Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

Abstract

Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus’ flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses.

Brachypodium: 20 years as a grass biology model system; the way forward?

“…This aligned with a niche competition hypothesis [33] that suggests the favouring of the newly formed allotetraploids in non-native habitats. Nonetheless, population analyses indicate that climate niche parameters and functional and phenotypic eco-physiological responses to environmental stress are more genotype-dependent within each species [32,34,35]. Phylogenomics of the pangenome has revealed up to five highly divergent Mediterranean lineages, which split from the common ancestor 0.16 Ma [27,36,37], showing some signs of geographic structure coupled with frequent long-distance dispersals.…”

“…Nonetheless, the extraordinary natural diversity of B. distachyon and its robust pangenome has served to launch a variety of studies into the sources of variation. These include potential interlineage isolation caused by different flowering times [36], the influence of the individual TEs in the genetic and epigenetic constitution of the host genomes [39] (Box 2), and drought stress [34]. Such studies illustrate ongoing intraspecific evolution of this Brachypodium species and how shifts in biodiversity could show the impact of environmental change.…”

“…At its most basic, an examination of Brachypodium inbred lines grown under range of soil % moisture contents indicated a nonlinear relationship, so simple pairwise comparisons between droughted and fully watered plants could be insufficient [75]. The variation in responses to drought in Brachypodium accessions has been assessed [34,76,77] and, in one case, the degree of drought tolerance related to rainfall in the original sampling sites [78]. The transcriptomic and metabolomic responses of B. distachyon to drought have been characterised and, amongst many changes, suggested the importance of the cell wall [76,79].…”

Patterns of pan-genome occupancy and gene co-expression under water-deficit in Brachypodium distachyon

“…21 out of the 25 most strongly upregulated genes did not cluster with other genes in the drought co-expression network (i.e., they were members of the grey D0 module), while the majority of these strongly upregulated genes did cluster in a module in the water network (Table S7). The 25 most strongly upregulated genes by drought showed a range of predicted functions which included two predicted dehydrins (Decena et al 2021), two ABA-associated proteins, and two lipid transfer proteins (LTPs) (Table S7). LTPs were among the most highly induced transcripts in an Arabidopsis thaliana experiment that imposed very similar soil drying conditions to those imposed in the present study (Des Marais et al, 2012).…”

Bioengineering and Molecular Biology of Miscanthus

“…In some species, it can convert caffeine-CoA into caffeic acid, but there are no orthologs in the genomes of B. distachyon, Z. mays and S. bicolor [48]. Devi et al showed that this diversity underscores the necessity to comprehend monolignol biosynthetic pathways in all lignocellulose cultures [21].…”