NCCC_old215: Potato Breeding and Genetics Technical Committee

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Inactive/Terminating

Project Menu

SAES-422 Reports

Annual/Termination Reports:

[02/01/2018] [02/09/2019] [07/29/2020] [01/01/1970] [03/07/2022]

Date of Annual Report: 02/01/2018

Report Information

Annual Meeting Dates: 12/04/2017 - 12/05/2017
Period the Report Covers: 12/01/2016 - 11/30/2017

Participants

Participants Attachment:

NCCC215 2017 attendees.xlsx

Brief Summary of Minutes

Minutes Attachment:

NCCC215 meeting minutes 2017.docx

Accomplishments

Publications

Impact Statements

Date of Annual Report: 02/09/2019

Report Information

Annual Meeting Dates: 12/10/2018 - 12/11/2018
Period the Report Covers: 12/01/2017 - 12/01/2018

Participants

Laura Shannon UMN
Husain Agha UMN
Beck Eddy UW-Madison
Ruth Genger UW-Madison
Susie Thompson NDSU
Sagar Sathuvalli OSU
Heather Tuttle UMN
Corin Curwen McAdams Bejo Seeds
Maher Alshlany MSU
Matt Zuehlke MSU
Thilani Jayakody MSU
Greg Steere MSU
Kate Shaw MSU
Ray Hammerschmidt MSU
Joe Coombs MSU
Dave Holm CSU
Caroline Gray CSU
Isabel Vales TAMU
Jeff Koym TAMU
Chen Zhang MSU
Alfonso del Rio UW-Madison
Max Martin USDA genebank
Douglas Scheuring TAMU
Lin Song UW-Madison
Asma Alkhaj UW-Madison
Han Tan University of Maine
Andy Hamernick UW-USDA
Maria Caraza-Harter UW-Madison
Felix Enciso MSU
Hari Karki UW
Benoit Bizimungu AAFC
Mark Clough NC State University
Meng Li UW-Madison
Shelley Jansky USDA-ARS
Walter DeJong Cornell
David Douches MSU
Natalie Kaiser MSU
Cari Schmitz Carley UMN
Charlie Higgins Potato USA
Greg Porter UMaine
Craig Yencho NCSU
Dennis Halterman USDA
Jeff Endelman UW-Madison

Brief Summary of Minutes

NCCC215 meeting Dec 10-11, 2018

Hyatt Regency Chicago O’Hare

Chair: Jeff Endelman (WI)

Vice-chair: Dennis Halterman

Secretary: Laura Shannon

Monday 12/10/18

Call to order by Jeff Endelman.

Agenda:

Monday

1-3:15 Research presentations

3:15 -3:45 Break

3:45 – 5:30 Research presentations

Introductions – see attached sign in list

Research Projects

Wisconsin

Maria Caraza-Harter – Endelman – Skin Set and Dormancy in Red Potatoes

Ruth Genger – Dawson – Participatory potato breeding and selection for Midwest organic systems

Li Meng – Jansky – Potato pollen analysis through impedance flow cytometry

Shelley Jansky (for Jim Busse and Paul Bethke) – Inbreeding Red Norland

Shelley Jansky -- Identifying CPB resistant clones, DM x M6 (F5, F6 populations), Dihaploid extraction

Dennis Halterman (for Sidrat Abdullah) – Development of diploid germplasm with late and early blight resistance

Dennis Halterman – Identifying host target(s) of infestans effector IPI-O1

Hari Karki – Halterman – Application of capture based NGS technology in mapping and cloning genes in potato

Alfonso del Rio (for John Bamberg) – USPG collecting trip SW-2018

Alfonso del Rio – Promoting sustainable potato agriculture in the Andean region by breeding for frost tolerance

Minnesota

Heather Tuttle – Shannon – Diversity analysis of diploids and tetraploids using GBS data

Husain Agha – Shannon – Dihaploid Seed Production

Cari Schmitz Carley – Shannon – Quantifying differentiation between South American collections and US breeding clones

Michigan

Felix Enciso-Rodriguez – Douches – Overcoming self-incompatibility in diploid potatoes using CRISPR/Cas-9

Kate Shaw – Douches – Dihaploid Potato Production at Michigan State University

Maher Alsahlany – Douches – Introgressing Self-compatibility to Solanum tuberosum dihaploids for diploid variety development

Chen Zhang – Douches—Application of molecular markers in marker assisted selection in Michigan State Breeding program

Thilani Jayakody – Douches -- Gene editing in diploid potato

Natalie Kaiser – Douches – Deploying durable Colorado potato beetle resistant diploid breeding lines

Matt Zuehlke -- Douches – Certified Seed Minituber Production

Greg Streere – Douches – Michigan State University Potato Grading Line Upgrade

Tuesday 12/11/18

Jeff Endelman called the meeting back to order and reminded us of the agenda.

Tuesday

8:15 – 9:00 Approve minutes, new business, scheduling 2019 meetings, officer elections, announcements

9-10:30 Breeder talks

10:30-11 Break

11-12 Breeder presentations

Susie Thompson moved to approve the minutes and Dave Douches seconded. Unanimously approved. Jeff reminded us that the North Central Region breeders we need to submit a report to Ray Hammerschmidt.

When should we meet? 12/9-12/10 or 12/2-12/3? We will meet 12/9-12/10, location TBD.

Elections for secretary, call for nominations: Dennis Halterman nominated Dave Douches. Dave accepted the nomination. Susie Thompson moved to close nominations. Dave Douches unanimously approved.

Announcements

Ray Hammerschmidt– When you write reports think about the difference between impacts and accomplishments. Work on diploids, grants that come out of the group, varieties being used all count as accomplishments.

USDA attempting to consolidate types of programs. Farm bill moving ahead, senate version getting traction. Two open positions at MSU – dry bean breeding and genetics position and plant resilience broadly defined.

Dave Douches – Steve Tanksley has a position open and there is a USDA ARS position at Aberdeen for a molecular geneticist to work with potato breeders (there’s also a post doc there). Jeff Stark’s position in University of Idaho has reopened – looking for a potato agronomist.

Craig Yencho – looking to hire a masters level position with field work and data base management components.

Dave Douches – Re-designing the SNP array, adding 14K SNPs from diploid germplasm and Glenn Bryan’s GBS analysis to the 22K array. Reduce ascertainment bias, increasing coverage, eliminating gaps. The price is probably going to stay at approx. $50.

Jeff Endelman – For the first time in 2018 Atlantic was unseated as the primary chip cultivar by Lamoka. Congrats to Walter!

Potato R gene KASP panel

Excellence in breeding initiative, High throughput genotyping service established for CIGAR breeding programs

Cheap KASP assay to screen breeding lines

~$3/sample for 10 SNPs (includes DNA extraction)

CIP breeding program has begun to utilize Ry-adg based on M6 amplicon

Exploring whether other public programs can utilize this service, adding Ry-sto, H1, and R8

Jeff is still working out the details with Intertek

It can be customized, everyone can have their own

Shelley Jansky – Diploid breeding update

We were funded for a planning grant

We had a planning meeting in October

We have submitted as SCRI pre-proposal with 6 PDs – Shelley Jansky, Dave Douches, Jeff Endelman, Laura Shannon, Paul Bethke, and Robin Buell

If asked to submit a full proposal we will need help with dihaploid extraction and evaluation and we’re hoping other programs are interested in participating.

Jeff Endelman – SCRI polyploid tools proposal

Isabel Vales and Jeff Endelman are working on the potato part

Breeders Presentations

Jeff Endelman – Wisconsin

Susie Thompson – North Dakota

Laura Shannon – Minnesota

Accomplishments

NCCC 215 Accomplishments   Douches (MSU) Application of Molecular Markers in MSU Potato Breeding With the development of molecular markers for potato breeding, marker-assist selection has been incorporated into our routine breeding practice and greatly facilitate the selection process. Some of the main markers that are used at MSU include: RYSC3 and M6, Potato virus Y (PVY) resistance markers; RxSP, a Potato virus X (PVX) resistance marker; TG689, a Golden Nematode resistance marker; RB and R8, Late Blight resistance marker. PVY markers have been the most frequently used tools to assist selection in our program due to the importance of PVY resistance. According to the pedigrees, selections from our single-hill trial (1st year of field selection) are screened for PVY markers every year. This allowed for a prioritization of the space in the field, and for earlier, more informed decisions in variety selection.  Decoding S. chacoense-derived Colorado potato beetle resistance Introgression of Colorado potato beetle resistance from S. chacoense-derived diploid recombinant inbred lines into cultivated backgrounds is being conducted. Subsequent marker assisted selection will yield diploid breeding lines with beetle resistance and desirable tuber traits. The spatio-temporal durability of this glycoalkaloid-based host plant resistance will be assessed using Colorado potato beetle populations from potato growing regions across the nation and examining 10 successive generations of beetles grown on host plant resistant material.  Furthermore, the development of cross-resistance by beetles grown on host plant resistant material to commercial insecticides will be examined to inform the most sustainable deployment of this germplasm."  New Grading line for trial plot evaluation at MSU Michigan State University's potato group updated its grading line in 2018. Variable speed drives control: a new lift; custom built barrel washer; grading table; and Kerian speed sizer. Incorporation of bar-coded labels, and scales synchronized to computer hot keys, have improved the speed, accuracy and efficiency of the grading process.  All entities of the potato group: Potato Breeding and Genetics; Potato Outreach Program; pathologists and soil fertility researchers have access to this new equipment.  Overcoming self-incompatibility in diploid potato using CRISPR-Cas9 The aim of this project was to generate a targeted knock-out (KO) of the S-RNase gene, involved in gametophytic self-incompatibility in diploid potatoes, using CRISPR/Cas9 technology in an effort to avoid self-pollen degradation. We identified S-RNase alleles with flower-specific expression in two diploid self-incompatible lines using genome resequencing data. S-RNase gene mapped to chromosome 1 within a low recombination region. S-RNase KO lines were obtained causing premature stop codons. Fruits were set in selected KO and produced viable T1 seeds, and a Cas9-free KO line. Our results suggest that creating S-RNase KO can contribute to generation of self-compatible lines as a first step for the generation of commercial diploid cultivars.  Gene editing in diploid potato MSU’s breeding program has developed diploid germplasm with important agronomic qualities. These lines can be further characterized on traits for the use of gene editing. Thus, the first objective of my thesis project is to characterize the MSU diploid germplasm for important molecular and morphological traits such as regeneration capability. The second major objective is to use gene editing, namely, CRISPR-Cas9 to knockout vacuolar invertase (VInv) in select diploid lines. The overall goal is to further advance the diploid breeding program by introducing economically important traits and proving the utility of gene editing in potato.    Introgressing Self-compatibility to Solanum tuberosum Dihaploids for Diploid Variety Development Dihaploids of cultivated potato (Solanum tuberosum L.) have been produced for over 50 years to reduce the breeding and genetic challenges of autopolyploidy. Most dihaploids are male sterile (MS) that reduces the benefit of lower ploidy level of cultivated tetraploid potato. In this study, we used three self-compatibility (SC) donors to introgress SC into a wide range of dihaploid germplasm through a series of crosses to dihaploids which we refer to as S. tuberosum backcrossing. The SC increased from 11% in the F1 generation to 33% in the BC2 generations. Over 6,000 genome-wide SNPs were used to characterize the germplasm diversity, heterozygosity, and structure in two backcrossing generations. The BC2 generation was significantly improved regarding maturity, scab resistance, average tuber number, however, the yield in BC2 was not greater than the F1 and BC1 generations.  Certified NFT Minituber production at Michigan State University For 2 years, the MSU Potato Breeding program has operated its own certified NFT minituber production greenhouse. The ability to produce certified seed allows faster introduction of early generation material to the potato industry. It also helps position the program for participation in international trials. This presentation will discuss some of the operational aspects involved in certified seed production as well as provide some insight into things we have learned through experience. Transgenic Approaches to Building Late Blight and Stress Tolerance into Commercial Potatoes MSU conducts genetic engineering research to introgress and test economically important traits into potato.  We have a USAID-funded project to create and commercialize 3-R-gene potato varieties in Bangladesh and Indonesia.  This a partnership with Simplot Plant Sciences.  Simplot has been creating the plants for the target countries.  Greenhouse trials show that a high level of resistance to late blight has been achieved in events that have no backbone and are single inserts.  Trials are planned for the fall of 2019.  We also are exploring the value of XERICO for drought tolerance.  We transformed Ranger Russet with constructs that constitutively and under drought stress express the XERICO gene.  A small field trial was conducted with transplants in 2018.  The XERICO events performed well and had a higher specific gravity than Ranger Russet.   Variety Development Michigan State University released Mackinaw, which is a storage chip-processing potato with PVY resistance, late blight resistance and moderate scab tolerance.  They also released Huron Chipper, which is a late blight-resistant storage chipper with a good size profile for the chip processing industry.   Endelman (UW-Madison)             Foundation seed of two new potato varieties was released to growers in 2018. W9576-11Y is a yellow tablestock variety with high yield potential, attractive tubers, and intermediate maturity. W9433-1rus is a light-skinned, tablestock russet variety that bulks very quickly but with late vine maturity and skin set. Our 2016 red tablestock release W8405-1R was named ‘Red Prairie’ in 2018, and production increased to 29 acres of certified seed. We also received notice that the USDA will issue PVP certificates for the varieties ‘Pinnacle’ and ‘Hodag’.             The Endelman Lab published two manuscripts on potato breeding and genetics in 2018. Endelman et al. (2018) demonstrated the use of genome-wide markers to predict breeding values, which enables superior clones to be selected as parents more accurately and quickly. Schmitz Carley et al. (2018) used six years of data from 10 locations of the National Chip Processing Trial to quantify the amount of genotype x environment interaction for yield and specific gravity. Endelman delivered five oral presentations on potato breeding and genetics at scientific conferences and three outreach presentations targeted to growers, processors, and other stakeholders in the potato industry.  Shannon (UMN) The Shannon lab completed the first field season of the reconstituted Minnesota potato breeding program in summer 2018. Their current focus is to develop new Minnesota germplasm through crossing and selecting from unselected families from other programs. Additionally they are evaluating the legacy material from the previous breeder, Dr. Christian Thill. The remaining cultivars from Thill were genotyped on the 22K SolCAP array and it was determined that the Minnesota program shared a genetic basis with neighboring breeding programs. Of the 34 remaining legacy cultivars which had been grown in the same production field for six years from harvested tubers rather than clean seed, 10 have tested virus free after heat treatment and 24 are still undergoing anti-viral tissue culture.             Shannon delivered four presentations at national and international scientific conferences and five talks targeted at growers and industry.   Jansky (USDA-ARS)             We are beginning our new CRIS project to identify and clonally maintain 200 wild species plants for use by breeders and geneticists.  We have screened for Colorado potato beetle resistance in five accessions from three wild species and will select the most resistant clones for the collection.  Self-compatible plants have been found in two of the accessions.  These will be valuable for our inbred-hybrid breeding efforts. We continue to create recombinant inbred lines (RILs) from interspecific hybrids.  Some have a higher than average proportion of cultivated germplasm and are highly fertile and self-compatible.  These will also be used for breeding.  During the summer of 2018, we evaluated a set of RILs for root development in the field.  Large differences were detected in root development.  In the summer of 2018, we also carried out a large dihaploid extraction effort, making over 31,000 pollinations on cultivars and generating 1091 potential dihaploids.  Three of the parents are russets, so they have the potential to produce russeted dihaploids, which will be especially valuable for breeding. Finally, we have been testing an impedence flow cytometer for measuring pollen viability.  This has been a challenging endeavor, but we have made good progress and developed a protocol that is producing consistent results.  Halterman (USDA-ARS) Molecular markers linked to Verticillium wilt resistance in potato germplasm Verticillium wilt (VW) of potato (Solanum tuberosum), caused by two different soil-borne fungi Verticillium albo-atrum R & B or V. dahliae Kleb., is a major limiting factor in potato production throughout North America. Yield losses in potato associated with the disease can reach up to 50% in severely infested fields. In tomato, resistance to race 1 of Verticillium dahliae is conferred by a dominant Ve gene that has been exploited in breeding programs from more than 50 years. However, previously developed markers within the Ve gene in potato are unreliable in predicting resistance. The goal of this project is to identify additional genomic regions that determine VW resistance in potato. An F2 mapping population was developed by selfing an F1 individual derived from two homozygous diploid parents, S. tuberosum DM1-3 (susceptible to VW) and S. chacoense M6 (resistant to VW). Using a rooted cutting protocol, the population was phenotyped and SNP genotyped. A major QTL in chromosome 1 was identified that explains 31% of the phenotypic variation. A total of 22 genes are located within the QTL region, and two genes have been selected for further functional validation studies. Using the sequence information of these two genes, are developing markers to distinguish between resistant and susceptible germplasm.  The marker information will be a valuable tool for potato breeders interested in selecting for VW resistance.  Molecular interactions that influence virulence contributions of the IPI-O family of Phytophthora infestans effectors Phytophthora infestans, causal agent of potato late blight, is a destructive pathogen that is a frequently recurring problem worldwide. Several resistance genes exist in potato to counter against this pathogen, but the majority have been overcome after introgression into popular potato varieties. The RB gene, derived from Solanum bulbocastanum, has effector recognition specificity to members of the IPI-O family. Recognition of the IPI-O1 allele by RB elicits a hypersensitive resistance response while IPI-O4 can suppress this response. We have carried out several experiments to determine the virulence contributions of IPI-O1 and IPI-O4 during infection, and to identify host proteins involved in IPI-O recognition/suppression using co-immunoprecipitation and yeast two-hybrid. Our results indicate that both IPI-O1 and IPI-O4 contribute to P. infestans virulence, but their impact is influenced by the pathogen genotype. Protein interaction studies have identified both cytosolic- and membrane-localized host proteins that interact with IPI-O and will help to elucidate the function of these effectors in pathogen virulence. Together, we hope that our understanding of the function of the ubiquitous IPI-O effector will assist us in identifying or developing improved host resistance genes in potato. This work has been included in two publications (Chen and Halterman, 2017a; Chen et al., 2017b) Foliar resistance to bacteria in potato Solanaceous crops including tomato, pepper, and eggplant are susceptible to many foliar bacterial pathogens. However, cultivated potato is immune to most pathogenic Pseudomonas and Xanthomonas species. The purpose of this project is to understand the mechanisms involved in limiting infection of bacteria in the foliage of potato. We have previously found that many popular potato cultivars are immune P. syringae pv. tomato DC3000, while many wild species accessions of potato are susceptible or tolerant, suggesting that resistance to foliar pathogens may have been selected during cultivation of potato as a food crop. We have used various DC300 strains defective in pathogenesis. Populations between wild and cultivated potato have also been developed to map the resistance locus using SNP genotyping. The identification of novel genes involved in bacterial resistance will facilitate the development of new varieties of Solanaceous crops.  Development of diploid potato germplasm containing disease resistance             Using a combination of diploid wild species hybrids and dihaploid cultivated germplasm from the programs of David Douches (Michigan State) and Shelley Jansky (USDA-ARS), we have developed populations segregating for resistance to potato late blight and early blight. Seventeen families from crosses between various parents were phenotyped using detached leaflet assays and whole plant inoculation assays (greenhouse) to identify individuals with increased resistance to either or both diseases. Three families contained individuals with high levels of late blight resistance and one family had individuals with increased early blight resistance. Selected individuals were grown in the field and assayed for agronomic characteristics including tuber size and shape, specific gravity, and chip quality. Three individuals were chosen for crossing with diploids containing resistance to other diseases, including PVY and Verticillium wilt. Bamberg (USDA-ARS) Collected 33 new germplasm accessions in the southwest USA.  Distributed almost 10,000 samples to germplasm to users in 34 states and 13 foreign countries.  Organized and supported screening of the microdontum core collection, resulting in discovery of strong resistance to Dickeya.  Cooperative cold hardiness breeding with Peru resulted in the release of the new cultivar “Wiñay” this year.  The three cultivar releases published in AJPR this year all have wild species in their pedigrees.  A link to the related NRSP6 project’s annual reports can be found on NIMSS and the USPG website, <a>https://www.ars-grin.gov/nr6/admin.html</a>  Grants awarded in 2018  Title <table> <tbody> <tr> <td width="125"> </td> <td width="125"> PIs </td> <td width="125"> Source </td> <td width="125"> Duration </td> <td width="125"> Budget </td> </tr> <tr> <td width="125"> Planning for a CAP proposal to convert potato into a diploid inbred-hybrid crop </td> <td width="125"> Shelley Jansky (USDA-ARS) </td> <td width="125"> USDA-NIFA </td> <td width="125"> 9/1/18 – 8/31/19 </td> <td width="125"> $50,000 </td> </tr> <tr> <td width="125"> Genome-wide evaluation of off-targets from gene editing reagents in seed vs. vegetatively propagated crop species </td> <td width="125"> David Douches (MSU) </td> <td width="125"> USDA-NIFA </td> <td width="125"> 9/1/18 – 8/31/21 </td> <td width="125"> $500,000 </td> </tr> <tr> <td width="125"> Development of biological pesticide(s) to combat late blight and other potato diseases </td> <td width="125"> Dennis Halterman (USDA-ARS), Jason Kwan (UW-Madison) </td> <td width="125"> USDA ARS </td> <td width="125"> 8/1/18 – 5/31/19 </td> <td width="125"> $67,500 </td> </tr> <tr> <td width="125"> Targeting a conserved structural module in Phytophthora effectors for disease resistance </td> <td width="125"> Dennis Halterman (USDA-ARS), Wenbo Ma (UC-Riverside) </td> <td width="125"> USDA-NIFA/NSF </td> <td width="125"> 9/1/18 – 8/31/21 </td> <td width="125"> $650,000 </td> </tr> </tbody> </table>

Publications

Publications   Abdullah S, Halterman D. 2018. “Methods for Transient Gene Expression in Wild Relatives of Potato,” in Plant Pathogenic Fungi and Oomycetes, vol. 1848, Methods in Molecular Biology, W. Ma, T. Wolpert, Eds., New York City: Humana Press. pp. 131–138. Bali S, Patel G, Novy R, Vining K, Brown C, Holm D, Porter G, Endelman J, Thompson A, Sathuvalli V. 2018. Evaluation of genetic diversity among Russet potato clones and varieties from breeding programs across the United States. PLoS ONE 13(8):e0201415. Bali S, Robinson BR, Sathuvalli V, Bamberg JB, Goyer A. 2018. Single nucleotide polymorphism markers associated with high folate content in wild potato species. PLoS ONE 13(2):e0193415 Bamberg, J.B.  2018.  Diurnal alternating temperature improves germination of some wild potato (Solanum) botanical seedlots.  American Journal of Potato Research 95:368-373.   Bisognin, D. A., N. C. Manrique-Carpintero, and D. S. Douches. 2018. QTL Analysis of Tuber Dormancy and Sprouting in Potato. American Journal of Potato Research 95:374–382. https://doi.org/10.1007/s12230-018-9638-0   Crossley, M.S., S.D. Schoville, D.M. Haagenson, and S.H. Jansky. 2018. Host plant resistance to Colorado potato beetle (Coleoptera:Chrysomelidae) in diploid F2 families derived from crosses between cultivated and wild potato. Journal of Economic Entomology.  doi: 10.1093/jee/toy120   Deperi, S. I., Ma. E. Tagliotti, M. Cecilia Bedogni, N. C. Manrique-Carpintero, J. Coombs, R. Zhang, D. Douches, and M. A. Huarte. 2018. Discriminant analysis of principal components and pedigree assessment of genetic diversity and population structure in a tetraploid potato panel using SNPs. PloS One 13:e0194398.   Ellis, D., O. Chavez, J. J. Coombs, J. V. Soto, R. Gomez, D. S. Douches, A. Panta, R. Silvestre, and N. L. Anglin. 2018. Genetic Identity in Genebanks: Application of the SolCAP 12K SNP Array in Fingerprinting and Diversity Analysis in the Global In Trust Potato Collection. Genome 61:523-537.   Enciso-Rodriguez, F., D. Douches, M. Lopez-Cruz, J. Coombs, and G.de los Campos. 2018. Genomic Selection for Late Blight and Common Scab Resistance in Tetraploid Potato (Solanum tuberosum). G3: Genes, Genomes, Genetics 8:2471-2481.   Endelman JB, Schmitz Carley CA, Bethke PC, Coombs JJ, Clough ME, da Silva WL, De Jong WS, Douches DS, Frederick CM, Haynes KG, Holm DG, Miller JC, Muñoz PR, Navarro FM, Novy RG, Palta JP, Porter GA, Rak KT, Sathuvalli VR, Thompson AL, Yencho GC. 2018. Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato. Genetics 209:77–87.   Graebner RC, Brown CR, Ingham RE, Hagerty CH, Mojtahedi H, Quick RA, Hamlin LL, Wade N, Bamberg JB, Sathuvalli V. 2018. Resistance to Meloidogyne chitwoodi identified in wild potato species.  American Journal of Potato Research 95:679-686.   Hirsch RL, Miller S, Halterman D. 2018. An inquiry-based investigation of bacterial soft rot of potato. The American Biology Teacher. 80: 594-599.   Jansky, S., D. Douches, and K. Haynes. 2018. Transmission of scab resistance to tetraploid potato via unilateral sexual polyploidization. American Journal of Potato Research. 95:272-277.   Jansky, S., D. Douches, and K. Haynes. 2018. Three tetraploid clones with resistance to common scab. American Journal of Potato Research. 95:178-182.   Jansky, S.H. and D.M. Spooner. 2018. The evolution of potato breeding. Plant Breeding Reviews. 41:169-214.   Leisner, C. P., J. P. Hamilton, E. Crisovan, N. C. Manrique‐Carpintero, A. P. Marand, L. Newton, G. M. Pham et al. 2018. Genome sequence of M6, a diploid inbred clone of the high‐glycoalkaloid‐producing tuber‐bearing potato species Solanum chacoense, reveals residual heterozygosity. The Plant Journal 94:562-570.   Li, M., H. An, A. Ruthie, C. Bagaza, A. Batushansky, L. Clark, V. Coneva, M.J. Donoghue, E.             Edwards, D. Fajardo, H. Fang, M. H. Frank, T. Gallaher, S. Gebken, T. Hill, S. Jansky, B. Kaur, P. C. Klahs, L. L. Klein, V. Kuraparthy, W. C. Otoni, J. C. Pires, E. Rieffer, S. Schmerler, E. Spriggs, C. N. Topp, A. van Deynze, K. Zhang, L. Zhu, B.M. Zink, and D. H. Chitwood. 2018. Topological data analysis as a morphometric method: Using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science 9:1-14.   Majeed, N., B. Javaid, F. Deeba, S. Muhammad Sa. Naqvi, and D. S. Douches. 2018. Enhanced Fusarium oxysporum f. sp. tuberosi Resistance in Transgenic Potato Expressing a Rice GLP Superoxide Dismutase Gene. American Journal of Potato Research  95:383–394. https://doi.org/10.1007/s12230-018-9639-z   Mambetova, S., W. W. Kirk, N. Rosenzweig, and D. S. Douches. 2018. Characterization of Late Blight Resistance Potato Breeding Lines with the RB Gene from Solanum bulbocastanum. American Journal of Potato Research 95:564–574. https://doi.org/10.1007/s12230-018-9664-y   Manrique-Carpintero, N. C., J. J. Coombs, G. M. Pham, F. P. E. Laimbeer, G. T. Braz, J. Jiang, R.E. Veilleux, C. R. Buell, and D. S. Douches. 2018. Genome reduction in tetraploid potato reveals genetic load, haplotype variation, and loci associated with agronomic traits. Frontiers in Plant Science 9, 944.   Schmitz Carley CA, Coombs JJ, Clough ME, De Jong WS, Douches, Haynes KG, Higgins CR, Holm DG, Miller Jr. JC, Navarro FM, Novy RG, Palta JP, Parish DL, Porter GA, Sathuvalli VR, Thompson AL, Yencho GC, Zotarelli L, Endelman JB. 2018. Genetic covariance of environments in the National Chip Processing Trial. Crop Science, published online ahead of print, Nov. 8, 2018. doi: 10.2135/cropsci2018.05.0314   Tai H, De Koeyer D, Sønderkær M, Hedegaard S, Lägue M, Goyer C, Nolan L, Davidson C, Gardner K, Neilson J, Paudel J, Murphy A, Bizimungu B, Wang HY, Xiong X, Halterman D, and Nielsen KL. 2018. Verticillium dahliae disease resistance and the regulatory pathway for tuberization in potato. The Plant Genome. 11: 170040.   Tagliotti, M. E., S. I. Deperi, M. C. Bedogni, R. Zhang, N. C. Manrique Carpintero, J. Coombs, D. Douches, and M. A. Huarte. 2018. Use of easy measurable phenotypic traits as a complementary approach to evaluate the population structure and diversity in a high heterozygous panel of tetraploid clones and cultivars. BMC Genetics 19:8.   Wu S, Zhang B, Keyhaninejad N, Rodriguez G, Kim H, Chakrabarti M, Illa-Berenguer E, Taitano N, Jose Gonzalo M, Diaz A, Pan Y, Leisner C, Halterman D, Buell CR, Weng Y, Jansky S, van Eck H, Willemsen J, Monforte A, Meulia T, and van der Knaap E. 2018. A common genetic mechanism underlies morphological diversity in fruits and other plant organs. Nature Communications. 9:4734.   Yong, YS and SH Jansky. 2018. Considerations for selecting disease resistant wild germplasm: Lessons from a case study of resistance to bacterial soft rot and Colorado potato beetle. Genetic Resources and Crop Evolution. 65:2287-2292.

Impact Statements

Date of Annual Report: 07/29/2020

Report Information

Annual Meeting Dates: 12/09/2019 - 12/10/2109
Period the Report Covers: 12/01/2018 - 12/01/2019

Participants

see attached file

Participants Attachment:

Participants.docx

Brief Summary of Minutes

NCCC215 Breeding and Genetics Technical Committee Meeting

December 9-10, 2019

Chair: Dennis Halterman; Vice-Chair: Laura Shannon; Secretary: Dave Douches

Administrative Advisor: Ray Hammerschmidt

Agenda

Monday, December 9

1:00 – Welcome and Introductions

1:15 – Tribute to Creighton Miller

1:20 – 3:15 Research presentations

3:15 – 3:45 Break

3:45 – 5:30 Research presentations

Order of research presentations:

Michigan

Minnesota

North Dakota

Wisconsin

Other contributors

Tuesday, December 10

7:30 – 8:15 SCRI Diploid potato discussion

8:15 – 8:45 Potato pan-genome discussion

8:45 – 9:05 Approve minutes, new business, scheduling 2020 meeting, officer elections, announcements

9:05 – 9:15 Administrative Advisor report

9:15 – 10:30 Breeder presentation

10:30 – 11 Break

11 – 12 Breeder presentations

Minutes of meeting and Research Project report titles

Michigan

Sarah Lee – Douches – Overcoming self-incompatibility in diploid potatoes using CRISPR/Cas-9

Paul Collins – Douches – Introgressing Self-compatibility to Solanum tuberosum dihaploids for diploid variety development

Thilani Jayakody – Douches -- Gene editing in diploid potato

Natalie Kaiser – Douches – Deploying durable Colorado potato beetle resistant diploid breeding lines

Douches – Dihaploid Potato Production at Michigan State University; Application of molecular markers in marker assisted selection in Michigan State Breeding program; Certified Seed Minituber Production

Will Behling – Interspecific crossing barriers and self-compatibility

Genevieve Hoopes – Circadian rhythm in potato

Wisconsin

Maria Caraza-Harter – Genetics of Skin Set Red Potatoes

Filipe Matias – FIELDimageR – A tool to analyze othologous data

Lin Song – diploid potato breeding and the selection for self-compatibility

Jansky (for Akito Nashiki) – Verification of cold stratification for TPS germination

Shelley Jansky (for Jim Busse and Paul Bethke) – Fixing red color through inbreeding Red Norland

Shelley Jansky (for Asma Aikhaja) – Creating dihaploids from Russet Nortotah

Shelley Jansky – RILS and germplasm releases

Dennis Halterman – Resistance breaking in PVY

Dennis Halterman – infestans effector IPI-O1 disruption of RB gene

Hari Karki – Halterman – Source of late blight resistance in Payette Russet

John Bamberg – summary of USPG reported above

Minnesota

Heather Tuttle – Shannon – Diversity analysis of diploids and tetraploids using GBS data

Husain Agha – Shannon – Dihaploid Seed Production – Using NIR spec to determine ploidy

North Dakota

Felicity Merritt – Identification of genes involved in sugar end disorder in 4x potato

Maine

Oluwafemi Alaba (with Han Tan) – Leveraging haploid induction in tetraploid potato

Tuesday 12/10/19

Dennis Halterman called the meeting back to order and reminded us of the agenda.

Shelley Jansky and Jeff Endelman– Diploid breeding grant update

We were funded starting October 1, 2019

The objectives were reviewed for the breeding and genetics community

Jeff Endelman – and Genevieve Hoopes – PanGenome update

Genevieve gave a presentation on the assembly of the Atlantic and Castle Russet genomes

Susie Thompson moved to approve the 2018 minutes and Dave Douches seconded. Unanimously approved.

It was determined that NCCC215 will meet 12/7-8/2020, at the Hyatt Place, Chicago (same as 2019).

Elections for secretary, call for nominations: Dennis Halterman nominated Josh Parsons. Josh accepted the nomination. Susie Thompson moved to close nominations. Josh Parsons was unanimously approved. Laura Shannon will be chair and Dave Douches will be vice-chair.

Announcements

Administrative Advisor Ray Hammerschmidt– Noted that 2020 is the International Year of Plant Health. He also gave a multistate committee update. We are due for a mid-term review. What is evidence of working together? Collaborations, enhanced education of graduate students and post docs, leadership opportunities, huge attendance and participation at the technical meeting. We should create an article for the potato industry popular press magazines (e.g. Spudman) describing the meeting.

Breeders Presentations

Jeff Endelman – Wisconsin

Susie Thompson – North Dakota

Laura Shannon – Minnesota

Dave Douches – Michigan

Isabel Vales – Texas A&M

Benoit Bizimungu – Agriculture and Agri-food Canada

Max Feldman – USDA/ARS Prosser, WA

Dennis closed the meeting at noon.

Minutes Attachment:

agenda and minutes.docx

Accomplishments

2019 Report for NCCC215   Accomplishments   Endelman (UW-Madison)             Variety development: In 2017, foundation seed of the fresh market russet variety W9133-1rus was released to the potato industry for commercial-scale evaluation. Based on the positive feedback from growers, this variety was named 'Plover Russet' in 2019. We also received notice from the USDA that our PVP application for Red Endeavor (W6002-1R) was approved. Certified seed acreage of the chip processing variety 'Hodag', which was released in 2015, exceeded 100 acres for the first time in 2019.   Research: A new diploid breeding project was initiated in 2016, and 2019 was the first field trial of over 200 dihaploid and F1 clones. QTL analysis allowed us to identify and select against "wild-type" (i.e., late) alleles at the CDF1 locus on Chromosome 5.    Invited talks: Endelman gave seven invited research seminars in 2019, including at three international locations (Peru, Netherlands, United Kingdom). He also delivered 5 outreach presentations to the potato industry.   Grants: UW-Madison is the lead institution on the 2019 award of $3.0M from USDA-NIFA-SCRI for the project "A new paradigm for potato breeding based on true seed."   Shannon (UMN) The Shannon lab completed the second field season of the reconstituted Minnesota potato breeding program in summer 2019. They are developing new Minnesota germplasm at the diploid and tetraploid level through crossing, dihaploid extraction, and selecting from unselected families from other programs. Additionally, they are evaluating the legacy material from the previous breeder, Dr. Christian Thill. All 30 remaining legacy cultivars have gone through anti-viral tissue culture and test negative for PVY. They will be evaluated in the 2020 field season. One legacy cultivar, MN13142, a dual-purpose long dormancy russet is in trials with industry this year.             Shannon delivered two presentations at national scientific conferences and five talks targeted at growers and industry.     Douches (MSU) Understanding the components of self-compatibility in Solanum chacoense   The S. chacoense inbred line M6 has been used by a wide variety of potato breeding programs to introgress self-compatibility to diploid germplasm. It is hypothesized that self-compatibility in M6 is primarily conferred by the Sli locus on chromosome 12. We are utilizing a S. chacoense F2 population derived from a cross between M6 and a self-incompatible, but largely homozygous, S. chacoense line 80-1 to examine other genetic factors that may contribute to self-compatibility and examine the environmental stability of this self-compatibility. SNP genotyping of 325 self-compatible F2 individuals revealed distorted segregation not only on chromosome 12 but also on chromosome 1, which harbors the S-locus. An additional 200 unselected F2 individuals will be grown and selfed in two locations: Michigan State University and University Wisconsin Madison. Historically, fruit and seed set have been used as an indicator of self-compatibility. However, these phenotypes are confounded by other fertility traits. To directly examine and quantify the compatibility reaction, we will conduct stylar analysis of pollen tube growth using a protocol that has been optimized in the Douches lab. The fact that F5 lines derived from this F2 population are still segregating for self-compatibility is further evidence that multiple genes may be involved. Residual heterozygosity observed in the F5 generation, specifically enriched on chromosomes 12 and 8, suggests that heterozygosity at these loci may be necessary for survival. Thus, in addition to phenotyping, we have cloned and sequenced several candidate genes, including SRNase, hypothesized to be involved in self compatibility in the F2 population. Understanding the genetic landscape of self-compatibility in S. chacoense M6 will facilitate the efficient development of diploid inbred lines.  Natalie Kaiser   The Implications of Endosperm Balance Number and Self-Compatibility on Inter specific Crosses.   Endosperm Balance Number cannot accurately categorize crossing behavior between species, as crossing behavior is species pair specific. The failure of species crosses has also been confounded by prezygotic barriers such as S-RNase, so S-RNase knock-outs could allow previously improbable crosses in the future. It is necessary to understand the exact specifics on why species crosses fail. EBN should not be used as a catch-all explanation of why interspecific incompatibility exists between species. Will Behling   De Novo Assembly of DM1S1   Based on its high regeneration rate, self-compatibility and quality tuber traits, the diploid line DM1S1 from Virginia Tech University has ideal characteristics for use in genome editing. The next step is creating a genomic resource to assist in designing guides and screening for off target effects. To do this, I am using a hybrid assembly approach combining long DNA reads from Oxford Nanopore Technologies using the MinION and short reads using Illumina HiSeq4000. Thilani Jayakody   Diploid Potato Breeding at MSU   Self-compatibility from diploid potatoes can be harnessed towards developing inbred lines to serve as parents for an F1 hybrid potato line development system. Work to introgress self-compatibility into breeding lines with good tuber traits and high yield was presented. A summary of the different types of crosses, and some of the best breeding lines was also presented. A section was presented which outlined the future plans for diploid potato breeding at MSU. Paul Collins   Investigating the Role of the Circadian Clock in Potato Domestication.                The circadian clock is composed of an endogenous oscillator which is regulated by environmental inputs which in turn drives the rhythmicity of molecular processes (e.g. gene expression over 24 hours) and corresponding physiological responses (e.g. leaf movement). No circadian period length difference was observed during potato domestication, in contrast to other crops analyzed, and we have developed a mapping population to assess the genetic architecture of the circadian period trait. We also developed time course transcriptomic data and luciferase reporter constructs to characterize downstream genes and pathways which are regulated by the circadian clock in potato.  Atlantic and Castle Russet NRGene Genome Assembly QC. Genome assemblies were generated by NRGene for two North American potato varieties, and basic quality control and preliminary anchoring of the scaffolds into haplotype resolved pseudomolecules has been conducted. While the gene content of both assemblies is nearly complete, many genomic regions only have 3 scaffolds instead of 4 scaffolds present. We’ve found that in many of these regions, the haplotypes were collapsed into a single scaffold potentially due to high nucleotide similarity between the haplotypes. Currently, we are working on anchoring the scaffolds into haplotype resolved pseudomolecules using phased GBS and HiC data.  Genevieve Hoopes   Generation of Self-Compatible Diploid Potato Via CRISPR-Cas9 Genome Editing   Development of self-compatible diploid potato lines is useful to the potato community in that these lines could help fix desirable alleles and create inbred lines that could later be used to take advantage of heterosis. The Gametic Self-Incompatibility (GSI) model has been well established in Solanaceae and shows that S-RNase is a major factor in self-incompatibility in potato lines. We hypothesize that there are other major factors that contribute to self-incompatibility; therefore we are targeting two genes in concert with S-RNase with CRISPR-Cas9 to establish robust self-compatible lines. We are also working to understand why M6, a Solanum chacoense line, is naturally self-compatible.  Sarah Lee     Jansky (USDA-ARS)             Germplasm Releases USDA-Madison   <table width="2089"> <tbody> <tr> <td width="66"> Clone </td> <td width="63"> Genebank Accession </td> <td width="1960"> Description </td> </tr> <tr> <td width="66"> BR03 </td> <td width="63"> BS 236 </td> <td width="1960"> 4x, resistance to early blight and late blight from S. palustre and S. bulbocastanum </td> </tr> <tr> <td width="66"> BR05 </td> <td width="63"> BS 237 </td> <td width="1960"> 4x, resistance to early blight and late blight from S. palustre and S. bulbocastanum </td> </tr> <tr> <td width="66"> BR85 </td> <td width="63"> BS 238 </td> <td width="1960"> 4x, resistance to early blight and late blight from S. palustre and S. bulbocastanum </td> </tr> <tr> <td width="66"> M1 </td> <td width="63"> BS 223 </td> <td width="1960"> 4x, resistance to cold-induced sweetening from S. chacoense and S. raphanifolium </td> </tr> <tr> <td width="66"> M2 </td> <td width="63"> BS 224 </td> <td width="1960"> 4x, resistance to cold-induced sweetening from S. chacoense and S. raphanifolium </td> </tr> <tr> <td width="66"> M3 </td> <td width="63"> BS 225 </td> <td width="1960"> 4x, resistance to cold-induced sweetening from S. chacoense and S. raphanifolium </td> </tr> <tr> <td width="66"> M4 </td> <td width="63"> BS 226 </td> <td width="1960"> 4x, resistance to cold-induced sweetening from S. chacoense and S. raphanifolium </td> </tr> <tr> <td width="66"> M5 </td> <td width="63"> BS 227 </td> <td width="1960"> 4x, resistance to cold-induced sweetening from S. chacoense and S. raphanifolium </td> </tr> <tr> <td width="66"> M6 </td> <td width="63"> BS 228 </td> <td width="1960"> 2x, self-compatible S. chacoense, formerly 523-3 </td> </tr> <tr> <td width="66"> M7 </td> <td width="63"> BS 229 </td> <td width="1960"> 4x long russet; bilateral sexual polyploid from US-W4 x S. infundibuliforme </td> </tr> <tr> <td width="66"> M8 </td> <td width="63"> BS 293 </td> <td width="1960"> 4x, resistance to common scab from S. chacoense </td> </tr> <tr> <td width="66"> M10 </td> <td width="63"> BS 231 </td> <td width="1960"> 2x, resistance to late blight from S. verrucosum </td> </tr> <tr> <td width="66"> M11 </td> <td width="63"> BS 232 </td> <td width="1960"> 2x, resistance to late blight from S. verrucosum </td> </tr> <tr> <td width="66"> M12 </td> <td width="63"> BS 233 </td> <td width="1960"> 2x, resistance to late blight from S. verrucosum </td> </tr> <tr> <td width="66"> M13 </td> <td width="63"> BS 234 </td> <td width="1960"> 2x, resistance to early blight, late blight, and cold-induced sweetening </td> </tr> <tr> <td width="66"> M14 </td> <td width="63"> BS 235 </td> <td width="1960"> 2x, resistance to early blight, late blight, and cold-induced sweetening. </td> </tr> <tr> <td width="66"> M16 </td> <td width="63"> BS 294 </td> <td width="1960"> 4x, resistance to common scab from S. chacoense </td> </tr> <tr> <td width="66"> M17 </td> <td width="63"> BS 295 </td> <td width="1960"> 4x, resistance to common scab from S. chacoense </td> </tr> <tr> <td width="66"> M19 </td> <td width="63">   </td> <td width="1960"> 2x, resistance to PVY from S. chacoense </td> </tr> <tr> <td width="66"> M20 </td> <td width="63">   </td> <td width="1960"> 2x, resistance to PVY from S. chacoense </td> </tr> <tr> <td width="66"> S438 </td> <td width="63"> BS 297 </td> <td width="1960"> 4x, processing quality </td> </tr> <tr> <td width="66"> S440 </td> <td width="63"> BS 298 </td> <td width="1960"> 4x, processing quality </td> </tr> <tr> <td width="66"> ver-cmm 1 </td> <td width="63"> GS 400 </td> <td width="1960"> 2x, S. verrucosum-bridge clone. ver 161173 x cmm 472839 hybrid </td> </tr> <tr> <td width="66"> ver-cmm 2 </td> <td width="63"> GS 401 </td> <td width="1960"> 2x, S. verrucosum-bridge clone. ver 161173 x cmm 472839 hybrid </td> </tr> <tr> <td width="66"> ver-cmm 21-1 </td> <td width="63"> GS 402 </td> <td width="1960"> 2x, S. verrucosum-bridge clone. ver 275256 x cmm 458319 hybrid </td> </tr> <tr> <td width="66"> ver-cph 8-1 </td> <td width="63"> GS 399 </td> <td width="1960"> 2x, S. verrucosum-bridge clone. ver 161173 x cph 283062 hybrid </td> </tr> <tr> <td width="66"> ver-pnt 1 </td> <td width="63"> GS 403 </td> <td width="1960"> 2x, S. verrucosum-bridge clone. ver 161173 x pnt 275233 hybrid </td> </tr> <tr> <td width="66"> ver-pnt 2 </td> <td width="63"> GS 404 </td> <td width="1960"> 2x, S.  verrucosum-bridge clone. ver 161173 x pnt 347766 hybrid </td> </tr> <tr> <td width="66"> C287 </td> <td width="63">   </td> <td width="1960"> 2x, resistance to Verticillium wilt developed by Christian Thill </td> </tr> </tbody> </table>   Halterman (USDA-ARS) Molecular markers linked to Verticillium wilt resistance in potato germplasm Verticillium wilt (VW) of potato (Solanum tuberosum), caused by two different soil-borne fungi Verticillium albo-atrum R & B or V. dahliae Kleb., is a major limiting factor in potato production throughout North America. Yield losses in potato associated with the disease can reach up to 50% in severely infested fields. In tomato, resistance to race 1 of Verticillium dahliae is conferred by a dominant Ve gene that has been exploited in breeding programs from more than 50 years. However, previously developed markers within the Ve gene in potato are unreliable in predicting resistance. The goal of this project is to identify additional genomic regions that determine VW resistance in potato. An F2 mapping population was developed by selfing an F1 individual derived from two homozygous diploid parents, S. tuberosum DM1-3 (susceptible to VW) and S. chacoense M6 (resistant to VW). Using a rooted cutting protocol, the population was phenotyped and SNP genotyped. A major QTL in chromosome 1 was identified that explains 31% of the phenotypic variation. A total of 22 genes are located within the QTL region, and two genes have been selected for further functional validation studies. Using the sequence information of these two genes, are developing markers to distinguish between resistant and susceptible germplasm.  The marker information will be a valuable tool for potato breeders interested in selecting for VW resistance.   Molecular interactions that influence virulence contributions of the IPI-O family of Phytophthora infestans effectors Phytophthora infestans, causal agent of potato late blight, is a destructive pathogen that is a frequently recurring problem worldwide. Several resistance genes exist in potato to counter against this pathogen, but the majority have been overcome after introgression into popular potato varieties. The RB gene, derived from Solanum bulbocastanum, has effector recognition specificity to members of the IPI-O family. Recognition of the IPI-O1 allele by RB elicits a hypersensitive resistance response while IPI-O4 can suppress this response. We have carried out several experiments to determine the virulence contributions of IPI-O1 and IPI-O4 during infection, and to identify host proteins involved in IPI-O recognition/suppression using co-immunoprecipitation and yeast two-hybrid. Our results indicate that both IPI-O1 and IPI-O4 contribute to P. infestans virulence, but their impact is influenced by the pathogen genotype. Protein interaction studies have identified both cytosolic- and membrane-localized host proteins that interact with IPI-O and will help to elucidate the function of these effectors in pathogen virulence. Together, we hope that our understanding of the function of the ubiquitous IPI-O effector will assist us in identifying or developing improved host resistance genes in potato. This work has been included in two publications (Chen and Halterman, 2017a; Chen et al., 2017b) Foliar resistance to bacteria in potato Solanaceous crops including tomato, pepper, and eggplant are susceptible to many foliar bacterial pathogens. However, cultivated potato is immune to most pathogenic Pseudomonas and Xanthomonas species. The purpose of this project is to understand the mechanisms involved in limiting infection of bacteria in the foliage of potato. We have previously found that many popular potato cultivars are immune P. syringae pv. tomato DC3000, while many wild species accessions of potato are susceptible or tolerant, suggesting that resistance to foliar pathogens may have been selected during cultivation of potato as a food crop. We have used various DC300 strains defective in pathogenesis. Populations between wild and cultivated potato have also been developed to map the resistance locus using SNP genotyping. The identification of novel genes involved in bacterial resistance will facilitate the development of new varieties of Solanaceous crops.   Development of diploid potato germplasm containing disease resistance             Using a combination of diploid wild species hybrids and dihaploid cultivated germplasm from the programs of David Douches (Michigan State) and Shelley Jansky (USDA-ARS), we have developed populations segregating for resistance to potato late blight and early blight. Seventeen families from crosses between various parents were phenotyped using detached leaflet assays and whole plant inoculation assays (greenhouse) to identify individuals with increased resistance to either or both diseases. Three families contained individuals with high levels of late blight resistance and one family had individuals with increased early blight resistance. Selected individuals were grown in the field and assayed for agronomic characteristics including tuber size and shape, specific gravity, and chip quality. Three individuals were chosen for crossing with diploids containing resistance to other diseases, including PVY and Verticillium wilt. Bamberg (USDA-ARS) We are organizing to propose a grant for combining phenotype, metabolites, and genetic markers for segregating pops we made resulting from past CGC projects on Dickeya and Zebra chip. A resource for the above is two CETS phytotron growth chambers for tuberizing we are installing at USPG.  In these we hope to propagate replicate genotypes for multifaceted evaluation in several locations without incurring the great effort and cost of in vitro maintenance, yet with very high phytosanitary security.  We expect these phytotrons to have many other applications that need uniform tuber samples for screening tuber traits.   We started a big archeology project with UT and OH collaborators.  Why should the genebank be involved in archeology?  USPG will benefit from a better understanding of factors that predict patterns of genetic diversity in the wild including the activities of ancient humans.  Collateral benefit is getting screening data on tuber size, frost tolerance, glycoalkaloids.   We previously reported a “MegaPop” for S.jamesii, a population from one place in the wild that captures most of the genetic diversity of the species.  That is the ultimate core subset!  Now we are pursuing identification of a parallel MegaPop for S. fendleri, the second species found in the US.   Using S. jamesii through S. verrucosum bridge crosses.  We took a good-flowering ver and made BC5 into tbr cytoplasm, selecting for self-incompatibility and good growth and flowers.  Now it crosses directly to S. jamesii without emasculation or double pollination with IvP.  We are going to repeat the whole experiment systematically this spring to confirm metrics of crossing success, including crosses with the other 1EBN species.   For the golden-fleshed specialty type Criolla, we created and selected S3 inbred families and a synthetic population both with high proportions of dark golden flesh and improved yield and type.  Preparing for S4 evaluation and selection next season.   Started core subset development of 92 populations of S. kurtzianum, including screening for differences in root vigor, fertilizer efficiency and drought tolerance.   Assessed inhibition of US native potatoes by invasive cheatgrass.  Preliminary results suggest cheatgrass inhibits sprouting of tubers, but not growth of potato shoots.  This study was first aimed at assessing how threatened USA native potato populations might be in the wild.  But if cheatgrass roots produce a safe, natural effective sprout inhibitor, it might have a valuable application for commercial storage.   Peru collaborative breeding and research continues.  Second named cultivar release pending.  New seedlots being bred and sent to Peru target high tuber calcium, frost and drought tolerance.      Susie Thompson (North Dakota State University)   Seventy-six genotypes were used as parents in hybridizing efforts in 2019; 213 new families were created.  Parental germplasm included named cultivars and advancing selections.  Traits of focus included processing (chip and frozen), fresh market quality, PVY, late blight, Colorado Potato Beetle, and Verticillium wilt resistance.   In 2019, irrigated trial sites were at Inkster, Larimore and Oakes, ND, and at Park Rapids, MN.  Three trials were planted at Inkster.  The metribuzin sensitivity screening trial was conducted in collaboration with Dr. Harlene Hatterman-Valenti’s program.  Trial results are being used to validate the model developed by a previous graduate student.  The sugar end screening trial was the second year of Felicity Merritt’s thesis research.  A new trial in 2019 was in response to ND certified seed growers concern about efficient vine kill after repeated use of mineral oils in aphid management, in collaboration with Drs. Gary Secor and Andy Robinson.  Eight vine-kill scenarios were evaluated.  The Larimore trial site included the Processing Trial (20 selections, cultivars and industry standards), the National French Fry Processing trial (46 selections compared to Russet Burbank and Ranger Russet; six were NDSU advancing selections), the preliminary processing trial with 58 entries (advancing dual-purpose russet selections compared to industry standards), an irrigate preliminary chip process trial (106 genotypes), and maintenance of out-of-state selections.  We were unable to harvest this site due to heavy rains, snow and freezing temperatures in September and October.  Trials at Oakes were focused on fresh market selections and 16 promising dual-purpose russet selections compared to industry standards; common scab was not as prevalent in the fresh market genotypes as in previous years.  Trials at Park Rapids, MN, included a processing trial with 15 entries, the common scab screening trial with 64 entries across market types, and the replicated screening trial for Verticillium wilt resistance (25 genotypes across market types) conducted in collaboration with Dr. Neil Gudmestad’s program.  Bannock Russet and Dakota Trailblazer continue to be the most resistant genotypes to Verticillium based on colony forming units of stem tissue collected right before vinekill/harvest.  Promising advancing processing russet selections include ND12108CAB-3Russ, ND12109CB-2Russ, ND13103B-1Russ, ND13245C-4Russ, ND13252B=6Russ, and ND13252B-12Russ, amongst others.   Non-irrigated research sites included Crystal and Hoople ND.  The Fresh Market trial had 30 entries, while the preliminary fresh market trial included 90 entries.  Several fresh market selections look very promising, including ND1232B-2RY, ND1241-1Y, ND102663B-3R, ND081571-2R, ND081571-3R, ND102990B-2R, and ND113091B-2RY. Chip processing trials were located north of Hoople, and included the Chip Processing Trial included 22 advancing chip selections compared to chip industry standards.  The Preliminary chip processing trial evaluated 30 selections and industry standards, and the National Chip Processing Trial (NCPT), included 98 unreplicated selections (Tier 1) and 22 replicated entries (Tier 2) from US potato breeding programs, compared to five industry chip selections.  Outstanding chip selections coming through the program include ND7519-1, ND7799c-1, ND102642C-2, ND102922C-3, ND113307C-3, ND1221-1, ND12180ABC-8, ND13228AB-3, ND14348AB-1, ND14437CAB-1, ND14437CAB-2, and many others.  The non-irrigated sites were hampered by a lack of rainfall during summer 2019, with significant rain developing in early September.  Late blight screening trials at Prosper, ND conducted in collaboration with Dr. Secor’s program were drown out in early June by excessive rain.   The seedling nursery, seed maintenance plots, and increase lots were planted south of Baker, MN.  All lots were entered for certification with the Minnesota Department of Agriculture and passed certification; all were submitted for winter testing.  The seedling nursery included single hills from NDSU (115 families) and out of state cooperators; 724 single hills were selected.  Of 776 second year selections 233 were retained; 40 of 118 third and 146 of 252 fourth year and older selections were saved.  Production from the seed maintenance and increase lots is used to maintain the genotypes via phenotypic recurrent selection and is the seed source for our research and collaborative trials at NDSU, and research and industry collaborators in ND, MN, and beyond.  As in previous years, several Chilean selections from the INIA program at Osorno, Chile, were evaluated in collaboration with Drs. Gary Secor and Julio Kalazich.  Three hundred-one genotypes were submitted for SNP genotyping in 2019.     Grants awarded in 2019   <table width="87%"> <tbody> <tr> <td width="15%">   </td> <td width="8%"> NAME         </td> <td width="24%"> SUPPORTING AGENCY </td> <td width="14%"> TOTAL $ AMOUNT </td> <td colspan="2" width="20%"> EFFECTIVE AND EXPIRATION DATES </td> <td width="16%"> TITLE OF PROJECT </td> </tr> <tr> <td width="15%"> Douches, Buell, Nadakuduti </td> <td colspan="2" width="33%"> USDA/BRAG </td> <td colspan="2" width="16%"> $500,000 </td> <td width="19%"> 09/01/2018-08/31/2021 </td> <td width="16%"> Genome wide evaluation of off-targets from gene editing reagents in seed vs. vegetatively propagated crop species </td> </tr> <tr> <td width="15%"> Jansky, Bethke, Buell, Douches, Endelmann, Shannon </td> <td colspan="2" width="33%"> USDA SCRI </td> <td colspan="2" width="16%"> $3M total </td> <td width="19%"> 9/1/19 – 8/31/23 </td> <td width="16%"> Creating a new paradigm for potato breeding and seed production based on true potato seed </td> </tr> <tr> <td width="15%">   Douches, Endelman, Thompson, Shannon </td> <td colspan="2" width="33%">   USDA/NIFA       </td> <td colspan="2" width="16%">   $708,000       </td> <td width="19%">   09/01/19 - 08/31/20     </td> <td width="16%">   Development of multipurpose potato cultivars with enhanced quality, disease and pest resistance – North Central Region, 2019-2021 </td> </tr> </tbody> </table>

Publications

Publications   Alsahlany, M., D. Zarka, J. Coombs, and D. Douches. 2019. Comparison of methods to distinguish diploid and tetraploid potato for applied diploid breeding. American Journal of Potato Research.  <a href="https://doi.org/10.1007/s12230-018-09710-7">https://doi.org/10.1007/s12230-018-09710-7</a>.   Caraza-Harter MV, Endelman JB (2019) Image-based phenotyping and genetic analysis of potato skin set and color. Crop Science, doi:10.2135/cropsci2019.07.0445   Enciso-Rodriguez F, Manrique-Carpintero NC, Nadakuduti SS, Buell CR, Zarka D and Douches D (2019) Overcoming Self-Incompatibility in Diploid Potato Using CRISPR-Cas9. Front. Plant Sci. 10:376. doi: 10.3389/fpls.2019.00376.   Fulladolsa, A.C., A. Charkowski, X. Cai, J. Whitworth, S. Gray, and S.H. Jansky. 2019. Germplasm with Resistance to Potato Virus Y Derived from Solanum chacoense: Clones M19 (39-7) and M20 (XD3). American Journal of Potato Research. 96:390-395.   Jansky, S., Haynes, K. & Douches, D. Am. J. Potato Res. (2019) Comparison of Two Strategies to Introgress Genes for Resistance to Common Scab from Diploid Solanum chacoense into Tetraploid Cultivated Potato. <a href="https://doi.org/10.1007/s12230-018-09711-6">https://doi.org/10.1007/s12230-018-09711-6</a>.   Satya Swathi Nadakuduti, Colby Starker, Dae Kwan Ko, Thilani B. Jayakody, C. Robin Buell, Daniel F. Voytas and David S. Douches (2019). Evaluation of methods to assess in vivo activity of engineered genome-editing nucleases in protoplasts. Frontiers in Plant Science, 10: 110.   Satya Swathi Nadakuduti, Colby Starker, C. Robin Buell, Daniel F. Voytas and David S. Douches (2019) “Genome editing in potato with CRISPR/Cas9”, Plant Genome Editing with CRISPR Systems: Methods and protocols, Methods in Molecular Biology, Springer Nature 1917: 183-201 (Book chapter).

Impact Statements

New diploid projects and new funding to support this work will help in the development of new potato lines and varieties

Date of Annual Report: 01/01/1970

Report Information

Annual Meeting Dates: 12/07/2020 - 12/08/2020
Period the Report Covers: 12/01/2019 - 12/01/2020

Participants

Participants Attachment:

NCCC215 attendees 2020.xlsx

Brief Summary of Minutes

Minutes Attachment:

2020 NCCC215 Meeting minutes.docx

Accomplishments

Breeding:  Tools for phenotyping tuber color have been developed; a fingerprinting system using SNP markers is available to answer variety identify questions; molecular and hyperspectral data are being used to help predict yield.  Genome sequencing:  research has been conducted to create a pan genome based upon 6 cultivars from the US and Europe; genome sequencing was used to look at relationships and diversity of the cultivated potato species.  Diploid potato breeding: self-compatibility is being genotyped in the germplasm using KASP markers for Sli; EBN1 wild species are being accessed using bridge crossing; dihaploids are being extracted by all the breeding programs to establish a diploid cultivated gene pool.  Gene editing:  potatoes have been gene edited to create self-compatible lines as well as late blight resistance.

Publications

Impact Statements

Several collbarative competetive grants were funded; a table of these is under meeting minutes

Date of Annual Report: 03/07/2022

Report Information

Annual Meeting Dates: 12/06/2021 - 12/07/2021
Period the Report Covers: 12/07/2020 - 12/06/2021

Participants

attached

Participants Attachment:

NCCC215 attendees.docx

Brief Summary of Minutes

attached

Minutes Attachment:

NCCC215 minutes.docx

Accomplishments

Accomplishments Breeding:  Tools for phenotyping tuber shape have been developed; Scab resistance and PVY resistance is being introgressed into advanced breeding lines. Software for genomic selection has been released, using potato as a case study.  Genome sequencing:  research has been conducted to create a pan genome based upon 6 cultivars from the US and Europe; genome sequencing was used to look at relationships and diversity of the cultivated potato species. Publication is expected in January 2022.  Diploid potato breeding: the genetics of self-compatibility is being studied; EBN1 wild species are being accessed using bridge crossing; dihaploids are being extracted by all the breeding programs to establish a diploid cultivated gene pool.  Gene editing:  potatoes have been gene edited to create self-compatible lines, PPO silenced lines as well as late blight resistance.  Multi-institution grants have been obtained as well as publications.   Outreach The Northern Plains Potato Growers Association Research Reporting Conference was held virtually February 16, 2021.  Susie Thompson presented ‘Potato Improvement and Cultivar Development for North Dakota and the Northern Plains‘and Laura Shannon ‘Program Through Breeding for Resistance and Cultural Practices’.   Tater Talk Panel (Drs. Robinson, Secor, Pasche, Rosen, McRae, and Thompson). Virtual. March 23, 2021.  Susie Thompson presented ‘New Potato Varieties‘at the Oakes Research Extension Field Day. August 4, 2021.  The Northern Plains Potato Growers Association held its annual Field Day on August 26, 2021, in person at Larimore, Inkster and Hoople, ND.  Laura Shannon (UMN) and Susie Thompson (NDSU) provided presentations ‘U of M Update‘and ‘NDSU Potato Breeding Trials‘, respectively.  Posters were exhibited by Xiaoxi Meng and graduate students from both programs at the Hoople site.  The Minnesota Area II Research Meeting was held as a hybrid on November 18, 2021.  Breeding program updates were provided by Laura Shannon (UMN) and Susie Thompson (NDSU). Tater Talk. Variety Trial Results 2021. NPPGA Offices/USDA-ARS Potato Worksite. December 1, 2021. Andy Robinson and Susie Thompson (NDSU).  Michigan Outreach activities for Dave Douches: Montcalm Research Center Field Day, August 2021; Variety Trial Field Day, Montcalm County, August 2021; Potato Variety Day, MI, February 2021.  Endelman JB. Feb 2, 2021. Creating a new paradigm for potato breeding based on true seed. UW Extension and WPVGA Grower Education Conference (Virtual). Endelman JB. April 4, 2021. A new paradigm for potato breeding. Board meeting of the Wisconsin Agricultural and Life Sciences Alumni Association (Virtual). Endelman JB. July 15, 2021. Potato Breeding Update. Field day at the UW Lelah Starks Elite Foundation Seed Potato Farm.   Current collaborative grants awarded <table width="88%"> <tbody> <tr> <td width="22%"> NAME (List/PD #1 first)   </td> <td width="17%"> SUPPORTING AGENCY AND AGENCY ACTIVE AWARD/PENDING PROPOSAL NUMBER </td> <td width="20%"> TOTAL $ AMOUNT </td> <td width="20%"> EFFECTIVE AND EXPIRATION DATES </td> <td width="20%"> TITLE OF PROJECT </td> </tr> <tr> <td width="22%">   </td> <td width="17%">   </td> <td width="20%">   </td> <td width="20%">   </td> <td width="20%">   </td> </tr> <tr> <td width="22%">   Douches, Endelman, Thompson, Shannon           </td> <td width="17%">   USDA/NIFA                 </td> <td width="20%">   $1,600,000                 </td> <td width="20%">   09/01/21 - 08/31/23               </td> <td width="20%">   Development of multipurpose potato cultivars with enhanced quality, disease and pest resistance – North Central Region, 2021-2023     </td> </tr> <tr> <td width="22%"> Endelman, Bethke, Buell, Douches, Shannon   </td> <td width="17%"> USDA SCRI </td> <td width="20%"> $3M </td> <td width="20%"> 9/1/19 – 8/31/23 </td> <td width="20%"> Creating a new paradigm for potato breeding and seed production based on true potato seed   </td> </tr> <tr> <td width="22%"> Karasev, Douches, Willbur, etc           Byrne/Endelman/Riera-Lizarazu/Zhang           Pasche/Thompson/Shannon                       Pasche/Thompson/Shannon   </td> <td width="17%"> USDA/SCRI           USDA/SCRI               North Dakota Department of Ag                   North Dakota Department of Ag   </td> <td width="20%"> $300,000           $4M               $176,720                     $186,338   </td> <td width="20%"> 10/1/2020-9/30/2024           9/1/20-  8/31/24               10/1/21- 9/30/23                 1   0/1/21- 9/30/23   </td> <td width="20%"> Development of sustainable system-based management strategies     Tools for Polyploids: Development of a Community Resource     Mining the soil and host genetics for sustainable answers to Verticillium wilt in potato         New technology to fight an old foe: characterizing resistance to potato powdery scab   </td> </tr> </tbody> </table>

Publications

Impact Statements

The committee reported 6 grants (listed unbder accomplishments)