Abiotic stress is any deviation from optimum growth conditions for plants caused by non-biological factors such as water, temperature, nutrients, salts, or light. Such stresses have been important drivers of plant adaptation in ecological settings and are important constraints on global agricultural yield. Climate change is projected to increase the frequency and severity of abiotic stress events in the future, including extreme weather events such as droughts and temperature fluctuations, as well as desertification and soil salinization, which will negatively impact agriculture. Many major crops, such as maize, wheat, rice, barley, and sorghum among others, are found in the grass family, Poaceae, which contains over 11,000 species and is also highly ecologically important. In particular, the subfamily Chloridoideae is highly resilient and contains most of the desiccation tolerant grasses. Understanding the mechanisms of abiotic stress response in both cereal crops and naturally resilient grasses is therefore important for improvement of agricultural resilience in the face of climate change. Each chapter of this dissertation examines abiotic stress response in one or more grass species from a genomics perspective. Chapter 1 gives an overview of abiotic stress responses and adaptations in the grasses, including desiccation tolerance, the ability to survive near-complete drying, which is found in 40 grass species. Chapter 1 also discusses the status of genome sequencing in the grasses; approximately 1% of the species in the family have at least one reference genome, with several important crops such as maize and wheat having multiple reference genomes for different genotypes. Chapter 2 is a meta-analysis of approximately 1,900 RNA-sequencing samples for six different stress conditions in maize: drought, salt, cold, heat, flooding, and low nitrogen. The goal of this study was to find core stress-responsive genes via two methods: set operations and random forest classification. We found that these two methods identified largely distinct sets of core genes; random forest identified core genes that were important for predicting if a sample was stressed or control, sometimes regardless of whether those genes were differentially expressed in any stress condition. Furthermore, core genes were enriched in transcription factors generally as well as specific families, such as bZIP, NAC, HSF, and ERF. We hypothesized that these transcription factors may regulate other core genes as well as stress-specific genes. In Chapter 3, the genome of desiccation tolerant grass Eragrostis nindensis was improved by high-fidelity long read sequencing. The new assembly is 20-fold more contiguous than the previous assembly, with a contig N50 of over 10 Mb for 828 contigs. The E. nindensis genome, already known to be tetraploid, was found to be likely autotetraploid using this improved assembly and annotation. In Chapter 4, the improved E. nindensis genome along with 85 others was used to find groups of orthologous genes across the grass phylogeny. Subsequently, expanded orthogroups were found for desiccation tolerant compared to sensitive Chloridoideae species, as well as conserved transcription factor-binding motifs in desiccation tolerant chloridoids. We thus concluded that both expansion of certain gene families (early light-induced proteins, thaumatin-like proteins, expansin precursors, and others) and gene expression regulatory changes (recruitment of motifs for TCP, BBR/BPC, and TIFY family transcription factors) have contributed to the evolution of desiccation tolerance in the Chloridoideae.
Read
