identified, and their interaction with mRNA targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.

Project description:Durum wheat requires high nitrogen inputs to obtain the high protein concentration necessary to satisfy pasta and semolina quality criteria. Optimizing plant nitrogen use efficiency is therefore of major importance for wheat grain quality. Here, we studied the impact on grain yield, protein concentration, and for the first time on protein composition of a marine (DPI4913) and a fungal (AF086) biostimulants applied to plant leaves. Plants were grown in a greenhouse and sampled at maturity for grain analysis. The protein concentration and quantity in grains per plant were determined, as well as water-use efficiency. A large-scale quantitative proteomics study of wheat flour samples was performed to determine the effect of biostimulant treatment on grain protein composition. Grain dry biomass and protein quantity were increased by 23.9% and 24.8% respectively with DPI4913, and by 27.4% and 25.9%, respectively, with AF086. A total of 1471 proteins were identified and 1391 were quantified. Quantitative proteomics analysis revealed 26 and 38 proteins with a significantly varying abundance after DPI4913 and AF086 treatment, respectively. Among these, 14 proteins were affected by both DPI4913 and AF086 treatments. The highest variations in proteins abundances were found for proteins involved in grain technological properties such as grain hardness, in storage functions with the substantial over-representation of the gluten protein gamma-gliadin, in regulation processes with the over-representation of proteins that play a transcription regulator role, and in stress responses with the over-representation of proteins implied in biotic and abiotic stress defense. The involvement of biostimulants in the abiotic stress response is suggested by the increase in water-use efficiency for DPI4913 treatment (15.4%) and for AF086 treatment (9.9%). In conclusion, our work, performed in greenhouse, has shown that DPI4913 and AF086 treatments promote grain yield while maintaining protein concentration in grains, and positively affect protein composition in term of grain quality. This study suggests that these biostimulants could be used to optimize durum wheat production and quality in field conditions.

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Multi-omics analysis of small RNA, transcriptome and degradome in T. turgidum – regulatory networks of grain development and abiotic stress response

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