Unraveling the Heterozygosity, Allelic Composition, and Copy Number Variation of Potato

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PI: C. Robin Buell (Michigan State University) Co-PIs: Yuehua Cui and David Douches (Michigan State University), Jiming Jiang (University of Wisconsin-Madison), and Richard Veilleux (Virginia Polytechnic Institute and State University)Potato is the third most important food crop in the world following rice and wheat and is cultivated for its tuber, a below-ground storage organ. Potato is distinct from many other major crops in that it is asexually propagated, has four sets of chromosomes (tetraploid), and all cultivars are highly heterozygous. As a consequence, potato has a greater probability of retaining deleterious gene mutations than sexually propagated diploids such as rice, maize, and soybean. These three characteristics make genetic improvement of potato slow and unpredictable due to a lack of understanding of the interaction of genetic elements in a complex background. Furthermore, there is limited knowledge regarding the molecular nature of heterozygosity and allelic composition in the potato genome and how these correlate with phenotype. The objectives of this project are to understand the contribution of genes/alleles, transcripts, copy number variation and epigenomic features to a complex of phenotypic traits associated with fitness in potato. Data to be generated from this project will include characterization of the genome, transcriptome and epigenome from multiple potato populations with differential degrees of chromosome number and heterozygosity and statistical analyses to identify genes and alleles associated with a set of phenotypes associated with vigor. These data will also facilitate modeling genomic features into phenotype. Many of the genetic and genomic questions associated with potato cannot be readily addressed by using diploid model plants. Project efforts to probe the genetic complexities of potato will serve as a model genomics system for other vegetatively propagated, highly heterozygous crops with similarly intractable breeding systems, including alfalfa, banana, cassava, grape, strawberry, sugarcane, sweet potato, yam and scores of minor horticultural crops, thereby improving the understanding of the genetic machinery underlying phenotypic diversity. Through outreach activities in this project, the public will gain knowledge of plant biology, specifically in the uses of potato and its unique biology, through a suite of activities with the Michigan State University Children's and Horticulture Garden involving all age groups. Through engagement of high school and under-represented groups, this project will provide opportunities for students to see science as a viable career opportunity and increase the representation of women in computer-related science/technology disciplines. The techniques and approaches used in this project will provide a rich training environment for graduate students and postdoctoral fellows in relevant and emerging disciplines of bioinformatics, genomics, and epigenomics. The data to be generated in this project through publication and deposition in public databases will provide the first high-resolution map of genome variation and its association with gene expression, epigenetic modifications, and phenotypic traits in potato. Sequence data will be made public through the project website (to be accessible via http://buell-lab.plantbiology.msu.edu/), the SOL Genomics Network (http://solgenomics.net/) and through the NCBI Sequence Read Archive and the NCBI Gene Expression Omnibus for permanent archiving. Germplasm developed and/or used in this project will be available on request and long-term through the NRSP-6 U.S. Potato Genebank (http://www.ars-grin.gov/nr6/).