Plant Breeding, Genetics, and Biotechnology

Dr. Zachary Lippman
Cold Spring Harbor Laboratory

Title: From Paralogs in Pan-Genomes to Eggplants in Africa

Abstract: Decades of research on the few model systems that dominate plant studies have revealed the genetic and molecular mechanisms that govern stem cell control and the natural and agricultural traits they influence. While the core factors and their interconnected regulation are highly conserved, recent advances in pan-genomes and genome editing have led to the emergence of new model systems that uncover previously hidden complexities of stem cell control within and between lineages. I will present our recent findings on using pan-genomics and pan-genetics in the Solanaceae family to expose critical roles for gene duplications, their diversifications, and interactions among stem cell regulators controlling flowering, inflorescence architecture, and fruit size. These findings have implications for the evolvability of phenotypes in nature and the engineering of traits in agriculture.

Dr. Allison J. Miller
Saint Louis University

Title: New crops, new rules? Genetic architecture, prediction, and the belowground in perennial grain and oilseed crops.

Abstract: Perennial crops are a cornerstone of regenerative agriculture, with the potential to produce food while rebuilding soil health, reducing erosion, retaining nutrients, and storing carbon. However, breeding perennial grains and oilseeds began relatively recently and presents unique challenges: selection cycles can be long, traits change as plants age across years, and breeding populations are still close to their wild ancestors. This presentation highlights ongoing work to dissect the genetic and environmental determinants of perennial plant phenotypes. First, I examine the genetic basis of complex traits in silflower (Silphium integrifolium), a perennial oilseed in the early stages of domestication. Second, I show how advanced understanding of perennial plant biology is being applied to optimize breeding through genomic and phenomic prediction in intermediate wheatgrass (Thinopyrum intermedium, Kernza®). Third, I describe ongoing efforts to understand relationships among grain yield, root traits, and soil properties in intermediate wheatgrass. Together, these genetic advances support the breeding of diverse perennial species that offer economically and ecologically viable options for regenerative agricultural systems.

Dr. Jeffrey Endelman
University of Wisconsin-Madison

Title: Advances in Quantitative Genetics and Their Application to Potato Breeding.

Abstract: In the US and most of the world, cultivated potato is autotetraploid, which complicates the use of quantitative genetics and genomics to accelerate breeding. In this talk, I will discuss recent advances in genetic mapping and genomic prediction for polyploids and the application of these methods for potato breeding. Despite these advances, there are inherent limitations to genetic improvement of autotetraploid potato. To address this, I am collaborating with a national consortium of researchers to reinvent potato as a diploid F1 hybrid crop that can be distributed as true seed.

Dr. Christine Diepenbrock
University of California, Davis

Title: Genomics-enabled breeding for crop nutritional quality and environmental stress tolerance

Abstract: Our research group works on improving nutritional quality and tolerance to environmental stresses, namely drought and high temperatures, in staple and specialty crops. I will present recent and ongoing work by our group and collaborative teams. For example, I will describe multiple approaches to sensing- and -omics-enabled dissection and prediction in grain legumes, cereals, and leafy greens, with a focus on field-collected agronomic traits and/or lab-collected compositional traits in the edible portion of the crop. I will also describe genotypic and phenotypic characterization of the lima bean USDA National Plant Germplasm System collection, much of which is photoperiod-sensitive, and the development of a conditional core collection. Finally, I will describe how we are using genetic/genomic information in our applied varietal development efforts, namely for lima beans (among other Phaseolus beans) and chickpea.

Dr. Taylor Ferebee

Title: Cultivating Genome Intelligence for Next-Generation Agricultural Solutions

Abstract: Computational biology and quantitative genetics have provided powerful approaches for connecting genomic variation with phenotypic diversity and advancing crop improvement. These approaches, however, have largely focused on exploiting existing genetic variation through association. Today with rapid advances in artificial intelligence and genome-editing technologies, there are new opportunities to design variation that can support the next generation of agricultural products. In this talk, I will explore how AI and experimental feedback advance genome intelligence and enable new products. I will also discuss the future of these feedback loop frameworks and how this approach can be extended to agricultural applications, including protein engineering for grain quality and gene editing for disease resistance. Finally, I will show how these innovations point toward a more prescriptive and purposeful future for crop improvement.