8:00am-8:15am
WiDiPo: A Collection of Wild Diploid Potato for Enhancement of Breeding Germplasm
Dennis Halterman, USDA-ARS

               Wild potato relatives are an invaluable breeding resource, as they contain genes for high priority traits, including disease resistance, processing quality, and culinary characteristics. Seeds collected from wild species at a single place and time are maintained in genebanks as populations of unique individuals. This approach preserves genetic diversity, but that diversity is unordered, largely unexplored, varies among populations, and has little value per se as a breeding resource. To facilitate the use of wild species more effectively for potato improvement, and to make use of the computational and genomics tools that are revolutionizing breeding and genetics, we developed a collection of more than 200 individual genotypes from 10 species and characterized them with respect to genotype, disease and pest resistance, and breeding value. This set of clonally maintained wild potatoes is available through the National Research Support Program-6 (NRSP-6) potato genebank and genotypic and phenotypic data for each clone is publicly available. Data describing these clones will become a community resource accessible to others interested in potato improvement and potato research. The phenotypic descriptions of each clone can be extended by incorporating data from users of the collection. Hybrid seed from crosses between select clones and inbred cultivated potato tester lines is available to breeders for evaluation of each clone’s potential to contribute to cultivar breeding efforts.

8:15-8:30am
USAID Feed the Future Global Biotech Potato Partnership: Deploying Stacked R-genes for Late Blight Resistance
David Douches, Michigan State University

               Potato (Solanum tuberosum L.) is an essential crop that can play an integral role in achieving global food security. Disease, particularly late blight (Phytophthora infestans), can be a major issue for farmers often resulting in total crop loss. The United States Agency for International Development (USAID) has funded the Feed the Future Global Biotech Potato Partnership (GBPP) to bring late blight disease resistant (LBR) potatoes in farmer-preferred varieties to the Southeast Asian countries of Bangladesh and Indonesia, and the Sub-Saharan Africa countries of Kenya and Nigeria. The GBPP focuses on the research and development and deregulation of the LBR potato through genetic engineering and is a collaboration between Michigan State University, the International Potato Center, the University of Idaho, African Agricultural Technology Foundation, and partner country National Agricultural Research Systems. Our team developed potato events in five different varieties stacked with three LBR R-genes.  We refer to these as our first-generation products and they have been tested in multi-location field trials in all four of our partner countries.  P. infestans diversity is also being evaluated in these countries to inform stewardship of the 3 R-gene potato varieties.  In-country field results have shown complete control of the pathogen. Molecular characterization, compositional analyses and regulatory studies of the events have been completed. Submissions of dossiers to the country regulatory agencies will start in 2024.  MSU has also developed disease resistant T-DNA constructs combining a new combination of late blight R-genes as well as R-genes for virus resistance.  These constructs are referred to as our second-generation products. The USAID goal is to sustainably reduce global poverty, hunger, and malnutrition. The GBPP expects to complete required research necessary to receive regulatory approvals for general release and commercialization of the LBR potato within the next three years for all four countries.

8:30am-8:45am
Potato Diversity: Implications of Heterozygosity and Paralog Interference
Sapphire Coronejo, University of Minnesota

               "Potato, an important global food crop, has a complex autotetraploid genome making genomic studies challenging. Its complexity impacts precision of sequence assembly, variant detection, and evaluation of genetic diversity. The high allele dosage in autotetraploids can lead to sequence misalignment and complicates the interpretation of genetic data, affecting population genetic inferences. Using dihaploids extracted from tetraploid parents enabled us to sequence tetraploid haplotypes with diploid technology, easing polyploidy complexities. We established a diversity panel from a collection of dihaploids derived from 60 tetraploid mothers across three market classes: chips, russets, and reds, sequenced to ~20X depth using Illumina short read technology. Initial findings revealed 12 completely fixed coding sequences and 34 with 200 alleles, averaging 27.86 alleles per locus indicating extensive genetic diversity, initially perceived as inter-genotypic variation. Further investigation on the synteny and orthology across the dihaploids and phased tetraploid genomes revealed that this diversity stemmed from paralogous sequences rather than true allelic variation. When focused on a more conservative gene set, where all the haplotypes are represented with only one gene, we identified two fixed coding sequences and one with 71 alleles, averaging 12 alleles per locus. In examining the genetic variation within the panel, we found that observed heterozygosity varied from 0.46%-0.69%, and nucleotide diversity ranged from 0.53%-0.98%. In comparison with the conservative set of genes, observed heterozygosity significantly increased to a range of 16.36%-26.43% whereas nucleotide diversity decreased at 0.046%-0.068%, emphasizing the impact of analysis scope on measuring genetic variation. Further exploration of the panel elucidated patterns of copy number variation, providing insights into the genome’s structural dynamics and its implication for potato breeding. This study not only offers a detailed view of the complexities of the potato genome but also highlights the critical need for precise analytical methods to differentiate between allelic and paralogous variations."

8:45am-9:00am            
Capturing the genetics of eastern United States potato germplasm for diploid breeding
Ek Han Tan, University of Maine

               One of our major undertakings for diploid potato breeding efforts at the University of Maine and the eastern United States is to access the genetics within the conventional varieties and clones developed by breeding programs in this region. Thus far, we have generated several primary dihaploid populations from these clones and are beginning to introgress self-compatibility and male fertility traits using these lines. We also utilize select Solanum phureja-stenotomum long-day adapted diploid clones developed by the USDA-ARS that carry desirable traits such as colored flesh, late blight resistance and resistance to Dickeya dianthicola, a member of the bacterial complex that causes potato blackleg and soft rot disease. In addition, through our collaborative within the Host-Virus Evolutionary Dynamics Institute, we are also focused on understanding the disease dynamics of Potato Virus Y using greenhouse and field methods in Maine. Through collaborations within the eastern network of cooperators, we hope to evaluate field performance in multi-location trials, perform disease phenotyping, continue to extract primary dihaploids and begin to test diploid clones that are representative of the region’s conventional potato germplasm and build upon the wide adaptability required in this region for diploid breeding.

9:00am-9:15am
Genetics of Diploid Breeding at UW-Madison
Maria Caraza-Harter, University of Wisconsin - Madison, Jeffrey Endelman, University of Wisconsin - Madison

               Genetic homozygosity of the haplotypes containing favorable alleles is of great importance for developing inbred parents for diploid potato breeding. Our diploid breeding program has made progress towards achieving this homozygosity while selecting against the accumulation of deleterious alleles through 3 cycles of inbreeding. Diploids included in this study were selected based on their self-compatibility, true potato seed yield, and tuber yield and morphology in the F1 and F2 generation. After genotyping using the potato SNP array, we reconstructed the haplotypes using the software PolyOrigin and calculated the homozygosity levels using the genotype probabilities. We evaluated greenhouse phenotypes for morphological traits. Tracking and identifying favorable haplotypes from diploid founders allowed us to make faster progress on the fixation of these haplotypes for maturity and skin color in our diploid breeding program. The genetic analysis results will reveal the signatures of selection in the F2 generation. The outcome of this breeding effort will be reported and results on the type of distorted segregation will be discussed.

9:15am-9:30am
Genome Sequence of ‘Ozette’ Potato Provides Insights into its Evolutionary Relationship
Hemant Kardile, Oregon State University

               The ‘Ozette’ potato is one of the oldest heirloom varieties  grown in the Pacific Northwest (PNW) region. It was grown for over two centuries by the Makah tribe native to PNW coast of  Washington and was rediscovered in the late 1980s. Apart from Ozette, there are other similar looking clones in this area cultivated by native people of Alaskan coast. However, it was unclear whether they are genetically identical to ‘Ozette’ or not. In addition, the precise genetic origin of these clones is not yet known. To address this issue, we collected these heirloom clones from different parts of PNW and performed genetic diversity analysis using SNP markers. Our results showed that all these clones are genetically identical, and the variation associated are merely clonal selection from ‘Ozette’. We chose a phylogenomic approach to study the evolutionary relationship of ‘Ozette’ with respect to modern day cultivated potatoes as well as clones which originated in North America, Mexico and Chile, and Central Andean regions. ‘Ozette’ clone from the potato gene bank was sequenced using PacBio HiFi Sequencing. We generated an average of 11.74 M high-fidelity (HiFi) raw reads.  The genome was assembled using the Hifiasm assembler. Primary assembly resulted in a contig N50 of 25 Mb . The contigs further assembled to scaffolds using high-throughput chromatin conformation capture (Hi-C) sequencing data. The completeness of assemblies was supported by BUSCO, with an average score of 98.7% (single-copy and duplicated). Finally, predicted gene models from Ozette, modern day cultivated potatoes and clones originating in North America, Mexico and Chile, and Central Andean regions will be used for identifying structural variants (presence/absence variants) and developing phylogenetic tress to study the evolutionary relationships. 

9:30am-9:45am
Genetic Basis for Broad Interspecific Compatibility in Solanum verrucosum        
William Behling, Michigan State University       

Solanum verrucosum (2x = 2n = 24) is a unique species with a perplexing evolutionary history.  It is one of the only fully self-compatible diploid potato species, and uniquely lacks prezygotic interspecific reproductive barriers allowing it to accept pollen from a broad range of Solanum species. This allows S. verrucosum to serve as “bridge” between the cultivated or primary potato gene pool and the distantly related species in the tertiary gene pool. The genetic mechanisms that underpin self-compatibility in Solanum often underpin interspecific compatibility interactions. In S. verrucosum, self-compatibility, and by extension interspecific compatibility, has been attributed to the lack of S-RNase expression. The lack of S-RNase expression in theory would remove the central barrier to self and interspecific pollen. However, this has never been confirmed and may not be the only important factor contributing to interspecific compatibility. In the tomato clade S-RNase alone cannot reject incompatible pollen tubes, a functioning copy of HT-A or HT-B must also be present. HT also mediates S-RNase-independent pollen rejection in interspecific pollination in tomato. The importance of HT in interspecific pollen rejection is supported by previous research where CRISPR-Cas9 knockouts of S-RNase alone in S. tuberosum could not replicate the phenotype observed in S. verrucosum. We created a true F2 mapping population (n = 150) segregating for interspecific reproductive barriers to elucidate the mechanisms responsible for lack of interspecific reproductive barriers in S. verrucosum. The F2 population was evaluated for the ability to accept pollen from two clade 1 species S. pinnatisectum and S. tarnii, and QTL analysis was used to identify associated markers. The results confirmed the central role of the S-locus, implicating S-RNase, but interestingly no other QTL’s were identified. In these pollinations S-RNase alone mediates interspecific compatibility in S. verrucosum, and HT and other factors did not play significant roles.