Currently Funded Projects

• Project 1: Genomics and epigenomics of subgenome dominance in hybrids and allopolyploids

  Many crop species are allopolyploids, formed by interspecific hybridization coupled with whole genome doubling, which has long been known to contribute to the emergence of important agronomic traits. Furthermore, one of the parental subgenomes in an allopolyploid is often more dominantly expressed over the other ‘submissive’ subgenome(s) in both hybrids and allopolyploids. This can result in certain pathways, and ultimately phenotypes, being dominated by a single parental subgenome. Despite its importance, the underlying genetic mechanisms determining subgenome dominance remain poorly understood. One hypothesis is that subgenome dominance may be the outcome of resolving genetic and epigenetic conflicts that arise from the merger of highly divergent (sub)genomes into a single nucleus. Similarly, little is known about the interplay of polyploidy, subgenome dominance and natural selection toward shaping phenotypic diversity. A major goal of this research is to understand subgenome expression dominance in order to better predict the expressivity of parental phenotypes. Strawberry is a well-suited system for studying polyploidy given its range of polyploid species, wealth of genetic resources, small diploid progenitor genome sizes, and efficient transformation system. Basic discoveries in strawberry will serve as a platform for elite cultivar development and mechanistic insights into subgenome dominance in strawberry can be translated to other complex polyploid crop systems. Using a comparative genomic platform, consisting of diploid progenitor and polyploid species genomes, combined with transcriptome and a diverse epigenomic dataset, we will uncover the epigenomic and transcriptomic changes that occur during the earliest stages of subgenome dominance using a set of inter- and intra-specific hybrids and in naturally established octoploid strawberry. Our specific objectives are: (1) Construct a comparative genomic platform to investigate subgenome expression dominance in naturally established octoploid strawberry, (2) Investigate the epigenome of dominant and submissive subgenomes in natural octoploid strawberry and a suite of resynthesized inter- and intra- specific hybrids, (3) Using 3D fluorescence in situ hybridization (FISH) data to investigate subgenome organization within the nucleus, (4) Assess the potential role of the environment on shaping and determining subgenome expression dominance patterns, and (5) Develop a series of educational outreach activities targeting K-5 grade students, and provide unique training opportunities for undergraduate and graduate students. My key collaborators on this project from Michigan State University are Drs. Jiming Jiang, Chad Niederhuth, and Jianrong Wang. This project is supported by the National Science Foundation (NSF-PGRP #2029959).

  Project personnel in the Edger Lab: Elizabeth Alger, Kevin Bird, Scott Teresi, Lexy Kelsey, Adrian Platts, Patrick Edger

  Relevent Publications:

  1. https://www.nature.com/articles/s41588-019-0356-4

  2. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15256

  3. https://www.sciencedirect.com/science/article/abs/pii/S1369526620300340?via%3Dihub

  

• Project 2: Multiple origins of tuber formation - Evolution of a unique storage organ

  In addition to sexual reproduction resulting in true seed borne on a fruiting structure, numerous plant species reproduce asexually via modified organs such as tubers, storage roots, corms, and bulbs. Tubers, derived from true stems, serve as storage organs enabling survival during the winter and/or prolonged periods of abiotic stress, a mechanism for perennialism, and a means to bypass sexual reproduction. Tuber crops provide significant calories and nutrition worldwide and are an especially important component of food security in developing countries as exemplified by potato, yam, oca, ulluco and mashua. The trait of tuber production has evolved multiple times throughout the history of angiosperms across taxa separated by ~130 million years of evolution. The goal of this project is to identify key gene modules underlying the transition from non-tuberizing to tuberizing by comparing gene regulatory and metabolic networks. We will address the following question: Which co-regulated gene modules in the global gene interaction network have been rewired to permit the evolution of the tuber in different lineages? Beyond a few putative candidate genes such as StSP6A and StCDF1, it remains largely unknown which genes (e.g. content and expression profile changes) have contributed to the evolution of tubers. My lab will generate and compare gene coexpression networks of three 'foundation' tuber species with their non-tuber 'sister' species. We hypothesize that the comparison between the three 'foundation' tuber species and nontuber 'sister' species will identify network changes required for the evolution of tubers, resulting in a narrow list of potential candidate genes distributed among a few gene modules. Additionally, we will generate co-expression networks from seven additional tuber-bearing 'validation' species and compare these networks with the genes associated with tuber formation in the three 'foundation' tuber species. This will be accomplished by identifying the shared network similarities and differences. Similar network analyses have been used by us to investigate the evolution of other novel traits, including novel chemical defense pathways and secondary woodiness. My key collaborator on this project from Michigan State University is Dr. Robin Buell. This project is supported by the National Science Foundation (NSF-PGRP #1929982).

  Project personnel in the Edger Lab: Lexy Kelsey, Claudia Miranda, Patrick Edger

• Project 3: Development of genetic and genomic resources to improve fruit quality attributes

  The U.S. Vaccinium (blueberry and cranberry) industry has identified the development of new cultivars with improved fruit quality, in particular fruit with firm texture, good flavor, appealing appearance (color, size, and free of diseases), and longer shelf life as its top research priority and the key for continued success. Currently, Blueberry and cranberry breeders have limited tools to guide breeding efforts to improve fruit quality. The goals of this project include: a) understand how and which fruit characteristics affect fruit quality, b) generate DNA information and develop innovative genotyping tools to routinely and efficiently select genotypes with improved fruit quality attributes, and c) identify specific fruit quality characteristics, and estimate the levels of such fruit quality characteristics that will increase and sustain consumer purchases. My lab is leading the effort to establish new genomic resources, including constructing a pangenome and identify novel genes associated with superior fruit quality, to enable effective association mapping studies in both blueberry and cranberry. Project outcomes will enable breeders to effectively select blueberry and cranberry cultivars with improved fruit quality attributes and to accelerate the integration of multiple traits (e.g., fruit quality and disease resistance), making the cultivar development process more cost-effective and sustainable in the long term. Commercial production of blueberries and cranberries with improved fruit quality will increase profitability and sustainability throughout the entire supply chain, enhance the global competitiveness of these industries, and help sustain the economies of rural communities in the United States. Consumers will benefit from access to a consistent supply of affordable and nutritious fruit with the sensory quality profile that meets their expectations and preferences. This will translate into increased per capita consumption and improved human health and well-being. My key collaborators on this project include Drs. Massimo Iorizzo (North Carolina State University), Nick Vorsa (Rutgers), Jim Polashock (USDA), Nahla Bassil (USDA), Patricio Munoz (University of Florida), Juan Zalapa (Wisconsin), and David Chagne (Plant and Food Reseach Ltd). This project is supported by the United State Department of Agriculture (AFRI #2019-51181-30015).

  Project personnel in the Edger Lab: Alan Yocca, Adrian Platts and Patrick Edger

  Relevent Publications:

  1. https://academic.oup.com/gigascience/article/8/3/giz012/5304886

• Project 4: Developing genomic tools to facilitate breeding of strawberry with improved salinity tolerance

  The United States is the top producer of strawberries in the world. However, the loss of production due to abiotic stressors, namely increasing soil salinity levels, results in the loss of millions of US dollars annually to growers. The primary goal of this project is to develop a cost-effective solution to address crop loss in strawberry associated with high levels of salt present in the soil or irrigation water. The proposed research will not only permit us to gain valuable insight into the underlying genetics of salinity tolerance in strawberry, but develop molecular markers that will enable breeding programs to release superior cultivars. We have the needed genomic resources and genetic mapping populations in hand for the proposed research, including a validated genetic source for high salinity tolerance. Furthermore, chromosome-scale reference genomes for both a high salinity tolerant and susceptible genotype, combined with genetic mapping populations, will enable high-resolution mapping of candidate genes and simplify molecular marker development. This is expected to enhance economic and environmental sustainability of strawberry production across the country. The specific objectives are to: 1) identify candidate gene(s) associated with improved salinity tolerance in strawberry, 2) validate and functionally characterize candidate genes and 3) develop diagnostic molecular marker for high salinity resistance. My key collaborators on this project include Dr. Steve Knapp (UC-Davis) and Dr. Guo-Qing Song (MSU). This project is supported by the United State Department of Agriculture (AFRI #2020-67013-30870).

  Project personnel in the Edger Lab: Elizabeth Alger, Sofia Fanelli, Claudia Miranda, Patrick Edger

• Project 5: Identify genetic source(s) of resistance to diverse blueberry stem gall wasp populations

  The blueberry stem gall wasp, Hemadas nubilipennis, has emerged in the past decade as a devastating pest for affected growers and it is a high risk for the nation’s blueberry industry. This pteromalid wasp species is native to the Midwest and north-eastern North America. It is currently causing significant economic loss to one of the major production regions east of the Rockies, and unfortunately has been increasing in prevalence. An estimated 10% of Michigan’s $120 million blueberry industry is planted with cultivars susceptible to this pest. For this project, my lab is leading efforts to; A) test resistant germplasm with BSGW from native populations. We hypothesize that resistant individuals to BSGW can be identified in our mapping population using no-choice assays. This is supported by our preliminary data having already screened nearly 200 individuals, with resistance segregating 1:1 across the population, and B) screening breeding populations for BSGW resistance from diverse populations. We hypothesize that blueberry plants will be either completely resistant to BSGW or will be resistant to only native populations of BSGW. My key collaborator on this project from Michigan State University is Dr. Rufus Isaacs. This project is supported by the United State Department of Agriculture (AFRI #2018-7006-28917).

  Project personnel in the Edger Lab: Scott Teresi, Alder Fulton and Patrick Edger

   

  

• Project 6: Developing genomic tools to facilitate breeding of blueberry for anthracnose fruit rot resistance

  Anthracnose fruit rot is the most destructive and widespread fruit disease of blueberries across the United States. Anthracnose fruit rot can lead to substantial losses, including reduced yield, shelf life, fruit quality, and unacceptable microbial levels. Pre-harvest yield losses of 10 to 20% annually have been reported, and postharvest losses during storage can approach 100%, as the fungus may lay dormant and not cause disease until after harvest. The primary goal of the proposed research is to gain insights into the genetics and molecular mechanisms that underlie resistance to anthracnose fruit rot in an effort to develop genomic tools for rapid screening and development of new anthracnose fruit rot resistant blueberry cultivars. We have identified genetic sources of superior resistance to anthracnose fruit rot. A large number of highly and moderately susceptible cultivars were also identified, reflecting the challenges faced by the industry. Thus, we have the necessary germplasm and genetic diversity needed to investigate anthracnose resistance in blueberry. Furthermore, we have the needed genomic resources, including a chromosome-scale reference genome for a highly resistant genotype, and genetic mapping populations in hand for the proposed research. The specific objectives are to: 1) identify candidate gene(s) associated with anthracnose fruit rot resistance, 2) validate and functionally characterize candidate defense-related genes to anthracnose and 3) develop diagnostic molecular marker for anthracnose fruit rot resistance. My key collaborators on this project at Michigan State University include Drs. Tim Miles and Guo-Qing Song. This project is supported by the United State Department of Agriculture (AFRI #2018-67013-27592).

  Project personnel in the Edger Lab: Lexy Kelsey, Maddie Berg, Josh Moses, Patrick Edger

   

  

• Project 7: Investigate global transcriptional and metabolic changes induced by fungal-plant-bacterial symbiosis.

  Symbioses between fungi, bacteria and plants are integral to plant and ecosystem productivity and health. Such inter-Kingdom interdependencies were likely a prerequisite for the terrestrialization of Earth, and are key components of modern plant holobionts - plant hosts and associated symbionts. In fact, early diverging lineages of terrestrial fungi under investigation here, the Mucoromycota, are so ubiquitous as plant symbionts that they even associate with algae and belowground tissues of plants that do not produce true roots including ferns, mosses, liverworts. The goal of this project is to identify the molecular basis underpinning plant-fungal symbiosis. To accomplish this, my lab will contrast species-specific co-expression gene networks in different combinations of plant, fungi and bacterial partners to better understand genome regulation between photobiont and mycobiont species. Co-expression networks will be constructed by analyzing gene expression in time-course datasets gathered over weeks and throughout a day at precise, comparable time points. This approach will also help in determining which differentially expressed genes are involved in these symbiotic interactions. My key collaborators at MSU, Drs. Greg Bonito and Björn Hamberger, will generate matching metabolomic data in order to correlate phenotypic and physiological data with our results from transcriptome analyses. We expect there to be many parallels in the way that arbuscular mycorrhiza fungi and Mortierella species interact with plants, including regulation of the symbiotic (SYM) pathway in plants by these fungi. We will address the following questions: i) Is there a core set of plant symbiotic pathways (i.e. conserved gene regulatory modules) across the major land plant clades? ii) Do endohyphal bacteria of Mortierella alter plant-fungal interactions and transcriptional regulation in land plants? This project is supported by the National Science Foundation (NSF-DEB #1737898).

  Project personnel in the Edger Lab: Alan Yocca and Patrick Edger