Pan-Genomes and the Genetics of Adaptation: Theory and Utility for Improving Resilience and Sustainability of Annual Crop Production

Abstract:
In domesticated species, there remains an ongoing hunt for single gene perturbations that will have a large effect on increasing adaptation. By now, tens of thousands of engineered or natural single gene variants have been hypothesized to be adaptive in crop species. Nearly all of these hypotheses have been rejected. The variants that seemed the most promising to cause major fitness jumps did not hold up when tested at scale in agriculturally relevant environments. Despite this overwhelming empirical evidence, enthusiasm and funding remains for finding or creating single genes or DNA constructs that increase adapation in agriculture, in part because of the simplicity of introducing or introgressing single events into elite germplasm. Success will be rare, but chances may be improved by utilizing theory.
Prior to the discovery of DNA and the concept of gene models, phenotypes underlying adaptation were modeled as highly polygenic. This quantitative genetic approach this assumes 1) any given mutation or polymorphism will have no effect or a very small effect on adaptive traits. 2) For the subset of mutations that do have large effects on fitness, most will be deleterious. We now have empirical data for pangenomes, where de novo whole genomes are assembled and annotated for multiple lineages in a species. These data reveal a massive level of variation in the degree of genetic redundancy among lineages within species, in the form of copy number variation in gene models. I will discuss efforts to incorporate these new observations into quantitative genetics and applied to design adaptations in domesticated species.

About the Speaker:
John McKay is a Professor of Evolutionary Genomics at Colorado State University where he leads a research group on the genetics of adaptation, with a focus on drought and improving sustainability of food and feed production. In addition, McKay is co-founder and CSO of New West Genetics, an Ag Tech company applying modern genomics and breeding to industrial hemp, a highly sustainable and productive grain, biomass, and fiber crop. His research examines evolution and gene function at both the phenotypic and molecular levels. McKay has established collaborations and technology to market strategies to increase chances that the most impactful of his genetic discoveries make it to the public and private sector breeding pipeline for multiple crops. McKay is invested in training the next generation of Biologists that can tackle global challenges; this includes conceptual and professional development for undergraduates, PhD students and postdocs. McKay has published 100 papers which have been cited over 13,000 times. He serves on funding agency and scientific review panels in the US and internationally. McKay is a fellow of the American Association for the Advancement of Science.

Contact

Jesse Lasky
jesserlasky@gmail.com