Jeffrey Dunne PhD

The objective of this research is to develop genomic resources that can be applied for improvement of winter wheat germplasm adapted to the eastern United States. Research done in the parent project relies heavily on a reference quality genome sequence, however relevant winter wheat germplasm is not currently represented in genome assembly projects. Specific objectives include: (1) Obtain and assemble long read DNA sequences of eastern winter wheat cultivars at low coverage, (2) Use annotation software to identify the gene content of an eastern winter wheat cultivar that will can serve as a relevant reference assembly,(3) Utilize these new genomic resources to identify gene variants underlying traits of importance in soft winter wheat, (4) Incorporate the new genomic resources into the development of improved high-throughput genotyping approaches used for selection in breeding populations.

The overall objective of this proposal is to ensure release of peanut cultivars resilient to the climate change to allow producers of the Virginia and Carolinas (VC) peanut growing region to maintain competitiveness in the marketplace. This will be realized through evaluation of the developed lines within the well-established Peanut Variety and Quality Evaluation (PVQE) multi-state program with the addition of new high-throughput methods and traits for accurate selection of 1) early maturing peanut cultivars with 2) tolerance to heat and dry conditions and 3), resistance to southern corn rootworm (SCR), using ���smart��� technologies and computer algorithms. Once validated, these new methods will be implemented in future PVQE testing.

Diploid species of the Arachis section have agronomically important traits that can be transferred to cultivated peanut through complex hybridization methods. The proposed work includes 1. the creation of a public core collection of wild derived, peanut compatible tetraploid that covers as strategic reserve of alleles, available to peanut breeders. These allotetraploids will be made available through the National Plant Germplasm System; 2. to genetically map disease resistances and advance this germplasm by backcrossing and/or rounds of selfing; and 3. to developed DNA markers for two new loci of resistance to Root Knot Nematode (from A. stenosperma) and two new loci of resistance to Late Leaf Spot (from A. cardenasii) for use in marker-assisted selection.

The U.S. is the third-largest peanut producer in the world. Besides being locally consumed, a large proportion of peanuts (over 500,000 metric tons valued at $675 million) is annually export to Canada, Mexico, and European Union countries. These countries also reported a high peanut allergy prevalence. Therefore, given peanuts' economic and nutritional importance, it is worthwhile to correct this primary health concern associated with peanut grains. The proposed project attains this problem from the prevention standpoint different from previous attempts that focused on therapeutics via developing reduced immunogenicity peanut genotypes following a molecular breeding approach. Specifically, this research project targets the FFAR's 'Health-Agriculture Nexus Challenge Area' by focusing on the research theme "breeding better nutrition." Under this research project, an interdisciplinary team comprised of a molecular biologist, a geneticist, a plant physiologist, peanut breeders, and immunologists will test the hypothesis that it is possible to develop reduced-immunogenicity peanut genotypes with high oleate content while maintaining agronomical and end-use properties. Following tasks will be undertaken to test this hypothesis: i) Identification of peanut genotypes deficient in major allergenic proteins. The team will achieve this task via screening an interspecific Arachis hypogea 'Gregory' ������������ A. diogoi population for genotypes with reduced content of major allergenic proteins. ii) Development of reduced-immunogenicity peanut genotypes with high oleate content via genome-editing. The team will achieve this task via inducing mutations in the genes coding major allergenic proteins, Ara h1, Ara h2, Ara h3, and Ara h6 in the high-oleate peanut background via CRISPR-based genome editing and backcross breeding . iii) Characterization of lines for reduced allergen and enhanced oleate content and agronomical properties. The team will achieve this task via detailed genetic, biochemical, immunological, and agronomical characterization of the derived lines.

The goal of this project is for investigator partners to perform bioinformatics analyses, develop and implement bioinformatics software focused on improving breeding tools. Organize breeding community projects around development of bioinformatics platforms that are commodity specific for specialty crops, including but not limited to: sugarcane, blueberry, peanut and turf. Work on development of genomics based tools within commodity groups to set the stage for future genomic selection projects.

The turfgrass industry is a multibillion dollar industry in the United States, and represents tens of thousands of jobs related to production, installation, and management of turfgrasses. Outside of its significant economic impacts, turfgrasses also provide significant environmental and social benefits. Despite these numerous benefits, the turfgrass industry faces many serious challenges. Greatest among these is the limited availability and reduced quality of water for irrigating turfgrass areas. Although sustainable landscapes are a concern throughout the country, severe droughts and limited water in California and the Southwestern United States are already forcing changes to the landscape. Due to increasingly limited water resources and the desire to have more sustainable landscapes, there is a growing need for turfgrasses which can withstand drought conditions. A transdisciplinary group from North Carolina State University (NCSU), Oklahoma State University (OSU), Texas A&M AgriLife Research (TAMUS), the University of Georgia (UGA), and the University of Florida (UF) was formed to address these problems and to develop turfgrasses with reduced irrigation requirements for use in southern landscapes. These efforts have focused on economically important warm-season turfgrass species, bermudagrass [Cynodon spp. (L.) Rich], zoysiagrass (Zoysia spp. Steud.), St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze], and seashore paspalum (Paspalum vaginatum Swartz), that have the potential to significantly reduce water use in future landscapes. To date eight improved cultivars have been released from this project. However, additional efforts are needed to continue the development pipeline for new cultivars and genetic tools, promote their adoption, and quantify their impact. Advancing this successful research relationship will allow for efficient progress towards improved screening methods and molecular markers using new tools and technologies, the dissemination of important information to stakeholders and end-users, and ultimately allow for the continued utilization of turfgrasses in sustainable landscapes.

Throughout its history, the NCSU peanut breeding program has successfully transferred genes from wild species to cultivated peanut. These transferred genes confer strong resistance to pathogens, particularly leaf spot and tomato-spotted wilt virus. Every NCSU cultivar released since Bailey has contained two segments of wild species DNA credited with conferring high levels of disease resistance. The overall objective of this proposal is to continue using wild species to develop cultivars with high levels of disease resistance and excellent yield potential for the peanut farmers of North Carolina. Improved disease resistance has the potential to significantly lower input costs, thus improving profit margins in an environmentally sustainable manner. The primary emphasis of this project is leaf spot but also includes other value-added traits important to North Carolina with root-knot nematode (RKN) resistance offering a high probability of rapid progress.

At peanut buying stations across the U.S. South East, peanut grading is currently implemented using labor-intensive equipment. Many of the steps related to grading have been unchanged for decades. A critical reason for this involves political pressures against updating or expediting the grading process. However, like many other economic sectors, new labor-force pressures are requiring that more be done with fewer people. Given that (1) labor is more challenging to come by; and (2) political pressure exists to maintain the status quo, we propose to update key steps in the existing process to simplify and/or expedite data collection. This project���s goal is to develop automated imaging and weighing technologies that can serve as a bridge, toward more fully automated systems, by addressing key bottlenecks in the existing grading process. We will achieve this by the following objectives: (1) Automate the weighing and grading of peanuts either traveling down or entering the rollers during pod pre-sizing; and (2) Automate the detection of splits and, if possible, sound versus unsound splits, by adding vision systems to the existing sheller.

Genomic selection (GS) has only been theorized rather than implemented in cultivated peanut. With the introduction of the progenitor and cultivated reference genomes, genomic selection becomes possible in a peanut breeding pipeline. GS requires the generation of genomic libraries suitable for Next-Generation Sequencing (NGS) that enable reduced representation sequencing (RRS) techniques like Genotype-by-Sequencing (GBS). The resulting molecular information collected (DNA markers and sequencing data) from the existing North Carolina State University (NCSU) peanut breeding lines, in addition to the extensive phenotypic data collected over the last decade, will provide accurate breeding values to compare and select novel breeding materials currently in development based solely on their molecular information. The ability to apply a genomic selection pipeline will improve the selection accuracy and efficiency of the breeding population, significantly improving breeding gains in comparison to conventional breeding methods. Initially, whole-genome sequencing can lay the groundwork for this genomic selection pipeline by providing information on regional and genome-wide single nucleotide polymorphisms (SNPs) within the NCSU peanut breeding program and the restriction enzyme pairs that will maximize read length and counts for RRS of larger sample sizes.

NCSU has successfully used wild peanut species for transferring desired genes from wild species into cultivars in the past 30 years. Several essential resistant genes were introduced, including early leaf spot, late leaf spot, and tomato spotted wilt virus (TSWV) resistance. However, the ploidy difference between cultivated peanuts (tetraploid, 4x) and wild peanuts (diploid, 2x) causes difficulties in gene introgression. The ploidy barriers, which means hybrid incompatibility between different ploid plants, have been a critical challenge in using wild germplasms. Frequently, polyploid manipulation has been used in conquering this problem by double diploid genomes. The overall objective of this proposal is to establish methods for converting diploid wild peanut into tetraploid to enhance their crossability to cultivated peanuts. The outcome will help NCSU peanut breeders to use wild germplasms much more efficiently.