Genomic Underpinning of Drought-Associated Phenotypes in a Keystone Shrub Species of Western North America
Authors: Dumaguit Carlos Dave Contreras 
Published: July 2024

Anthropogenic climate warming and habitat loss threaten species and ecosystem sustainability. Given this, it is urgent to determine whether populations can adapt at a rate sufficient to combat climate change or if human intervention is needed to preserve community ecosystem health. Assessing whether populations could adapt includes inferring whether key phenotypic traits associated to abiotic tolerance are under genetic control and therefore heritable. This thesis focused on the imperiled western North American sagebrush steppe and its widespread eponymous keystone species Artemisia tridentata, (common name, big sagebrush). To determine the adaptive capacity of any population, standing variation for phenotypic traits across its climatic range must be known, allowing for predictions of performance under climate change conditions. For sagebrush populations, we investigated phenotypic trait variation by examining leaf stomata density and size to infer water use efficiency as well as xylem diameter to infer relative risk of embolism, then used comparative genomic analyses to test for signature of natural selection driven by climatic conditions. A common garden greenhouse experiment included 41 seedlings from four populations from Idaho, Nevada, and Utah, sampled across a cline which represent a potential evapotranspiration gradient. If distinct phenotypes were observed under optimum conditions, then this would provide evidence for genetic control of these traits. Light microscopy observations to leaf epidermis and roots were used to record phenotypes associated with performance under drought stress and comparative statistical analysis was conducted to determine phenotypes at population level. This study showed that seedlings from Utah exhibited significantly more dense stomata, a trait associated with increasing transpiration water loss, but greater allocation of large diameter xylem vessels, which would increase the risk of embolism. In contrast, seedlings from Idaho and Nevada exhibited significantly less stomata density, a trait known to decrease transpiration water loss, and greater allocation of small diameter xylem vessels mitigating risk of embolism. The genetic underpinning of phenotypes was investigated by reconstructing 12 individual genomes from three significantly different stomata phenotypes by applying a genome reconstruction approach using Illumina short reads. To test for the signature of local adaptation, single nucleotide polymorphisms were called and a PCA was conducted. The latter analysis returned the same climatic and phenotypic clustering as previously observed with Utah seedlings being separated from those from Idaho and Nevada. Combining phenotypic and genomic data support a hypothesis of genetically controlled phenotypic traits reflecting local adaptation. In all populations, individuals with less dense and smaller-sized stomata increasing drought tolerance as well as smaller diameter xylem with greater tolerance to embolism exist. Future work should explore gene expression responsible for phenotypic trait development under controlled drought, with continued work informing practices to improve ecosystem restoration of big sagebrush and maintenance of this keystone species in the face of climate change.