Collaborative Research: The ecological genomic basis of parallel serpentine adaptation in Mimulus

University Of California-Davis, Davis CA

Investigators

Abstract

A major challenge in 21st century biology is to understand how organisms adapt to complex and often unpredictable environments. Environmental heterogeneity results in divergent selective pressures that are important for creating and maintaining biological diversity; however, little is known about how organisms respond to such spatially varying selection at the genetic level. This project investigates the genetic basis of plant adaption to variation in soils. Serpentine soils present particularly challenging environments for plants ? they are deficient in several essential plant nutrients, notably calcium (Ca), and contain toxic levels of magnesium (Mg) and heavy metals. However some species, such as Mimulus guttatus, are able to grow both on and off of these harsh soils. This research will characterize soil, climatic, and fitness traits related to serpentine adaptation from populations of M. guttatus distributed on and off serpentine soils from British Columbia to southern California, and investigate whether serpentine tolerance in these widespread populations has evolved via the same or different genetic and physiological mechanisms. Establishing the genetic basis of plant adaptation to and the degree of parallelism across widespread populations will contribute to a broader understanding of plant physiology, ecology and evolution that will advance the ability to conserve and subsequently to exploit genetic diversity to produce new crops and plant communities with greater resilience to emerging changes in the environment, including salinity and mineral nutrient stress. Serpentine tolerance in Mimulus provides an integrative and accessible example of plant adaptation, so in addition to mentoring of postdocs, graduate and undergraduate students, and underrepresented minority high school students, the investigators will develop and test the effectiveness of data generated by this work to demonstrate core concepts in biology for undergraduates. This resource would be developed in part through a new capstone undergraduate course at Duke University. The investigators will also train a public school high school teacher and assist in the development, teaching, assessment, and modification of teaching modules for introductory and AP biology classes. The molecular genetic basis of adaptation to serpentine soil will be investigated in M. guttatus , an ecological genomic model species with a rapid generation time, high quality annotated genome sequence, extensive genomic resources, and well developed methods for stable transformation. Serpentine soils are usually lethal, but hundreds of populations of M. guttatus have repeatedly adapted to these soils across geographically and geologically distinct regions in western North America, from British Columbia to southern California. The four aims in the project will result in one of the most complete and detailed studies of how plant species evolve in response to spatially varying selection and elucidate the physiological, cellular, and molecular genetic mechanisms underlying parallel adaptation. In Aim 1, reciprocal transplant experiments, ionomic profiling, and detailed soil analysis will be conducted for 20 pairs of adjacent serpentine and non-serpentine M. guttatus populations from five geographically and geologically diverse regions. Aim 2 will utilize pooled population genomic sequence data from each of the 40 populations to identify candidate genes and SNPs underlying parallel serpentine adaptation, and evaluate whether individual candidate genes and molecular pathways are shared across widespread serpentine regions or have evolved in response to particular serpentine sites. In Aim 3, new, highly efficient and cost-effective methods for QTL mapping combined with physiological, ionomic, and soil transplant experiments, will be used to identify the loci that are most important for local adaptation to serpentine soils at each of the eight serpentine regions, determine whether QTLs are unique or shared across regions, and for each major QTL evaluate the likely physiological mechanisms involved in tolerance. Aim 4 involves using fine-scale genetic mapping, positional cloning, and transgenic experimental approaches combined with tests of physiological and biochemical function to identify the most important genes involved in local adaptation to serpentine soils and characterize their cellular and molecular mechanisms.