2017 Faculty Update: Nevin Young
In the Cargill Building across the street from Christensen Lab, plant pathology has an outpost exploring the genomics of plant-microbe symbiosis. Nevin Young and his colleagues use DNA sequencing technology to discover genes that enable plants and microbes to form symbiotic relationships. His lab focuses on legumes (the family comprising species such as soybean, pea and alfalfa) with a special interest in their symbiotic association with rhizobial bacteria, a relationship that leads to the formation of root nodules and biological nitrogen fixation.
Young and his colleagues use next generation DNA sequencing plus computational data-mining to search for undiscovered symbiosis genes. The starting point for their research is the reference genome sequences of two important legume models, soybean and Medicago truncatula, a close relative of alfalfa. In fact, the Young lab led the worldwide effort to create a genome sequence for Medicago, culminating in its 2011 publication in Nature magazine, still one of the best and most complete reference genome sequences in any legume species.
Since then, the lab’s focus has been on creating a “Hapmap Platform” to enable the use of genome-wide association mapping (commonly called “GWAS”) to discover undescribed genes important in nodulation. This has been a large, NSF-funded, multi-year initiative that involves collaborations with Peter Tiffin (Plant and Microbial Biology), Mike Sadowsky (Soil, Water and Climate) and Bob Stupar (Agronomy and Plant Genetics) – plus many others from around the world. In the Young lab, team manager Roxanne Denny has led much of the greenhouse work while former graduate students, Peng Zhou and Joseph Guhlin, have led much of the bioinformatic data-mining. Along the way, the lab coordinated Medicago research across campus, advised post-docs and graduate students in multiple programs, and hosted dozens of undergraduate students as part of the university’s Life Sciences Summer Undergraduate Research Program. An example is the work of current graduate student, Diana Trujillo, who has mined Medicago, soybean and other legume genomes to discover nodule-expressed gene families that have expanded in just one legume species, revealing a new family (called the PLAT-domain proteins) that is essential for successful nodule development.
Using the Medicago genome sequence as a starting point, the multi-lab research team discovered millions of SNP (single nucleotide polymorphisms) and compared this massive data set to a corresponding set of greenhouse phenotypes. The outcome was the discovery of previously unknown symbiosis genes, genes that have since been validated through the use of new genome engineering techniques like CRISRPs (clustered regularly interspaced short palindromic repeats). Former lab member, Shaun Curtin, was the leader in this research and his work appeared earlier this year in a high profile publication in Plant Physiology. Curtin has since gone on to work with Matt Rouse, Debby Samac and David Garvin in the USDA-ARS Cereal Disease Lab to extend these powerful techniques to small grains and alfalfa.
Young and colleagues participate in projects beyond the NSF-funded Medicago nodulation work. One of the longest running has been marker-assisted breeding in soybean, first with Jim Orf and more recently with Aaron Lorenz, both in Agronomy and Plant Genetics. This work, which began way back in 1992, led to the intial discovery and description of the most important soybean cyst nematode (SCN) resistance gene, Rhg1, a discovery that is the basis of SCN breeding ever since. The plant pathology graduate student who led this work, Vergel Concibido, was the recipient of the 2017 Distinguished Alumnus Award from plant pathology and he’ll be visiting campus next year to give a presentation about his current research and interests.
Genomics research in systems like Medicago and soybean still has plenty of potential for new discoveries. In recent months, Young, along with Peter Tiffin and Dean Malvick, has been exploring the possibility of sequencing either symbiont or pathogen communities as they associate with legume hosts to discover more about the dynamics of plant-microbial communication. This is just one example of the directions where sequence-based biology can build on the discoveries from three decades of legume genomics research at the University of Minnesota.