<em>Hordeum erectifolium</em>, a physiological and genomic study of drought-adaptive traits

Abstract

Drought stresses plants at multiple levels, affecting water uptake, stomatal evaporation, and intracellular stability, which in turn impacts plant fitness and yield. To develop climate-resilient crops, I investigated barley’s tertiary gene pool, focusing on the crop wild relative <em>Hordeum erectifolium</em>. <br/> First, I explored leaf anatomy of <em>H. erectifolium</em>, <em>H. vulgare cv.</em> Morex, a modern cultivar, and a wild accession of barley <em>H. vulgare spontaneum</em> B1K-04-12. I found anatomical characteristics only in the leaves of <em>H. erectifolium</em> which have been described as adaptive to xeric conditions. <br/> Next, I generated a chromosomal scale reference genome of <em>H. erectifolium</em> using Oxford Nanopore Technology long-read sequencing, and structural gene annotation was aided by tissue-specific PacBio IsoSeq full-length transcript sequencing. Comparing the three genomes, I investigated chromosomal structural rearrangements and the composition of long terminal repeats retrotransposons. <br/> Further, I compared the hierarchical phylogenetic orthologs of seven monocot species and one dicot for genetic signatures for gene gain or loss of abiotic stress-related gene families on the phylogenetic branch of <em>H. erectifolium</em>. I uncovered gene family expansions related to adaptation to drought, saline, and cold tolerance. <br/> Lastly, I investigated the transcriptional response of <em>H. erectifolium</em> and Morex during a controlled dry-down drought and recovery experiment in soil. Transcriptional changes were detected on the second day of dry-down in Morex but not in <em>H. erectifolium</em>, and most differentially regulated genes in <em>H. erectifolium</em> reached control expression levels 24 hours after rewatering, but not in Morex. During dry-down, <em>H. erectifolium</em> was enriched in pathways related to photosynthesis, detoxification, and various localizations and transport. Whereas, Morex was mainly enriched in the biosynthesis of small molecules and proteins. The enriched pathways in <em>H. erectifolium</em> hinted at the capacity for drought tolerance. <br/> This work thus demonstrates the potential of <em>H. erectifolium</em> as a model species for extensive drought adaptation. It shows the morphological and genetic complexities for adaptations to xeric environments and illustrates how the tertiary gene pool of barley can be used to study anatomical, physiological, and genetic features that can aid in producing stress-resilient crops.