Location: Vegetable Crops Research
2023 Annual Report
Objectives
Objective 1: Identify and maintain a set of wild potato plants, determine the DNA sequence of each, evaluate the distribution of genetic diversity among these wild potatoes, and use this information to guide breeders in developing improved potato germplasm.
Objective 2: Characterize the set of wild potato plants from Objective 1 for resistance to major potato diseases and pests, including late blight, early blight, Verticillium wilt, and Colorado potato beetle, and map these resistance traits to identify the genetic regions responsible for these traits.
Objective 3: Create hybrids between diploid cultivated potato and the set of wild potato plants from Objective 1, characterize these hybrids for plant and tuber traits, and provide the data to the breeding community to use in developing improved potato germplasm.
Approach
Objective 1: We have identified 10 wild diploid Solanum species with demonstrated utility in potato breeding. Within each species, we will choose 10 accessions for this project based on published resistance data, personal experience, and genebank passport data. Multiple individuals from each wild species will have their S-locus RNase alleles sequenced. Fertility of individuals will be assessed by assaying for pollen viability and production of berries with viable seeds. Disease and pest resistance screens will be carried out on multiple plants in each accession for which a specific resistance trait has been reported previously. Based on these data, twenty individuals from each species will be selected for SNP genotyping, detailed phenotyping and clonal maintenance.
Objective 2: Individual clones identified in Objective 1 will be characterized for resistance to major potato diseases and pests, including late blight, early blight, Verticillium wilt, and Colorado potato beetle. For each disease or pest, we will perform disease inoculations or beetle challenges that generate quantitative resistance scores using previously published methods. R-genes within each individual will be sequenced using RenSeq and the position of R-genes will be mapped to the potato genome.
Objective 3: We will create hybrids by crossing flowers of diploid cultivated potato with pollen from the 200 wild potato plants identified in Objective 1. Resulting hybrids will be characterized for plant growth and tuber traits including size, shape, color and yield. These phenotypic data will be shared with the potato breeding community to use in developing improved potato germplasm. Phenotypic data and genotypic data will be deposited into GRIN and the clones used for this research will be donated to the NRSP-6 potato genebank for use by others.
Progress Report
This is the final report for this project which terminated in March 2023. See the report for the replacement project, 5090-21220-006-000D, “Introgression of Disease Resistance and Tuber Quality Traits from Wild Species Relatives into Diploid Cultivated Potato” for additional information.
The goal of this project is to select and characterize a total of 200 clones from 10 wild species relatives of potato that have valuable genetic traits. Our vision for this collection is that it will be a data-rich genetic resource for potato breeding and research. Clones for the collection were identified by screening accessions from the U.S. Potato Genebank for disease and pest resistance, as well as for plant vigor, fertility and tuber formation under a long-day environment. Clones selected based on one trait have been evaluated for other traits, and genetic data related to each clone has been collected. Additional DNA sequence data are being generated. Each individual in the collection is a clone that can be maintained vegetatively and the utility of each clone increases as more information about it is obtained. Our next 5-year research plan builds on the foundation established in this project and uses this collection of wild species clones to develop additional resources for potato breeding, especially for the introgression of traits from wild species relatives into cultivated potato. Progress on the current 5-year project is summarized below.
Objective 1. The 200-clone diversity panel has been assembled from accessions of wild species relatives of potato that are likely to be useful for improving cultivated potato. Members of the panel were screened for growth vigor, fertility, and tuber production under long-day conditions and tuber size.
Objective 1. Sequences for the S-locus ribonuclease (RNase) genes expressed in the diversity panel are being acquired. These genes determine if a clone is self-fertile, and this trait is important for germplasm enhancement and potato breeding efforts.
Objective 1. Genotyping by sequencing of the diversity panel is progressing. These data will facilitate development of genetic markers linked to traits of interest within the panel.
Objective 2. Clones in the diversity panel were screened for early blight and late blight resistance using replicated detached leaf assays and multiple resistant clones were identified. Tubers were screened for soft rot resistance in two replicated trials using wound inoculations and soft rot resistant clones were identified. A field screen for Colorado potato beetle resistance is being conducted in summer of FY23.
Objective 2. We determined that whole genome sequencing is a more cost-effective method than capture sequencing. We have initial candidates with robust and unique sources of disease resistance to begin sequencing. We have completed whole genome sequencing of S. microdontum and are currently working to identify R gene sequences within that accession.
Objective 3. Members of the diversity panel were crossed with other diploid lines to determine male and female fertility and produce families of progeny seeds that may be used for genetic analysis.
Objective 3. Clones are being screened for potato virus Y, potato virus X and potato spindle tuber viroid as a cautionary step prior to submission to the U.S. Potato Genebank. As needed, potato virus Y and potato virus X have been removed using heat and chemical treatment. Multiple methods for detecting potato spindle tuber viroid have been evaluated for sensitivity and reliability. Related subordinate work. The S-locus inhibitor gene was sequenced from diverse wild species relatives and cultivated potato. The product of this gene interacts with S-locus ribonucleases and the interaction determines, to a large extent, if pollination will result in seed production.
Related subordinate work. Wild species relatives of potato most commonly have two copies of each chromosome; they are diploid. Cultivated potato has four copies of each chromosome and this increase in chromosome number complicates potato genetics and slows breeding progress. As part of a larger effort to reinvent potato by reducing chromosome number to two, we received a NIFA planning grant and used it to organize a meeting on diploid potatoes that was attended by 38 potato industry representatives and researchers from 11 states and Canada. Participants included commercial and seed potato growers, state commissioners, company representatives, extension potato specialists, breeders from 10 of the 14 public U.S. programs, and one breeder from Canada. Based on discussions at this meeting, we wrote and submitted an SCRI SREP proposal, including contributions from industry. We published research papers on true potato seed germination and a high throughput method for generating dihaploids, providing tools for future research on diploid potato. We generated dozens of diploid potato lines from russet, chip and red skinned potato cultivars including Pike, superior, Castle Russet, La Belle Russet, Payette Russet, Ranger Russet, Pacific Russet, Mercury Russet, Russet Norkotah, Silverton Russet and Red Norland. Genomic sequences for approximately 15 of these clones have been obtained. Our research in developing diploid hybrid potatoes has been highlighted in prominent journals, including the cover stories of the February 8 2019 issue of Science and the May 2019 issue of Genetics.
Accomplishments
1. Novel form of resistance gene regulation discovered in potato. Introduction of resistance (R) genes into plants can confer a high level of disease resistance, but improper expression of R genes can cause plant stress leading to yield losses. Understanding how plants balance growth with disease resistance is important for the improvement of crop germplasm. ARS researchers in Madison, Wisconsin, have determined the molecular mechanisms involved in expression of the R gene RB (resistance from S. bulbocastanum), which confers resistance to potato late blight. RB undergoes alternative splicing of its intron, resulting in two transcriptional isoforms, which coordinately regulate plant immunity and growth homeostasis. During normal plant growth, RB mainly exists as intron-retained isoform encoding a truncated lost-function RB protein to to avoid plant stress and maintain normal plant growth without pathogen infection. Upon late blight infection, the causal pathogen Phytophthora infestans induces intron splicing of RB, increasing the abundance of a full-length and active resistance protein. We identified the P. infestans effector IPI-O1 as a facilitator of RB alternative splicing. Importantly, IPI-O1 directly interacts with potato splicing factor StCWC15 to promote RB splicing for activation of RB-mediated resistance. Thus, our study reveals that StCWC15 serves as a surveillance facilitator sensing the pathogen-secreted effector maintaining the trade-off between RB-mediated plant immunity and growth, expanding our understanding of molecular plant-microbe interactions. Our understanding of the molecular mechanisms involved in proper RB gene expression provides guidance for how to improve the deployment of RB into cultivated potato to avoid plant-stress-associated yield losses. The introduction of resistance genes into new crops should utilize the genomic copy of the gene, with introns and the native promoter, in order to ensure proper gene regulation and avoid plant stress during normal growth.
2. Screening of wild potatoes identifies new sources of late blight resistance. While most cultivated potato varieties are susceptible to the potato late blight, wild relatives of potato are an excellent source of resistance. Late blight, caused by the oomycete pathogen Phytophthora infestans, remains the most destructive disease of potato worldwide, causing annual losses estimated at up to six billion dollars. ARS researchers in Madison, Wisconsin, received 384 accessions of 68 wild potato species from the U.S. Potato Genebank and screened them for resistance to the late blight pathogen Phytophthora infestans in a detached leaf assay. From this screen, 39 accessions were identified with strong disease resistance and another 33 accessions contained a mixture of resistant and susceptible individuals. Resistance to late blight was found in Solanum albornozii, Solanum agrimoniifolium, Solanum chomatophilum, Solanum ehrenbergii, Solanum hypacrarthrum, Solanum iopetalum, Solanum palustre, Solanum piurae, Solanum morelliforme, Solanum neocardenasiI, Solanum trifidum and Solanum stipuloideum. These species will be a valuable source of novel late blight resistance for potato breeding.
3. Modification of a late blight resistance gene to avoid effector-mediated suppression. Plant breeders are interested in the identification and incorporation of simply inherited genes that confer robust resistance to diseases. These resistance (R) genes typically encode proteins that recognize the presence of very specific pathogen molecules, termed effectors, and activate plant defense responses. We previously identified a late blight (Phytophthora infestans) effector that suppresses the activity of the RB (resistance from S. bulbocastanum) resistance protein through direct protein to protein interaction. ARS scientists in Madison, Wisconsin, mined the sequences of natural genetic variants of RB from wild potato relatives and identified specific amino acids in the RB resistance protein that allow it to avoid disease suppression from the blight effector and maintain its ability to activate defense responses. The specific sequence variants of the RB resistance protein identified in this research are excellent candidates for introducing strong late blight resistance into potato. Late blight resistant varieties would substantially decrease costs of production by minimizing expenses associated with fungicide sprays and preventing yield losses caused by reduced tuber production and post-harvest spoilage.
4. Transfer of resistance to common scab from wild to cultivated potatoes. Common scab, caused by the soil-borne bacterium Streptomyces scabies, is a persistent threat to the potato industry. It causes unsightly pits on the surface of potatoes and results in economic losses and waste due to rejection for all potato market classes. ARS scientists in Madison, Wisconsin, identified strong scab resistance in a wild relative of potato and demonstrated that resistance can be transferred to cultivated potato. Through a series of crosses, we incorporated resistance into parental lines and released them to breeders who are using them to develop their own resistant cultivars. The development of cultivars with enhanced levels of resistance to common scab will address a major cause of marketable yield loss for potato growers and will provide more attractive potatoes to consumers.
Review Publications
Bethke, P.C., Halterman, D.A., Francis, D.M., Jiang, J.M., Douches, D.S., Charkowski, A.O., Parsons, J. 2022. Diploid potatoes as a catalyst for change in the potato industry. American Journal of Potato Research. (2022) 99:337–357. https://doi.org/10.1007/s12230-022-09888-x.
Bethke, P.C. 2023. Cool soil Increases potato (Solanum tuberosum) tuber number in multiple varieties and alters skin color intensity of ‘Red Norland’ and ‘Adirondack Blue’. American Journal of Potato Research. (2023) 100:79-86. https://doi.org/10.1007/s12230-022-09901-3.
