Source: MICHIGAN STATE UNIV submitted to NRP
DEVELOPMENT OF MULTIPURPOSE POTATO CULTIVARS WITH ENHANCED QUALITY, DISEASE AND PEST RESISTANCE – NORTH CENTRAL REGION, 2017-2018
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
SPECIAL GRANT
Reporting Frequency
Annual
Accession No.
1010193
Grant No.
2016-34141-25707
Cumulative Award Amt.
$1,896,578.00
Proposal No.
2016-06079
Multistate No.
(N/A)
Project Start Date
Sep 1, 2016
Project End Date
Aug 31, 2019
Grant Year
2018
Program Code
[AN]- Potato Research
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Plant Soil & Microbial Science
Non Technical Summary
Potato production is in the North Central US is vital to the regional economy and plays an important role in the national potato supply. In 2015 the four states of Michigan, Minnesota, North Dakota, and Wisconsin accounted for 22% of the US acreage, with a farm-gate value of $856 million. All sectors of the potato market are present in this region, dominated by fry and chip processing markets, with a successful fresh market and expanding specialty market niches. This proposal, which is a joint effort of the potato breeding and genetics programs at four North Central land-grant universities (UW, MSU, NDSU, UM). There are four specific objectives detailed: 1) to identify new varieties with superior agronomics and end-used quality via hybridization and selection, 2) to screen elite germplasm for resistance to key pests., 3) to use genetic markers to improve breeding efficiency, and 4) to transfer new varieties from the breeding programs to the commercial sector. The four project directors and their collaborators have the requisite experience, facilities, and stakeholder relationships to successfully complete these objectives. The expected outcomes from the one-year grant include the release of new varieties, the selection of new breeding lines, new markers for marker-assisted selection, and preliminary data on the feasibility of using genome-wide marker analyses for improving variety development.
Animal Health Component
90%
Research Effort Categories
Basic
10%
Applied
90%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011310108170%
2011310108030%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1310 - Potato;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Our state potato research advisory boards (Michigan Potato Industry Commission, Minnesota Area II Potato Research and Promotion Council, Northern Plains Potato Growers Association, and the Wisconsin Potato and Vegetable Growers Association) have identified a critical need for the development of improved potato varieties exhibiting superior agronomic performance, quality attributes, and host plant resistance to diseases and insect pests.Our specific objectives are to:1. Identify new varieties with superior agronomics and end-used quality via hybridization and selection.2. Screen elite germplasm for resistance to key pests. 3. Use genetic markers to improve breeding efficiency.4. Transfer new varieties from the breeding programs to the commercial sector.
Project Methods
The four cooperating breeding programs will establish crossing blocks at university greenhouses using favorable clones as parental lines from within and among breeding programs. Elite clones are intercrossed to synthesize new segregating seedling populations. We also make crosses to less adapted clones (e.g., wild-elite hybrids) developed by USDA collaborators (e.g., from the Vegetable Crops Research Unit, Madison, WI) to incorporate novel genes for disease resistance and other key traits. True potato seed will be sown in greenhouses and harvested to generate seedling tubers for the first field generation. Phenotypic evaluation of clones over time and locations is the current state of art for potato breeding. As much as 200,000 unique clones will be evaluated as single-hill plots, over 95% of which will be culled based on visual selection. Around 5,000 second-year clones will be planted in larger plots (4, 8, or 12-hill), and the number of third-year clones is typically 1,000-2,000. Across the four breeding programs, 500 Year 4 clones will be evaluated in replicated trials within their originating state. To accelerate the evaluation and selection process in the early generation phase we are incorporating marker-assisted-selection procedures for late blight, PVY, PVX, PLRV, cold sweetening, and Golden Nematode resistance into the evaluation of yr 2, 3 and 4 selections.Late BlightMSU will screen clones that have pedigrees with a known source of late blight resistance. A US23 P. infestans isolate will be applied through the irrigation system. The advanced breeding lines are evaluated as three replicates of 5-hill plots, whereas the early generation material is a 5-hill single plot observation. The border of the field is planted to susceptible lines to promote disease development. MSU has the capacity to screen up to 500 early generation and 200 advanced breeding lines per year. NDSU employs a detached leaf assay evaluating more than 5000 genotypes annually at the greenhouse seedling production stage using a cocktail of P. infestans genotypes representing all 11 virulence genes. Replicated field trials in subsequent generations are used to quantify foliar resistance and to test for tuber resistance.Colorado potato beetleThe Montcalm Research Farm (MSU) has developed field a nursery to evaluate foliar damage by the Colorado potato beetle. Border field rows will be planted to a susceptible variety and used to attract over-wintering Colorado potato beetle adults. The percent plot defoliation data will be collected throughout the growing season and resistant clones identified. Clones showing promise from the field study are further evaluated in 2x2x2 m cages on the MSU campus. Adult beetles or egg masses are placed in the cages and percent defoliation is recorded. NDSU also screens for CPB defoliation in the field at Grand Forks, ND, using a similar field design as at the MSU site.Common scabThe Sand Plains Research Farm in Becker, MN, has been a long-term common scab testing site and also is one of the sites of the National Common Scab Trial. Clones with a source of resistance in their pedigree are evaluated in replicated 4-hill plots. The evaluation criteria include number, severity, and percent area of lesions observed after washing harvested tubers. Advanced and early generation lines are also evaluated at the Montcalm Research Center, Entrican, MI, at university fields dedicated to maintaining high disease pressure. Furthermore, a commercial site in Michigan with extremely high disease pressure is being used to evaluate elite chip-processing crosses for scab resistance. Advanced breeding lines as well as first, second and third year selections are screened. NDSU is utilizing a commercial site to evaluate selections across market types for scab resistance.Verticillium wiltNDSU evaluates genotypes representing all market types, in a replicated field trial, with known Verticillium dahliae levels, at the NPPGA Research site at Inkster, ND. Selections are visually assessed twice weekly for symptoms and stem colonization is assessed using qPCR. Yield and grade are also determined in order to ascertain if production is reduced for susceptible selections.Use genetic markers to improve breeding efficiencyThe progeny of the crosses segregating for these marker-linked traits are produced as greenhouse seedling tubers in the first year. The second year these tubers are planted in the field as single hill selections. This evaluation process selects only lines with marketable tuber types and reduces the number of selections to a manageable number for DNA sampling. In the fall, a tuber is sampled for DNA isolation, followed by PCR-based marker analysis. The marker data, in combination with the field and storage data, are used in deciding which lines from the early generation phase should be advanced to replicated trials. Furthermore, some lines may be designated as parents for the following year's crossing block. In 2016, we will continue pursuing the identification of new markers in nine mapping populations that can improve the efficiency of cultivar development. Having collected phenotypic data for seven biparental families, including common scab resistance, chip processing quality, sugars, and specific gravity, we will complete the QTL analysis and identify potential markers for MAS. We now are developing additional SNP-derived markers for late blight resistance, scab resistance and chip-processing traits (glucose, sucrose, acrylamide, and asparagine). Two new populations (Manistee x Lamoka and Atlantic x MSR127-2) are being phenotyped so that QTL analysis can be conducted. Version 2 of the TetraploidMap software will be used.To complement these biparental mapping studies, genome-wide association studies (GWAS) are planned for 2016 to identify markers linked to key agronomic and processing traits, such as yield, size, chip color, glucose, and acrylamide. We now have 410 elite lines from the National Chip and Fry Processing Trials genotyped with either the 8303 or 12K SNP array and phenotyped across multiple locations and years. Analyses will be done using the GWASpoly software.

Progress 09/01/18 to 08/31/19

Outputs
Target Audience:Potato breeding and genetics community and the state/national potato industries (growers, processors and marketers). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Each breeding program has graduate students and post docs that are conducting research. During their graduate and post graduate training and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. These same experiences occur for the undergraduates in the breeding programs. How have the results been disseminated to communities of interest? Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. They four state researchers also get together at the NCC215 meeting to discuss and report research results each December. What do you plan to do during the next reporting period to accomplish the goals? The research cycle is yearly. Breeding material is advanced according to the current 2019research studies in the field andgreenhouse. Publications for research are written when data is collected and analyzed.

Impacts
What was accomplished under these goals? Variety development scheme The foundation of the North Central breeding programs is the generation of segregating populations by sexual hybridization and multiple years of phenotypic selection. Across our four states, more than 1000 segregating populations were created in 2018 and over 180,000 seedling were evaluated in the first year. Over 3,000 clones were evaluated in year 2 of selection with over 900 advancing to the third year. Due to the autotetraploid genetics of potato, the vast majority of the progeny have undesirable tuber appearance or maturity, and can be removed based on visual, single-plant selection in the first field year. After 3 to 4 years of field evaluation within each state, each clone is entered in the appropriate regional or national trial. Chip processing selections participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA, and for which Douches, Thompson, and Endelman manage test sites. In 2018, there were 62 clones entered in the NCPT from the North Central Region breeders. Fry processing selections enter the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which Thompson and Endelman manage test sites. In 2018, there were 4 clones entered in the NFPT from the North Central Region breeders. As there is no national trial for fresh market selections, we manage a North Central Regional Trial (NCRT) for table russets, reds, yellows, and specialty types, with all four breeders hosting test sites. In 2018, there were 24 clones in the NCRT. After multiple years in regional and national trials, we begin the process of producing foundation seed for large-scale commercial evaluations by potato growers, which takes 2-3 years. Advanced selections entering commercial seed production are listed below: Table 1. Advanced clones for which commercial seed is being developed Chip MSZ219-1 Scab, LB and PVY resistance, as well as chip quality MSZ219-13 Scab, LB and PVY resistance, as well as chip quality MSZ219-14 Scab, LB and PVY resistance, as well as chip quality MSV030-4 Scab resistance combined with high specific gravity and long-term storage W12078-76 Good tuber type, size profile, and long-term storability Russet W9742-3rus Excellent type, high specific gravity, under commercial evaluation by fry processing companies ND8068-5Russ Very early maturing, dual-purpose russet, excellent French fry quality ND050032-4Russ Dual-purpose russet, early tuber bulking, excellent processing quality ND060735-4Russ Dual-purpose russet, medium russet skin, excellent processing and consumer quality attributes MN13142 Long dormancy, excellent appearance, thick skin CW08071-2rus Dual-purpose russet with high yield and good shape Red ND081571-2R Medium-early maturity, round, excellent bright red skin color, smaller tuber size profile MN12009PLWR-02R Dark color, good skin set, good size profile MN12054PLWR-02R Dark color MN12054PLWR-03R Dark color Yellow MSV093-1Y Scab resistance with round shape and bright skin MST252-1Y Scab resistance with round shape and bright skin MN04844 Round shape, bright skin, good flavor Specialty MN07112 Purple/yellow skin, purple flesh, keeps color after chipping and mashing Disclosed Inventions Huron Chipper, late blight resistant chip processing variety Mackinaw, PVY, scab and late blight resistant chip processing potato Blackberry, purple skin and flesh tablestock variety with scab resistance CW08071-2rus, a russet tablestock variety W9742-3rus, a processing russet variety W8890-1R, a red tablestock variety W6511-1R, a red tablestock variety PVP:Applications for Red Endeavor, Huron Chipper and Mackinaw were submitted in 2018. Research over the past 20 years has elucidated over 20 R-genes for late blight resistance in various Solanum species, but relatively few are being deployed for variety development. In the last two years, research has shown both Jacqueline Lee and Missaukee from the MSU program contain the R8 gene on chromosome 9, which was inherited from their common parent Tollocan. MSU conducts large field trials to evaluate LB resistance in the field: in 2018, late blight was not able to be generated in the trials due to hot and dry conditions. Although it has not been formally characterized, a second late blight resistance gene on chromosome 5, derived originally from the chip processing clone NY121, is present in several advanced selections from the North Central region that have been used for crossing, such as Saginaw Chipper and MSX540-4. Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields. Reistant selections continue to be advanced through the evaluation process. Potato virus Y (PVY) is a major concern throughout the US, including the North Central region. Molecular markers have been linked with PVY resistance genes that are effective against all PVY strains, providing what is referred to as extreme resistance. The Ryadggene fromS. tuberosum ssp. andigenaand Rystogene fromS. stoloniferumare present in a number of elite parents used for crossing in the North Central region, including W8946-1rus (Rysto), W12003-3rus (Ryadg), Saginaw Chipper (Ryadg), and MSX540-4 (Ryadg). In 2018more than 1000 clones were screened for PVY resistance using molecular markers in the North Central region. Colorado potato beetleis the most important insect pest of potato in the U.S. At MSU a diploidS. chacoenseF2 mapping population was field screened in a beetle nursery at the Montcalm Research Center.The segregating progeny ranged from highly susceptible to highly resistant. A F4 RIL population is currently being has been developed from this F2 population to better understand the genetics of the resistance in a more inbred background. We are also pursuing marker-based approaches for agronomic and quality traits, including yield, size, specific gravity, fry color, tuber dormancy, tuber protein, and fry color. A key enabling technology for potato molecular breeding is our Infinium SNP array, which was originally developed with 8303 markers as part of the SolCAP project led by Douches. Thanks to the continuing efforts, Version 2 of the array with 12K markers became available two years ago, and version 3 with 22K markers has been used since Jan 2017. UW-Madison is using the genomic-estimated breeding values to select FY3 clones for crossing and dihaploid extraction in 2018, which is 1-2 years earlier than normal. This shortening of the breeding cycle is expected to compound over time and improve the rate of genetic gain.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 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. https://doi.org/10.1007/s12230-018-09711-6
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Massa, A.N. N.C. Manrique-Carpintero, J. Coombs, K.G. Haynes, P.C. Bethke, T.L. Brandt, S.K. Gupta, G.C. Yencho, R.G. Novy and D.S. Douches. Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato. BMC Genetics (2018) 19:87 https://doi.org/10.1186/s12863-018-0672-1
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Endelman, J. B., C. A. Schmitz Carley, P. C. Bethke, J. J. Coombs, M. E. Clough, W. L. da Silva, W. S. De Jong et al. 2018. Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato. Genetics 209, 77-87.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: 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 https://doi.org/10.1007/s12230-018-9664-y.


Progress 09/01/16 to 08/31/19

Outputs
Target Audience:Potato Breeding and Genetics community and the state potato industries (growers, processors and marketers). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Each breeding program has graduate students and post docs that are conducting research. During their graduate and post graduate training and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. which provides practical training in potato breeding. These same experiences occur for the undergraduates and post docs in the breeding programs. How have the results been disseminated to communities of interest?Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days.Information about new varieties and breeding technologies has been presented to stakeholders at several forums, including the National Potato Expo, the National Chip and Fry Processing programs of Potatoes USA, the USDA multi-state project NCCC215 (Potato Breeding & Genetics Technical Committee), the annual meeting of the Potato Association of America. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? 1. Identify new varieties with superior agronomics and end-used quality via hybridization and selection. The foundation of the North Central breeding programs is the generation of segregating populations by sexual hybridization and multiple years of phenotypic selection. Across our four states, more than 3000 segregating populations representing over 500,000 unique genotypeswere created during the grant. Due to the autotetraploid genetics of potato, the vast majority of the progeny have undesirable tuber appearance or maturity that were removed based on visual, single-plant selection in the first field year.After 3 to 4 years of field evaluation within each state at least 400 selections per year have beenadvanced for furthertrialing. Eachclone is entered in the appropriate state, regional or national trial. Chip processing selections participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA, and for which Douches, Thompson, Shannon and Endelman manage test sites. Since 2016 over 160clones entered in the NCPT andthe National Fry Processing Trial (NFPT) from the North Central Region breeders. Thompson and Endelman manage NFPT test sites. As there is no national trial for fresh market selections, we manage a North Central Regional Trial (NCRT) for table russets, reds, yellows, and specialty types, with all four breeders hosting test sites. 24 clones per year are tested. 2. Screen elite germplasm for resistance to key pests. Based on linkage mapping (Massa et al. 2015) and genome-wide association analysis (Enciso et al. 2018), two regions appear to be mainly responsible for the LB resistance observed in elite chip clones at MSU. The first is the distal end of Chromosome 9, which contains a large number of R genes, including the R8 and R9a genes from the wild relative Solanum demissum (Jo et al. 2015). Vossen et al. (2016) confirmed that at least two clones from the MSU program-Missaukee and Jacqueline Lee-contain R8, which we can deduce was inherited from their common LB-resistant parent Tollocan. In 2018, we developed a presence/absence SCAR marker for R8 and have started using it to identify LB-resistant progeny in segregating populations (Christensen et al. 2018). The other source of LB resistance is on chromosome 5, which coincides with a QTL for resistance first identified in NY121, a breeding line from Cornell (Mayton et al. 2010). No R genes for LB have been cloned from this region as of yet. Recent variety releases from MSU are believed to contain the Chr 5 QTL, including Saginaw Chipper (2016) and Mackinaw (2018).For russet varieties, much less is known about the genetic basis of LB resistance in elite germplasm. Based on published reports of field resistance in Palisade Russet (Novy et al. 2012) and Payette Russet (Novy et al. 2017), both clones have been used as parents at UW-Madison. In 2019, Payette Russet was confirmed to have strong resistance to the US-23 pathotype via detached leaf assay, whereas neither Palisade nor Jacqueline Lee (which contains R8) demonstrated resistance. Segregation has been confirmed in an F1 population derived from Payette and is being used for genetic mapping. Common scab is a prevalent soil borne disease in the US and the North Central Regionand is therefore an important trait for selection. Progress in breeding for scab tolerance has been made by conducting phenotypic selection in dedicated scab fields. Sixty-four genotypes across market types were evaluated for common scab in a scab screening trial conducted by NDSU. information is used in determining continuation in the breeding pipeline, parental selection, and in development of cultivar specific management guidelines. Entrants ranged from resistant to highly susceptible. We have conducted a number of research projects to develop molecular breeding strategies for common scab resistance. Braun et al. (2017) used a diploid biparental mapping population to identify a QTL for resistance on chromosome 11 in S. chacoense. Enciso-Rodriguez et al. (2018) used a Bayesian regression model to identify a QTL on chromosome 9 in a collection of 370 tetraploid clones. Potato virus Y (PVY) is a major concern throughout the US, including the North Central region. Molecular markers have been linked with PVY resistance genes that are effective against all PVY strains, providing what is referred to as extreme resistance. The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region. In the past two years over 1000 clones have been screened for PVY resistance using molecular markers in the North Central region. Colorado potato beetleis the most important insect pest of potato in the U.S.Sixty-four segregating families, in addition to 164 individual genotypes were evaluated for resistance to defoliation in 2018 by NDSU at Grand Forks, ND; materials segregated from highly susceptible to highly resistant. At MSU a diploid S. chacoense F2 mapping population was field screened in a beetle nursery at the Montcalm Research Center in 2017 and 2018. The segregating progeny ranged from highly susceptible to highly resistant. QTL mapping has identified a major QTL on Chromosome 2 partially explaining the observed foliar resistance and leptine production. A F4 RIL population is currently being developed from this F2 population to better understand the genetics of the resistance in a more inbred background. Additional screening trials for disease resistance and cultivar specific management information included a Verticillium wilt trial. Twenty-five genotypes were included in the replicated trial which evaluates colony formation in fresh potato stems. MSZ120-4 was identified as having very little colony formation in a Wisconsin field trial. The line also has scab resistance and chip processing quality. 3. Use genetic markers to improve breeding efficiency. Reducing the length of the breeding cycle (the time from cross to cross) while maintaining or even increasing selection accuracy is important to increasing genetic gain (Cobb et al. 2019), and genomic selection (GS) is a powerful method to achieving this goal. Starting in 2016, UW-Madison began genotyping 120 FY3 clones per year from the potato chip breeding program with thousands of SNP markers on a microarray (Hamilton et al. 2011; Felcher et al. 2012). Phenotypes for total yield, tuber size (median weight), specific gravity, and fry color were collected at a single location. The same data were collected for clones from the National Chip Processing Trial (at the same location) to generate a training set of 600 clones for GS (Endelman et al. 2018). Genomic-estimated breeding values (GEBV) for unphenotyped clones had expected accuracies of 0.5-0.7, depending on the relationship between the clone and training set. When phenotypes for the selection candidates were included (i.e., genome-wide marker-assisted selection), the expected accuracy increased to 0.7-0.8. GEBVs were used to select clones for crossing in 2019 at UW-Madison, in conjunction with data for other phenotypes and markers linked to disease resistance. Compared to historical practice, in which clones were not typically selected for crossing until after FY5, this represents a reduction of two years for the breeding cycle. 4. Transfer new varieties from the breeding programs to the commercial sector. Since 2016 twelve advanced selections have been placed in the commercialization track. Six applications for PVP have been submitted and invention disclosures have been submitted for 6 lines. Ramping up seed production in potato is a challenge. In 2018 there was over 1,700 acres of commercial seed of North Central potato varieties released since 2010.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kolech, S.A., Halseth, D., Perry, K., Wolfe, D., Douches, D.S., Coombs, J. and De Jong, W., 2016. Genetic Diversity and Relationship of Ethiopian Potato Varieties to Germplasm from North America, Europe and the International Potato Center. American Journal of Potato Research, 93(6), pp.609-619.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Rosyara, U.R., De Jong, W.S., Douches, D.S. and Endelman, J.B., 2016. Software for genome-wide association studies in autopolyploids and its application to potato. The Plant Genome, 9(2).
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bali, S., Sathuvalli, V., Brown, C., Novy, R., Ewing, L., Debons, J., Douches, D., Coombs, J., Navarre, D., Whitworth, J. and Charlton, B., 2016. Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program. American Journal of Potato Research, pp.1-10.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Carley, Cari A. Schmitz, Joseph J. Coombs, David S. Douches, Paul C. Bethke, Jiwan P. Palta, Richard G. Novy, and Jeffrey B. Endelman. "Automated tetraploid genotype calling by hierarchical clustering." Theoretical and Applied Genetics (2017): 1-10.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mambetova, S., D. Douches, W. Kirk and N. Rosenzwieg. 2018. Characterization of Late Blight Resistance Potato Breeding Lines with the RB Gene from Solanum bulbocastanum. American Journal of Potato Research. DOI: 10.1007/s12230-018-9664-y
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Braun SR, Endelman JB, Haynes K, Jansky S (2017) Quantitative trait loci for resistance to common scab and cold-induced sweetening in diploid potato. Plant Genome 10:3.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang Y, Snodgrass LB, Bethke PC, Bussan AJ, Holm DG, Novy RG, Pavek MJ, Porter GA, Rosen CJ, Sathuvalli V, Thompson AL, Thornton MT, Endelman JB (2017) Reliability of measurement and genotype x environment interaction for potato specific gravity. Crop Science 57:17.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 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. https://doi.org/10.1007/s12230-018-09711-6
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Massa, A.N. N.C. Manrique-Carpintero, J. Coombs, K.G. Haynes, P.C. Bethke, T.L. Brandt, S.K. Gupta, G.C. Yencho, R.G. Novy and D.S. Douches. Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato. BMC Genetics (2018) 19:87 https://doi.org/10.1186/s12863-018-0672-1
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Endelman, J. B., C. A. Schmitz Carley, P. C. Bethke, J. J. Coombs, M. E. Clough, W. L. da Silva, W. S. De Jong et al. 2018. Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato. Genetics 209, 77-87.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 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
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: 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.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 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. https://doi.org/10.1007/s12230-018-09710-7.


Progress 09/01/17 to 08/31/18

Outputs
Target Audience:Potato Breeding and Genetics community and the state potato industries (growers, processors and marketers). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Each breeding program has graduate students and post docs that are conducting research. During their graduate and post graduatetraining and research they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. These same experiences occur for the undergraduates in the breeding programs How have the results been disseminated to communities of interest?Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. They four state researchers also get together at the NCC215 meeting to discuss and report research results each December. What do you plan to do during the next reporting period to accomplish the goals?The research cycle is yearly. Breeding material is advanced according to the current 2018research studies in the field and greenhouse. Publications for research are written when data is collected and analyzed.

Impacts
What was accomplished under these goals? The foundation of the North Central breeding programs is the generation of segregating populations by sexual hybridization and multiple years of phenotypic selection. Across our four states, more than 1000 segregating populations were created in 2017, with family sizes ranging from 10 to 1000 progeny. Due to the autotetraploid genetics of potato, the vast majority of the progeny have undesirable tuber appearance or maturity and can be removed based on visual, single-plant selection in the first field year. After 3 to 4 years of field evaluation within each state, each clone is entered in the appropriate regional or national trial. Chip processing selections participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA, and for which Douches, Thompson, and Endelman manage test sites. In 2017, there were 60 clones entered in the NCPT from the North Central Region breeders. Fry processing selections enter the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which Thompson and Endelman manage test sites. In 2017, there were 17 clones entered in the NFPT from the North Central Region breeders. As there is no national trial for fresh market selections, we manage a North Central Regional Trial (NCRT) for table russets, reds, yellows, and specialty types, with all four breeders hosting test sites. In 2017, there were 24 clones in the NCRT. After multiple years in regional and national trials, we begin the process of producing foundation seed for large-scale commercial evaluations by potato growers, which takes 2-3 years. Advanced selections that are entering commercial seed production are listed below: Chip W9968-5 High specific gravity, good scab tolerance, only short-term storage MSZ219-1,13 and 14 Scab. LB and PVY resistance combined with chip quality MSX540-4 Combines scab, late blight and PVY resistance with high specific gravity MSW485-2 MSZ109-10PP Broad adaptable yield and specific gravity combined with late blight resistance Purple skin/purple fleshed table potato with round shape and scab resistance ND7519-1 High specific gravity, resistance to cold induced sweetening ND7799c-1 High specific gravity, excellent yield and uniform tuber size profile Russet W9433-1rus High yield and large size profile, light-skinned russet W9742-3rus Excellent type, high specific gravity, developed for processing ND8068-5Russ Very early maturing, dual-purpose russet, excellent French fry quality ND050032-4Russ Dual-purpose light skinned russet WND8625-2Russ Dual-purpose russet, excellent appearance, blocky type Red W8890-1R High yield, dark color, good skin set, smaller (60% A) than Norland (80% A) ND6002-1R Medium maturity, shape/size profile similar to Red Norland, excellent red skin color ND7132-1R Medium maturity, high yield, good red skin color Yellow MST252-1Y Scab resistance with round shape and bright skin Specialty MSZ109-10PP Scab tolerance, round shape and deep pigmented flesh In 2017, UW-Madison developed a SCAR marker unique to the R8 haplotype and used it to screen 10 clones derived from MSU parents. MSU conducts large field trials to evaluate LB resistance in the field: in 2017, 31 advanced lines were identified with late blight resistance, while 35 lines in the early generation observation plots had late blight resistance. These were from various late blight resistance sources in the pedigree of the selections (LBR9, Malinche, Kenya Baraka, Monserrat, Torridon, Stirling, NY121, Tollocan, B0718-3, Chaposa, S. bulbocastanum, S. microdontum, Muruta, Enfula, Perkoz, Basadre, etc.). Most notable lines with late blight resistance include MSX540-4, MSZ219-01, MSZ219-13, MSZ219-14, MSX497-06, MSW485-2, MSW121-2R and MSV235-2PY. In 2018 we recently published a genome wide association study for late blight resistance (Enciso et al. 2018). QTLs for LB resistance were identified on Chromosomes 5 and 9 in the MSU breeding germplasm as well as a few smaller QTL on other chromosomes. Although it has not been formally characterized, a second late blight resistance gene on chromosome 5, derived originally from the chip processing clone NY121 (Mayton et al. 2010), is present in several advanced selections from the North Central region that have been used for crossing, such as Saginaw Chipper and MSX540-4. In 2017 we conducted an initial greenhouse late blight test using a tetraploid mapping population. We will take this population to the field in 2018 and conduct QTL mapping with a set of genome-wide SNPs from the 22K SNP array. We have conducted a number of research projects to develop molecular breeding strategies for common scab resistance. Braun et al. (2017) used a diploid biparental mapping population to identify a QTL for resistance on chromosome 11 in S. chacoense. Enciso-Rodriguez et al. (2018) used a Bayesian regression model to identify a QTL on chromosome 9 in a collection of 370 tetraploid clones.The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region, including W8946-1rus (Rysto), W12003-3rus (Ryadg), Saginaw Chipper (Ryadg), and MSX540-4 (Ryadg). In 2017 more than 500 clones were screened for PVY resistance using molecular markers in the North Central region. MSU was also able to identify dihaploids that carry the RYSC3 marker linked to PVY resistance. In 2018 we published two papers demonstrating the feasibility of genome-wide prediction in potato (Endelman et al. 2018; Enciso-Rodriguez et al. 2018). UW-Madison is using the genomic-estimated breeding values to select FY3 clones for crossing and dihaploid extraction in 2018, which is 1-2 years earlier than normal. This shortening of the breeding cycle is expected to compound over time and improve the rate of genetic gain. In 2018 we will continue to expand the training population for chips and make predictions for russets for the first time.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: 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 (accepted for publication)
  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Mambetova, S., D. Douches, W. Kirk and N. Rosenzwieg. 2018. Characterization of Late Blight Resistance Potato Breeding Lines with the RB Gene from Solanum bulbocastanum. American Journal of Potato Research. DOI: 10.1007/s12230-018-9664-y
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Braun SR, Endelman JB, Haynes K, Jansky S (2017) Quantitative trait loci for resistance to common scab and cold-induced sweetening in diploid potato. Plant Genome 10:3.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang Y, Snodgrass LB, Bethke PC, Bussan AJ, Holm DG, Novy RG, Pavek MJ, Porter GA, Rosen CJ, Sathuvalli V, Thompson AL, Thornton MT, Endelman JB (2017) Reliability of measurement and genotype x environment interaction for potato specific gravity. Crop Science 57:17.


Progress 09/01/16 to 08/31/17

Outputs
Target Audience:Potato Breeding and Genetics community and the state potato industry (growers, processors and marketers). Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Each breeding program has graduate students that are conducting research. During their graduate training they are participating in the breeding program activities of hybridization, planting, field variety trials, disease assessment, grading of trials, post-harvest assessment, data analysis, etc. These same experiences occur for the undergraduates in the breeding programs. How have the results been disseminated to communities of interest?Research results from this project are reported to the state potato industries in Michigan, Wisconsin, Minnesota and North Dakota through written reports, winter research meetings and summer field days. They four state researchers also get together at the NCC215 meeting to discuss and report research results each December. What do you plan to do during the next reporting period to accomplish the goals?The research cycle is yearly. Breeding material is advanced according to the current 2017 research studies in the field and greenhouse.

Impacts
What was accomplished under these goals? 1. The foundation of the North Central breeding programs is the generation of segregating populations by sexual hybridization and multiple years of phenotypic selection. Across our four states, more than 1000 segregating populations were created in 2016, with family sizes ranging from 10 to 1000 progeny. Due to the autotetraploid genetics of potato, the vast majority of the progeny have undesirable tuber appearance or maturity and can be removed based on visual, single-plant selection in the first field year. After 3 to 4 years of field evaluation within each state, each clone is entered in the appropriate regional or national trial. Chip processing selections participate in the National Chip Processing Trial (NCPT), which is managed by Potatoes USA, and for which Douches, Thompson, and Endelman manage test sites. In 2016, there were 46 clones entered in the NCPT from the North Central Region breeders. Fry processing selections enter the National Fry Processing Trial (NFPT), which is also managed by Potatoes USA, and for which Thompson and Endelman manage test sites. In 2016, there were 11 clones entered in the NFPT from the North Central Region breeders. As there is no national trial for fresh market selections, we manage a North Central Regional Trial (NCRT) for table russets, reds, yellows, and specialty types, with all four breeders hosting test sites. In 2016, there were 26 clones in the NCRT. 2. The North Central programs place strong emphasis on breeding for disease resistance using both phenotypic and marker-based selection. Potato late blight (Phytophthora infestans Mont. de Bary) is a significant constraint to potato production, and due to conducive climatic conditions and growing practices, the mid-western states of the US are particularly vulnerable. Dakota Trailblazer also has good field resistance and breeding value for the trait. Saginaw Chipper (MSR061-1) is the latest variety to express late blight resistance to strain US-23 of the pathogen. Late blight resistance expressed in these varieties has been shown to be effective in reducing both the rate and frequency of fungicide applications, thereby reducing production costs for growers and mitigating environmental and consumer concerns. In the last two years, research has shown both Jacqueline Lee and Missaukee from the MSU program contain the R8 gene on chromosome 9, which was inherited from their common parent Tollocan (Massa et al., 2015). MSU has developed a KASP marker linked to R8 that was used for marker-assisted selection of approximately 100 clones in 2016. In inoculated field trials in Michigan, 150 advanced breeding lines and over 200 early generation lines were screened using the US23 isolate; 32 advanced breeding lines from 18 different parental sources of resistance, 56 early generation lines from 19 different late blight resistant parents and 12 diploid selections from three sources of resistance (mcd, ber, phu) were identified. Although it has not been formally characterized, a second late blight resistance gene on chromosome 5, derived originally from the chip processing clone NY121 (Mayton et al. 2010), is present in several advanced selections from the North Central region that have been used for crossing, such as Saginaw Chipper and MSX540-4. Common scab is a prevalent soil borne disease in the US and the North Central Region however, no major genes for scab resistance have been reported, despite decades of research, only minor QTL explaining < 20% of the variance. As a result, our scab resistance breeding efforts are currently based only on phenotypic selection. Potato virus Y (PVY) is a major concern throughout the US, including the North Central region. Molecular markers have been linked with PVY resistance genes that are effective against all PVY strains, providing what is referred to as extreme resistance. The Ryadg gene from S. tuberosum ssp. andigena and Rysto gene from S. stoloniferum are present in a number of elite parents used for crossing in the North Central region, including W8946-1rus (Rysto), W12003-3rus (Ryadg), Saginaw Chipper (Ryadg), and MSX540-4 (Ryadg). In 2016 more than 500 clones were screened for PVY resistance using molecular markers in the North Central region. Storage diseases, such as silver scurf, pink rot, and Pythium leak, occur widely in NC region production areas, reducing tuber quality and causing economic losses. Pink rot (caused by Phytophthora erythroseptica Pethyb.) and leak (caused by Pythium ultimum Trow.) are particularly problematic under conditions of high soil moisture. Thompson et al. (2007) reported efforts to develop genetic resistance to pink rot and leak, simultaneously, and identified a clone derived from S. berthaultii and S. etuberosum as a source of resistance to both. Eight advanced selections and parental genotypes were screened in 2016 compared to four check genotypes. Colorado potato beetle is the most important insect pest of potato in the U.S. Estimates of combined pesticide costs and crop loss are in the hundreds of millions of dollars for U.S. potatoes alone. Dakota Diamond (Thompson et al., 2008) possesses good field resistance to CPB attributed to glycoalkaloid-mediated resistance from S. chacoense. Fifty segregating families, in addition to 230 individual genotypes were evaluated for resistance to defoliation in 2016. 3.In addition to using validated markers for selection, the North Central breeding programs are actively pursuing the development of new markers. Great strides have been made in the methods and software available for QTL mapping in tetraploid F1 populations in the past several years (Hackett et al., 2013; Hackett et al., 2014; Bourke et al., 2016; Zheng et al., 2016). The Douches group is at the forefront of using these methods. As mentioned earlier, a marker linked to the R8 late blight resistance gene present in both the tetraploid Jacqueline Lee and Missaukee varieties was identified by QTL mapping (Massa et al. 2015). Scab resistance, chip and fry processing quality, and several other traits are currently being studied in three tetraploid populations by the Douches group: Premier Russet x Rio Grande Russet, Tundra x Kalkaska, and MSV507-121 x MSV507-99. A key enabling technology for potato molecular breeding is our Infinium SNP array, which was originally developed with 8303 markers as part of the SolCAP project led by Douches (Hamilton et al., 2011; Felcher et al., 2012). Thanks to the continuing efforts of the Douches group, Version 2 of the array with 12K markers became available two years ago, and version 3 with 22K markers is being used as of Jan 2017. In addition to QTL mapping, these arrays have been proven invaluable for genetic fingerprinting and quality control applications. Endelman and Douches have led a national effort to SNP genotype all clones submitted to the national chip and fry processing trials. One important near-term accomplishment from this effort was the discovery that many clones had errors in the recorded pedigree (Endelman et al., 2017). In most cases, we were able to identify the true parents in the dataset. 4.The new varieties Saginaw Chipper and Hodag were released with seed and commercial production currently increasing.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kolech, S.A., Halseth, D., Perry, K., Wolfe, D., Douches, D.S., Coombs, J. and De Jong, W., 2016. Genetic Diversity and Relationship of Ethiopian Potato Varieties to Germplasm from North America, Europe and the International Potato Center. American Journal of Potato Research, 93(6), pp.609-619.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Rosyara, U.R., De Jong, W.S., Douches, D.S. and Endelman, J.B., 2016. Software for genome-wide association studies in autopolyploids and its application to potato. The Plant Genome, 9(2).
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bali, S., Sathuvalli, V., Brown, C., Novy, R., Ewing, L., Debons, J., Douches, D., Coombs, J., Navarre, D., Whitworth, J. and Charlton, B., 2016. Genetic Fingerprinting of Potato Varieties from the Northwest Potato Variety Development Program. American Journal of Potato Research, pp.1-10.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Endelman, Jeffrey B., Cari A. Schmitz Carley, David S. Douches, Joseph J. Coombs, Benoit Bizimungu, Walter S. De Jong, Kathleen G. Haynes et al. "Pedigree Reconstruction with Genome-Wide Markers in Potato." American Journal of Potato Research (2017): 1-7.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Carley, Cari A. Schmitz, Joseph J. Coombs, David S. Douches, Paul C. Bethke, Jiwan P. Palta, Richard G. Novy, and Jeffrey B. Endelman. "Automated tetraploid genotype calling by hierarchical clustering." Theoretical and Applied Genetics (2017): 1-10.