Vardanega, I. | bioRxiv Science

bioRxiv2023

The transcriptome landscape of developing barley seeds reveals H3K27me3 dynamics in endosperm tissues

Cereal grains are an important food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley, we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination. Weighted gene co-expression network and motif enrichment analyses pointed out specific groups of genes and transcription factors with possible impacts on regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of transcription factors for functional studies of the pathways controlling barley grain development. Assessment of selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely to play a major role during barley endosperm development. Repressive modification H3K27me3 is globally reduced in endosperm tissues and at specific developmental and storage compound genes. Altogether, this atlas uncovers the complexity of the developmental regulation of gene expression in barley grains. TeaserSpatiotemporal profiling of developing barley seeds revealed loss of H3K27me3 and changes in gene expression in endosperm.

plant biology↗

bioRxiv2021

ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIVE containing protein that controls root growth angle in barley and wheat

The root growth angle defines how roots grow towards the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience and as a consequence yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin independent higher responsiveness to gravity compared to wild type plants. We cloned the EGT2 gene by a combination of bulked segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. Subcellular localization experiments revealed that EGT2 localizes to the nucleus and cytoplasm. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA-seq, we observed that seven expansin genes were transcriptionally downregulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals. Significance StatementTo date the potential of utilizing root traits in plant breeding remains largely untapped. In this study we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gravity which is conserved in barley and wheat and could be a promising target for crop improvement in cereals.

plant biology↗