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

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. Overall design: Analysis of small RNA transcriptome in 118 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates); Analysis of mRNA transcriptome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates); Analysis of mRNA degradome in eight libraries (2 genotypes × 4 treatments × 1 time-point × 1 pool of 3 biological replicates)