Enhancing Potato Quality and Resistance through Genetic Improvement and Variety Development

ENHANCING POTATO QUALITY AND RESISTANCE THROUGH GENETIC IMPROVEMENT AND VARIETY DEVELOPMENT

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

COMPLETE

Funding Source

HATCH

Reporting Frequency

Annual

Accession No.

1010438

Grant No.

(N/A)

Cumulative Award Amt.

(N/A)

Proposal No.

(N/A)

Multistate No.

(N/A)

Project Start Date

Oct 1, 2016

Project End Date

Sep 30, 2021

Grant Year

(N/A)

Program Code

[(N/A)]- (N/A)

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
Plant, Soil and Microbial Science

Non Technical Summary
The MSU breeding program has been operating for over 25 years and we have developed advanced breeding lines that will lead to elite varieties that also offer disease resistance to scab, late blight and PVY (in some combination). We have the genetic variation to combine tuber shape, skin type, scab resistance and low sugars, yield and storability as well as late blight, PVY, PLRV, Colorado potato beetle and golden nematode resistances. By optimizing our breeding methods we have been able to define more precisely the commercial needs of the new varieties and make better decisions more quickly in the first three years of the breeding program cycle. This is a critical 3-year phase in which we are evaluating over 60,000 combinations a year and sorting down to 100 of the most promising material for advanced testing. In addition, we have been able to increase our efficiency because we are conducting an integrated selection based upon our scab and late blight disease nurseries, post-harvest evaluations for specific gravity and chip quality and DNA tests. The MSU potato breeding program continues to test MSU-bred lines in replicated trials (over 160 lines) and on grower farms (~18 lines). We also enter 8 lines in the North Central regional trials, 2-4 lines in the USPB/SFA trials and send many of the advanced breeding lines to Ohio, Pennsylvania, Florida, California, North Dakota, Nebraska, Minnesota, North Carolina, Maine, Washington, Wisconsin, Ontario and Quebec, Canada for testing. We have also sent germplasm and advanced breeding lines to Japan, South Korea, China, Ethiopia, Australia, Canada, Brazil and Honduras. The USPB-supported NCBT allows us to test the over 40 MSU lines at 11 locations around the country. Through a cooperative effort of MPIC, commercial growers, seed growers, Chris Long (MSU potato specialist), the MSU breeding program and the processors, we are working together to help advance the best lines towards larger scale commercial testing and have chip-processing lines evaluated in the Commercial Demonstration Storage facility (500 cwt bins).

Animal Health Component

50%

Research Effort Categories

Basic

40%

Applied

50%

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1310	1081	50%
201	1310	1080	50%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1310 - Potato;

Field Of Science
1081 - Breeding; 1080 - Genetics;

Keywords

Goals / Objectives
1. Optimize conventional breeding techniques to generate seedlings for varietal selection and development of new breeding methods and schemes to introgress economic traits from exotic Solanum germplasm for the purposes of variety development. Conduct replicated trials at the Montcalm Research Center (MRC) and other sites in Michigan and throughout the nation that are designed to evaluate the marketable maturity and adaptability of advanced selections and new releases with emphasis upon yield, chip-processing, general appearance, dry matter, and blackspot bruise resistance, external and internal defects that affect specific markets.2. Conduct screening procedures (in the field and lab) to evaluate early generation breeding material and advanced selections for chip-processing from storage, resistance to Colorado potato beetle and diseases such as late blight, scab, PVY, PLRV and golden nematode.3. Integrate transformation techniques into the breeding program to introduce genes for insect (Bt-cry3A), late blight resistance (RB), abiotic stress (IPT, Xerico, mannose-6-phosphate and alanine amino transferase), low reducing sugars (acid invertase silencing, invertase inhibitor), tuber quality (starch ratio and carotenoids) and PVY resistance.4. Conduct breeding studies to improve early generation selection (EGS) strategies and develop novel technologies to enhance cultivar commercialization5. Combine the phenotypic evaluation of mapping populations with the genome-wide SNP genotype data to identify marker-trait associations for genes with large effects for market-limiting traits.6. Continue to name, commercially release, and intellectually protect new potato varieties that are of value to the potato industry. Using cryotherapy to generate a) virus-free seed for the testing of advanced selections that will be evaluated in production management studies and grower industry trials, and b) virus-free tissue culture plantlets of the superior advanced selections from the MSU breeding program for the industry.

Project Methods
In 2016 and future years the MSU breeding program will cross elite germplasm to generate and evaluate 65,000 new seedlings for adaptation to Michigan. In the subsequent years these selections are then advanced to 12?hill (year 2), 30-hill (year 3), 50-hill, and 100-hill plots, with increasing selection pressure for agronomic, quality and disease and/or insect resistance parameters. We now have in place field sites for early generation selection for late blight, scab and Colorado potato beetle resistant lines. Early generation evaluation of these key traits increases our effectiveness in identifying commercially valuable advanced selections. These lines are also placed in tissue culture to minimize the risk of PVY in the lines. We are also producing the field year one (FG1) and FG2 level seed of these most promising selections from the MSU breeding program for in-state grower-cooperator trials, out-of-state trials, North Central Regional trials, national USPB/SFA trials and MSU trials. Elite clones will be tested for at MRC for agronomic performance, marketable maturity, chip processing at harvest and in storage, resistance to pitted scab, potato early die and late blight (Clarksville Research Center (CRC)). We are also using a new technique (developed in our lab) to remove virus (cryotherapy) that is showing great promise. We are now establishing a hydroponic nutrient film technology (NFT) certified seed production greenhouse for seed increase of MSU lines for the commercial industry. Currently, the breeding program has in tissue culture over 1800 clones (advanced breeding lines, GM events, genetic stocks and mapping populations) in the MSU tissue culture bank and at least 100 new candidates that are in process for transfer to tissue culture. We want to continue to work closely with the commercial growers and seed industry to test and provide seed for more intensive evaluation. Through this linkage we identify the breeding selections that have merit to achieve varietal status in Michigan. Each year our breeding program will establish a crossing block in greenhouses using favorable clones as parental lines from within and among breeding programs. Superior clones are intercrossed to synthesize new segregating seedling populations. In the crossing blocks, superior parents (based upon previous progeny evaluations) are used as tester lines for crosses to resistance sources, unadapted germplasm, and parents from other breeding programs. Crosses are also made to combine disease resistance (e.g. scab and late blight resistance), quality traits and/or pyramiding resistance (eg. late blight resistance). For example, our parental material has a broad genetic base with over 15 sources of late blight resistance, 14 sources for scab resistance, 12 sources for chip-processing, and 10 Solanum species for trait introgression. Segregating progenies for various fresh market and processing market classes will be planted as single-hill F1 hybrid progenies across regional selection environments. Single or double 3m row spacing x 3m single-hill plant spacing in family field plots will be established. Family plots will have between 25 and 500 progeny per family. Harvested progeny segregating for important market limiting traits will be selected, clonally maintained, and advanced. Small tuber samples will be scored for presence or absence of internal physiological defects. Tubers will be cut longitudinally and defects counted for (HH) hollow heart, (BC) brown center, (IBS) internal brown spots, and (VD) vascular discoloration. As selected clones advance in the programs, the numbers of hills of each clone will increase to accommodate expanded testing from breeder's seed. Marker-assisted breeding (MAB) is initiated after single hill selection or later depending upon the trait's value. Larger plot sizes and more growing environments allow for assessment of the market limiting traits, and disease and pest resistances in the field and laboratory. Elite clones will be tested at the Montcalm Research Farm for agronomic performance, marketable maturity, chip processing at harvest and in storage, resistance to pitted scab, potato early die and late blight. For all field experiments each site will be soil sampled and then analyzed for standard chemical and physical properties. Plots will be grown under local Best Management Practices (BMPs) for the intended production environment at each testing location. Standard commercially available agrochemical products will be used to control disease and insect pests should the experimental plots require. We will collect agronomic parameters such as percent emergence, plant vigor, maturity, and yield, grade and quality attributes from harvested tuber samples. Additional post harvest samples will be evaluated for chip processing color and specific gravity. Tubers will be cut longitudinally and defects counted for (HH) hollow heart, (BC) brown center, (IBS) brown spots, and (VD) vascular discoloration. Chip-processing is the key market trait. The Commercial Demonstration Storage facility enhances our ability to characterize advanced breeding lines from our breeding program. We screen advanced breeding lines from MRC, the Commercial Demonstration Storage, and on-farm trials for chip-processing out-of-the-field, and 50°F and 45°F storage. We also screen early generation breeding material from the 12-, 30- and 50-hill stages for chip processing out-of-the-field, and 50°F and 45°F storage. About 1,200 samples are processed and this data is computerized and used in the selection and decision making process in the breeding program in the following evaluation phase.Diploid Germplasm Enhancement: The Solanum germplasm offers opportunities to broaden the genetic base of the tetraploid potato and introduce traits of economic importance. The benefits of germplasm enhancement are not subject to speculation, yet the enhancement time-line has been unattractively long. We now have a new initiative (USDA/NIFA-funded) to exploit a newly found gene that allows self-pollination (previously not possible). Self-pollination will allow us to develop a diploid breeding approach similar to hybrid corn. Moreover, the "diploid" breeding program simplifies the genetic system in potato and will exploit more efficient selection of desirable traits. We expect to broaden our germplasm base and improve our genetic gain for yield and resistance to major diseases and pests. In addition we are extracting haploids from our potato varieties that can be crossed with the diploid germplasm. In essence, we propose to make many traits more true breeding such as tuber shape, size, specific gravity, maturity, etc., hence making potato breeding a significantly more efficient process. We have expanded our potato breeding effort to focus on exploiting the diploid germplasm of potato. One direction is to extract haploids (2n=2x=24) from elite tetraploids (2n=4x=48). In the past few years we have developed hundreds of haploid lines. Some of our target germplasm has been cultivars and advanced breeding lines with scab resistance. This material needs to be examined in the scab nursery so that our cultivated germplasm base at the diploid level has scab resistance. We have also developed a recurrent selection population for photoperiod adaptability, self-compatibility and cultivated tuber traits. The germplasm is composed of a mixture of six species (S. berthaultii, S. chacoence, S. microdontum, S. tuberosum Grp. Phureja, S. tarijense and S. tuberosum). We are selecting this germplasm for self-fertility, tuber production and photoperiod adaptation. We are in our third cycle of selection and have selections with acceptable tuber traits. This material needs to be screened for scab resistance (as well as other agronomic and economic traits).

Progress 10/01/16 to 09/30/21

Outputs
Target Audience:Potato breeding and genetics researchers along with commerial potato growers and potato processors. Changes/Problems:Covid still creates logistical problems and as a result we are short-staffed. We are putting more emphasis on diploid breeding approaches by developing the germplasm base as well as expaning the number of wild species we are accessing for traits. Excessive rainfall has damaged the late blight research plots in 2021. What opportunities for training and professional development has the project provided?Three graduate students presented results at the national Potato Association of America meeting in July 2021 held virtually. One technician presented results as a poster. Three staff and 4 graduate students attended virtually. Staff and students also attended the MSU potato field day in August. Three technicians participated in manuscript preparation. How have the results been disseminated to communities of interest?Two reports are submitted to the Michigan Potato Industry Commission. Three peer-reviewed papers were published in scientific journals. Oral presentations were made at the regional (North central), national meetings (PAA), Michigan field days and MSU classrooms. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Breeding: The MSU potato breeding and genetics program is actively producing new germplasm and advanced seedlings that are improved for long-term storage chipping, and resistance to scab, late blight, and Colorado potato beetle. For the 2020 field season, progeny from about 300 crosses were planted and evaluated. Of those, the majority were crosses to select for round whites (chip-processing and tablestock), with the remainder to select for yellow flesh, long/russet types, red skin, and specialty market classes. During the 2020 harvest, about 1,500 selections were made from the 37,000 seedlings produced. Most of these first-year selections are segregating for PVY resistance. All second, third or fourth- year potential chip-processing selections will be tested in January and April 2021 directly out of 45°F (7.2°C) storage. Atlantic, Lamoka and Snowden are chip-processed as check cultivars. Selections have been identified at each stage of the selection cycle that have desirable agronomic characteristics and chip-processing potential. At the 12-hill and 30-hill evaluation state, about 200 and 100 selections were made, respectively; based on chip quality, specific gravity, scab resistance, late blight resistance and DNA markers for PVY and Golden nematode resistance. Selection in the early generation stages has been enhanced by the incorporation of the scab and late blight evaluations of the early generation material. Unfortunately, in 2020 we were unable to get effective late blight infection to collect useful data. We are pushing our early generation selections from the 30-hill stage into tissue culture to minimize PVY issues in our breeding and seed stock. We are now using a cryotherapy method as well as the traditional methods that was developed in our lab to remove viruses. This technique predictably and quickly removes virus from tissue culture stocks. Our results show that we are able to remove both PVY and PVS from lines, but PVS can still be difficult to remove in certain lines. We tested the removal of PLRV and succeeded. Over 1500 different varieties and breeding lines are maintained in tissue culture for the breeding and genetics program. Chip-Processing: Over 80% of the single hill selections have a chip-processing parent in their pedigree. Our most promising advanced chip-processing lines are Mackinaw (MSX540-4) (scab, late blight and PVY resistant), Petoskey (MSV030-4) (scab resistant), Huron Chipper (MSW485-2) (late blight resistant), MSZ242-13 (scab resistant), MSW474-1 (scab resistant) and MSZ219-1 (scab, late blight and PVY resistant). We have some newer lines to consider, but we are removing virus from those lines. We are using the NCPT trials to more effectively identify promising new selections. Manistee was licensed to Canada and Chile. Saginaw Chipper and Mackinaw are being tested in Australia and South Korea. Tablestock: Efforts have been made to identify lines with good appearance with an attractive skin finish, low internal defects, good cooking quality, high marketable yield and resistance to scab, late blight and PVY. Our current tablestock development goals now are to continue to improve the frequency of scab and PVY resistant lines, incorporate resistance to late blight along with marketable maturity and excellent tuber quality, and select more russet, red-skinned, and yellow-fleshed lines. We have also been selecting some pigmented skin and tuber flesh lines that fit some specialty markets. There is also interest in some additional specialty mini-potatoes for the "Tasteful Selections" market. We have interest from some western specialty potato growers to test and commercial these lines. From our breeding efforts we have identified mostly round white lines, but we also have a number of yellow-fleshed and red-skinned lines, as well as some purple skin selections that carry many of the characteristics mentioned above. We are also selecting for round white, red-skin, and improved Yukon Gold-type yellow- fleshed potatoes. Some of the tablestock lines were tested in on-farm trials in 2020, while others were tested under replicated conditions at the Montcalm Research Center. Promising tablestock lines include MSV093-1Y (yellow, scab resistant), MST252-1Y (scab resistant), MSV179-1 (scab resistant), and MSX324-2R (scab resistant). MSZ109-8PP and MSZ109-10PP (Blackberry) are purple-fleshed chippers with deep purple flesh, round shape and attractive skin as well as scab resistance. Jacqueline Lee (late blight resistant) was licensed to Australia and is being grown in Central America for its late blight resistance. Spartan Splash, Raspberry, Blackberry, MSQ558-2RR (Ruby Rose) and our PVY resistant Red Marker #2 potato are being marketed in the specialty markets. Blackberry is also being chip-processed by the Great Lakes Chip Co. in Traverse City, MI. Disease and Insect Resistance Breeding: Scab: In 2020, we had two locations to evaluate scab resistance: a commercial field with a history of severe scab infection and a highly infected site at the Montcalm Research Center. In 2020, the commercial site and the Montcalm Research Center both gave us very high scab infection levels. The susceptible checks of Snowden and Atlantic were highly infected with pitted scab. Promising resistant selections were MST252-1Y, MSV179-1, MSX324-1P, MSW474-01, MSZ219-1, MSZ219-13, MSZ219-14, as well as the Z-series selections MSZ242-07, MSZ242-09 and MSZ242-13 from the commercial scab site. If you examine the variety trials at MRC you will notice that many of the lines are scab resistant. We need to continue in this direction of many selections with scab resistance so we can find the great scab resistant chipper as well as table yellow and red. The high level of scab infection at the on-farm site with a history of scab infection and MRC has significantly helped with our discrimination of resistance and susceptibility of our lines. The MRC scab site was used for assessing scab susceptibility in our advanced breeding lines and early generation material and is summarized below. All susceptible check plots (Snowden and Atlantic) were scored as susceptible. PVY: We are using PCR-based DNA markers to select potatoes resistant to PVY. The gene is located on Chromosome 11. In our first round we made crosses in 2013 to generate over 7,000 progeny segregating for PVY resistance. Each year since 2013 we are making new crosses, making selections and expanding the germplasm base that has PVY resistance. In the past year we tested over 1,100 progeny for the PVY resistance marker. The 550 that were marker positive were evaluated at Lake City. About 170 selections were made to advance for further evaluation. We are also using DNA markers to also screen for PVX resistance, PLRV resistance, late blight resistance and Golden nematode resistance. As a result of this work, Mackinaw has PVY resistance. More PVY resistant advanced selections are in the queue that will be evaluated in 2021. We have identified an advanced breeding line, MSCC725-232 that combines three virus resistance genes (PVY, PVX and PLRV). Application of Molecular Markers in MSU Potato Breeding. With the development of molecular markers for potato breeding, marker-assisted 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 more informed decisions in variety selection.

Publications

Type: Journal Articles Status: Published Year Published: 2021 Citation: Alsahlany, M., Enciso-Rodriguez, F., Lopez-Cruz, M. et al. Developing self-compatible diploid potato germplasm through recurrent selection. Euphytica 217, 47 (2021). https://doi.org/10.1007/s10681-021-02785-0
Type: Journal Articles Status: Published Year Published: 2021 Citation: Zhang, C., Zarka, K. A., Zarka, D. G., Whitworth, J. L., & Douches, D. S. Expression of the Tomato pot-1 Gene Confers Potato Virus Y (PVY) Resistance in Susceptible Potato Varieties. American Journal of Potato Research, 1-9.
Type: Journal Articles Status: Published Year Published: 2021 Citation: Otieno, S. A., Collins, P., Coombs, J., Allen, C., & Douches, D. S. (2021). Screening for Ralstonia solanacearum Resistance in Solanum commersonii. American Journal of Potato Research, 98(1), 72-77.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Potato breeding and genetics community. Commercial potato farmers and potato processors. Changes/Problems:Covid-19 pandemic limited both field and lab work. Excessive rain destroyed 2 field trials this year. What opportunities for training and professional development has the project provided?Three graduate students presented results at the national Potato Association of America meeting July 2020 held virtually. Two technicians also presented results via posters. Staff and students also attended the virtual Michigan potato field day. How have the results been disseminated to communities of interest?A report is submitted to the Michigan Potato Industry Commission. Peer-reviewed publications are written. Oral presenations are made at national meetings (PAA, Potato Expo, PAG), Michigan field days and in MSU classrooms. What do you plan to do during the next reporting period to accomplish the goals?We will continue the breeding work. Cycle takes one year. Transformation experiments are under way to study new traits. We expect to release some new varieties for the chip-processing and table markets.

Impacts
What was accomplished under these goals? The MSU potato breeding and genetics program is actively producing new germplasm and advanced seedlings that are improved for long-term storage chipping, and resistance to scab, late blight, and Colorado potato beetle. For the 2019 field season, progeny from about 400 crosses were planted and evaluated. Of those, the majority were crosses to select for round whites (chip-processing and tablestock), with the remainder to select for yellow flesh, long/russet types, red skin, and novelty market classes. During the 2019 harvest, about 1,000 selections were made from the 45,000 seedlings produced. All of these first-year selections are segregating for PVY resistance. All second, third or fourth- year potential chip-processing selections will be tested in January and April 2020 directly out of 45°F (7.2°C) and 50°F (10°C) storages. Atlantic, Lamoka and Snowden are chip-processed as check cultivars. Selections have been identified at each stage of the selection cycle that have desirable agronomic characteristics and chip-processing potential. At the 12-hill and 30-hill evaluation state, about 300 and 100 selections were made, respectively; based on chip quality, specific gravity, scab resistance, late blight resistance and DNA markers for PVY and Golden nematode resistance. Selection in the early generation stages has been enhanced by the incorporation of the scab and late blight evaluations of the early generation material. We are now using a cryotherapy method as well as the traditional methods that was developed in our lab to remove viruses. This technique predictably as well as quickly remove virus from tissue culture stocks. Our results show that we are able to remove both PVY and PVS from lines, but PVS can still be difficult to remove in certain lines. We tested the removal of PLRV and succeeded. Over 1700 lines are maintained in tissue culture for the breeding and genetics program. Chip-Processing Over 80% of the single hill selections have a chip-processing parent in their pedigree. Our most promising advanced chip-processing lines are Mackinaw (MSX540-4) (scab, late blight and PVY resistant), Petoskey (MSV030-4) (scab resistant), Huron Chipper (MSW485-2) (late blight resistant), MSW075-2 (scab resistant), MSZ242-13 (scab resistant) and MSZ219-1, MSZ219-13 and MSZ219-14 ( all three sibs are scab, late blight and PVY resistant). We have some newer lines to consider, but we are removing virus from those lines. We are using the NCPT trials to more effectively identify promising new selections. Manistee was licensed to Canada and Chile. Saginaw Chipper and Mackinaw are being tested in Australia and Korea. Tablestock Efforts have been made to identify lines with good appearance with an attractive skin finish, low internal defects, good cooking quality, high marketable yield and resistance to scab, late blight and PVY. Our current tablestock development goals now are to continue to improve the frequency of scab resistant lines, incorporate resistance to late blight along with marketable maturity and excellent tuber quality, and select more russet, red-skinned, and yellow-fleshed lines. We have also been selecting some pigmented skin and tuber flesh lines that fit some specialty markets. There is also interest in some additional specialty mini-potatoes for the "Tasteful selections" market. We have interest from some western specialty potato growers to test and commercial these lines. From our breeding efforts we have identified mostly round white lines, but we also have a number of yellow-fleshed and red-skinned lines, as well as some purple skin selections that carry many of the characteristics mentioned above. We are also selecting for round white, red-skin, and improved Yukon Gold-type yellow-fleshed potatoes. Some of the tablestock lines were tested in on-farm trials in 2019, while others were tested under replicated conditions at the Montcalm Research Center. Promising tablestock lines include MSV093-1Y (yellow, scab resistant), MST252-1Y (scab resistant), MSV179-1 (scab resistant), Isle Royale (MSX569-1R) (scab resistant) and MSX324-1P (scab resistant). MSZ109-8PP and MSZ109-10PP (Blackberry) are purple-fleshed chippers with deep purple flesh, round shape and attractive skin as well as scab resistance. Jacqueline Lee (late blight resistant) was licensed to Australia and is being grown in Central America for its late blight resistance. Spartan Splash, Raspberry, Blackberry, MSQ558-2RR and our PVY resistant Red Marker #2 potato are being marketed in the specialty markets. Blackberry is also being chip-processed by the Great Lakes Chip Co. in Traverse City, MI and receiving local and national press. Disease and Insect Resistance Breeding Scab: In 2019 we had two locations to evaluate scab resistance: a commercial field with a history of severe scab infection (we thankfully acknowledge the support of Sackett Potatoes for this important trial) and a highly infected site at the Montcalm Research Center. In 2019 the commercial site and the Montcalm Research Center both gave us very high scab infection levels. The susceptible checks of Snowden and Atlantic were highly infected with pitted scab. Promising resistant selections were MST252-1Y, MSV179-1, MSX324-1P, MSW474-01, MSZ219-1, MSZ219-13, MSZ219-14, as well as the Z-series selections from the commercial scab site. If you examine the Advanced Chip trial you will notice that almost all the lines are scab resistant. We need to continue in this direction of many selections with scab resistance so we can find the great scab resistant chipper. The high level of scab infection at the on-farm site with a history of scab infection and MRC has significantly helped with our discrimination of resistance and susceptibility of our lines. The MRC scab site was used for assessing scab susceptibility in our advanced breeding lines and early generation material and is summarized below. All susceptible check plots (Snowden and Atlantic) were scored as susceptible. PVY: We are using PCR-based DNA markers to select potatoes resistant to PVY. The gene is located on Chromosome 11. In our first round we made crosses in 2013 to generate over 7,000 progeny segregating for PVY resistance. Each year since 2013 we are making new crosses, making selections and expanding the germplasm base that has PVY resistance. We are also using DNA markers to also screen for PVX resistance, PLRV resistance, late blight resistance and Golden nematode resistance. As a result of this work, Mackinaw has PVY resistance as well as MSZ219-1,13 and 14. More PVY resistant advanced selections are in the queue. We have identified an advanced breeding line, MSCC725-232 that combines three virus resistance genes (PVY, PVX and PLRV). ? We have also generated lines with the genes for water use efficiency. The XERICO gene is showing the most promise. In 2018 and 2019 we conducted preliminary trials at MRC with Ranger Russet events. These results are indicating that we are not seeing a yield reduction from the XERICO gene and the XERICO events also had a higher specific gravity than Ranger Russet. Meanwhile the greenhouse experiments are showing an ability to refrain from wilting under sub-optimal soil water levels. In 2020 we continued field trials at MRC. Lastly, we have generated and selected a Kalkaska invertase silencing line (Kal91.03) that has resistance to accumulating reducing sugars in cold (40°F) storage. We tested the agronomic characteristics of Kal91.03 from 2016-2019. The initial results are suggesting that the invertase silencing line has good tuber type, size and similar specific gravity. This suggests that we can correct sugar issues in a chip processing lines with this genetic engineering strategy. In 2020 we will be producing XERICO events and Kal91.03 in the NFT greenhouse to run larger trials in 2021.

Publications

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.
Type: Journal Articles Status: Published Year Published: 2019 Citation: 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
Type: Book Chapters Status: Published Year Published: 2020 Citation: Ghislain M., Douches D.S. (2020) The Genes and Genomes of the Potato. In: Campos H., Ortiz O. (eds) The Potato Crop. Springer, Cham doi.org/10.1007/978-3-030-28683-5_5

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:US potato industry and potato breeding and genetics community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?My graduate students and post docs report research at the Potato Association of America meetings and the NCCC215 North Central Potato Breeding and Genetics meetings. Undergraduates have presented posters at undergraduate research meetings at Michigan State University. How have the results been disseminated to communities of interest?A report is submitted to the Michgan Potato Industry Commission annually. There is also a field day each summer at the Montcalm Research Center we report progress. We also publish in peer-reviewed journals. What do you plan to do during the next reporting period to accomplish the goals?We will continue with the advancement of breeding material and evaluate its commercial potential. Disease resistance breeding continues to increase the frequency of lines with PVY, common scab and late blight resistance. We are also continuing to introgress self compatibility into the diploid germplasm. GE lines will continued to be assessed for their commercial value.

Impacts
What was accomplished under these goals? 1. Optimize conventional breeding techniques to generate seedlings for varietal selection and development of new breeding methods and schemes to introgress economic traits from exotic Solanum germplasm for the purposes of variety development. Conduct replicated trials at the Montcalm Research Center (MRC) and other sites in Michigan and throughout the nation that are designed to evaluate the marketable maturity and adaptability of advanced selections and new releases with emphasis upon yield, chip-processing, general appearance, dry matter, and blackspot bruise resistance, external and internal defects that affect specific markets. For the 2018field season, progeny from about 350 crosses were planted and evaluated. Of those, the majority were crosses to select for round whites (chip-processing and tablestock), with the remainder to select for yellow flesh, long/russet types, red skin, and novelty market classes. During the 2018harvest, over 1,200 selections were made from the 45,000 seedlings produced. 2. Conduct screening procedures (in the field and lab) to evaluate early generation breeding material and advanced selections for chip-processing from storage, resistance to Colorado potato beetle and diseases such as late blight, scab, PVY, PLRV and golden nematode. In 2018 we had two locations to evaluate scab resistance: a commercial field with a history of severe scab infection (Sackett Potatoes) and a highly infected site at the Montcalm Research Center in the commercial production area. The commercial site and the Montcalm Research Center both gave us high infection levels. The susceptible checks of Snowden and Atlantic were highly infected with pitted scab. Over 70 promising resistant selections were identified. In 2018we conducted late blight trials at the the MSU Plant Pathology farm. We inoculated with the US23 genotype. Due to the dry conditons, no late blight infection data was collected. 3. Integrate transformation techniques into the breeding program to introduce genes for insect (Bt-cry3A), late blight resistance (RB), abiotic stress (IPT, Xerico, mannose-6-phosphate and alanine amino transferase), low reducing sugars (acid invertase silencing, invertase inhibitor), tuber quality (starch ratio and carotenoids) and PVY resistance. Regarding late blight resistance, we have many lines with the RB gene for late blight resistance transformed into MSU lines. The addition of the RB gene allows us to test the effect of multiple resistance genes on the strength of resistance. Our data supports the need to pyramid the late blight resistance R-genes to achieve the best levels of resistance. The RB gene is in Jacqueline Lee and MSL268-D. We now have generated some lines with 3-R-genes stacked with one transformation. We have also generated lines with the genes for water use efficiency (WUE). The XERICO gene is showing the most promise. The XERICO lines are showing higher specific gravity in a preliminary field trial. Lastly, we have generated and selected a Kalkaska invertase silencing line (Kal91.03) that has resistance to accumulating reducing sugars in 40F storage. We tested the agronomic characteristics of Kal91.03 in 2016-18. The results are suggesting that the invertase silencing line has good tuber type, size and similar specific gravity. This suggests that we can correct sugar issues in a chip processing lines with this genetic engineering strategy and also store the potatoes for 6 months at 4C and maintain low reducing sugars. 4. Conduct breeding studies to improve early generation selection (EGS) strategies and develop novel technologies to enhance cultivar commercialization. During the 2018harvest, over 45,000 seedlings produced. In addition, about 700first year selections from elite chip-processing crosses segregating for PVY resistance were made. Selections have been identified at each stage of the selection cycle that have desirable agronomic characteristics and chip-processing potential. At the 12-hill and 30-hill evaluation state, about 300 and 70selections were made, respectively; based upon chip quality, specific gravity, scab resistance, late blight resistance and DNA markers for PVY and Golden nematode resistance. Almost all the 2019 crosses are segregating for PVY resistance. Selection in the early generation stages has been enhanced by the incorporation of the scab and late blight evaluations of the early generation material. We are pushing our early generation selections from the 30-hill stage into tissue culture to minimize PVY issues in our breeding and seed stock. 5. Combine the phenotypic evaluation of mapping populations with the genome-wide SNP genotype data to identify marker-trait associations for genes with large effects for market-limiting traits. We evaluated six mapping populations. One population BB040 was for specific gravity and woind healing, one population for protein content, one population for leptine based insect resistance, one population for trichome-based insect resistance and two populations for late blight resistance. Candidate SNP markers have been identified for the significant QTLs. 6. Continue to name, commercially release, and intellectually protect new potato varieties that are of value to the potato industry. Using cryotherapy to generate a) virus-free seed for the testing of advanced selections that will be evaluated in production management studies and grower industry trials, and b) virus-free tissue culture plantlets of the superior advanced selections from the MSU breeding program for the industry. We named MSX540-4, a PVY, scab and late blight resistant storage chipper, Mackinaw. MSV030-4, a scab resistant storage chipper, will be named Petosky.

Publications

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.
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: 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

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:US potato industry and potato breeding and genetics community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? My graduate students and post docs report research at the Potato Association of America meetings and the NCCC215 North Central Potato Breeding and Genetics meetings. Undergraduates have presented posters at undergraduate research meetings at Michigan State University. How have the results been disseminated to communities of interest? A report is submitted to the Michgan Potato Industry Commission annually. There is also a field day each summer at the Montcalm Research Center we report progress. We also publish in peer-reviewed journals. What do you plan to do during the next reporting period to accomplish the goals? We will continue with the advancement of breeding material and evaluate its commercial potential. Disease resistance breeding continues to increase the frequencyof lines with PVY, common scab and late blight resistance. We are also continuing to introgress self compatibility into the diploid germplasm. GE lines will continued to be assessed for their commercial value.

Impacts
What was accomplished under these goals? 1. Optimize conventional breeding techniques to generate seedlings for varietal selection and development of new breeding methods and schemes to introgress economic traits from exoticSolanumgermplasm for the purposes of variety development. Conduct replicated trials at the Montcalm Research Center (MRC) and other sites in Michigan and throughout the nation that are designed to evaluate the marketable maturity and adaptability of advanced selections and new releases with emphasis upon yield, chip-processing, general appearance, dry matter, and blackspot bruise resistance, external and internal defects that affect specific markets. For the 2017 field season, progeny from about 400 crosses were planted and evaluated. Of those, the majority were crosses to select for round whites (chip-processing and tablestock), with the remainder to select for yellow flesh, long/russet types, red skin, and novelty market classes. During the 2017 harvest, over 1,000 selections were made from the 40,000 seedlings produced. 2. Conduct screening procedures (in the field and lab) to evaluate early generation breeding material and advanced selections for chip-processing from storage, resistance to Colorado potato beetle and diseases such as late blight, scab, PVY, PLRV and golden nematode. In 2018we had two locations to evaluate scab resistance: a commercial field with a history of severe scab infection (Sackett Potatoes) and a highly infected site at the Montcalm Research Center in the commercial production area. The commercial site and the Montcalm Research Center both gave us high infection levels. The susceptible checks of Snowden and Atlantic were highly infected with pitted scab. Over 50 promisingresistant selections were identified as well as the 18Z-series selections from the commercial scab site. In 2017we conducted late blight trials at the Clarksville Research Center. We inoculated with the US23 genotype. 3. Integrate transformation techniques into the breeding program to introduce genes for insect (Bt-cry3A), late blight resistance (RB), abiotic stress (IPT, Xerico, mannose-6-phosphate and alanine amino transferase), low reducing sugars (acid invertase silencing, invertase inhibitor), tuber quality (starch ratio and carotenoids) and PVY resistance.Regarding late blight resistance, we have many lines with the RB gene for late blight resistance transformed into MSU lines. The addition of the RB gene allows us to test the effect of multiple resistance genes on the strength of resistance. Our data supports the need to pyramid the late blight resistance R-genes to achieve the best levels of resistance.The RB gene is in Jacqueline Lee and MSL268-D.We now have generated some lines with 3-R-genes stacked with one transformation. We have also generated lines with the genes for water use efficiency (WUE).Field trials with reduced fertilizer and non-irrigated conditions were conducted for a subset of these lines from 2014 to 2017.The XERICO gene is showing the most promise. Lastly, we have generated and selected a Kalkaska invertase silencing line (Kal91.03) that has resistance to accumulating reducing sugars in 40F storage.We tested the agronomic characteristics of Kal91.03 in 2016 and 2017. The initial results are suggesting that the invertase silencing line has good tuber type, size and similar specific gravity. This suggests that we can correct sugar issues in a chip processing lines with this genetic engineering strategy. 4. Conduct breeding studies to improve early generation selection (EGS) strategies and develop novel technologies to enhance cultivar commercialization. During the 2017 harvest, over 40,000 seedlings produced. In addition, about 500 first year selections from elite chip-processing crosses segregating for PVY resistance were made. All potential chip-processing selections will be tested in January and April 2018 directly out of 45F (7.2C) and 50F (10C) storages. Atlantic, Pike (50F chipper) and Snowden (45F chipper) are chip-processed as check cultivars. Selections have been identified at each stage of the selection cycle that have desirable agronomic characteristics and chip-processing potential. At the 12-hill and 30-hill evaluation state, about 200 and 80 selections were made, respectively; based upon chip quality, specific gravity, scab resistance, late blight resistance and DNA markers for PVY and Golden nematode resistance. Selection in the early generation stages has been enhanced by the incorporation of the scab and late blight evaluations of the early generation material. We are pushing our early generation selections from the 30-hill stage into tissue culture to minimize PVY issues in our breeding and seed stock. 5.Combine the phenotypic evaluation of mapping populations with the genome-wide SNP genotype data to identify marker-trait associations for genes with large effects for market-limiting traits. We evaluated six mapping populations. One population BB040 was for specific gravity and woind healing, one population for protein content, one population for leptine based insect resistance, one population for trichome-based insect resistanceand two populations for late blight resistance. 6.Continue to name, commercially release, and intellectually protect new potato varieties that are of value to the potato industry. Using cryotherapy to generate a) virus-free seed for the testing of advanced selections that will be evaluated in production management studies and grower industry trials, and b) virus-free tissue culture plantlets of the superior advanced selections from the MSU breeding program for the industry. We named MSX540-4 Mackinaw. It is a chip-processing variety with PVY, scab and late blight resistance. We also named MSW485-2 Huron Chipper. It is a late blight resistant chip-processing variety. Over 20 lines are being treated with cryotherapy to remove PVY and PVS from advanced selections from the breeding program.

Publications

Type: Journal Articles Status: Published Year Published: 2018 Citation: Bisognin, D. A., Manrique-Carpintero, N. C., & Douches, D. S. (2018). QTL Analysis of Tuber Dormancy and Sprouting in Potato. American Journal of Potato Research, 1-9. DOI: 10.1007/s12230-018-9638-0
Type: Journal Articles Status: Published Year Published: 2018 Citation: Majeed, N., Javaid, B., Deeba, F., Naqvi, S. M. S., & Douches, D. S. (2018). Enhanced Fusarium oxysporum f. sp. tuberosi Resistance in Transgenic Potato Expressing a Rice GLP Superoxide Dismutase Gene. American Journal of Potato Research, 1-12. DOI: 10.1007/s12230-018-9639-z
Type: Journal Articles Status: Published Year Published: 2018 Citation: Deperi, S. I., Tagliotti, M. E., Bedogni, M. C., Manrique-Carpintero, N. C., Coombs, J., Zhang, R., Huarte, M. A. (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(3), e0194398. http://doi.org/10.1371/journal.pone.0194398
Type: Journal Articles Status: Published Year Published: 2018 Citation: Tagliotti, M. E., Deperi, S. I., Bedogni, M. C., Zhang, R., Manrique Carpintero, N. C., Coombs, J.,Douches, D., Huarte, M. A. (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. http://doi.org/10.1186/s12863-017-0556-9

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The potato industry and the potato breeding and genetics community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?My graduate students and post docs report research at the Potato Association of America meetings and the NCCC215 North Central Potato Breeding and Genetics meetings. Undergraduates have presented posters at undergraduate research meetings at Michigan State University. How have the results been disseminated to communities of interest?A report is submitted to the Michgan Potato Industry Commission annually. There is also a field day each summer at the Montcalm Research Center we report progress. We also publish in peer-reviewed journals. What do you plan to do during the next reporting period to accomplish the goals?We will continue with the advancement of breeding material and evaluate its commercial potential. Disease resistance breeding continues to increase the frequencing of lines with PVY, common scab and late blight resistance. We are also continuing to introgress self compatibility into the diploid germplasm. GE lines will continued to be assessed for their commercial value.

Impacts
What was accomplished under these goals? 1. Optimize conventional breeding techniques to generate seedlings for varietal selection and development of new breeding methods and schemes to introgress economic traits from exoticSolanumgermplasm for the purposes of variety development. Conduct replicated trials at the Montcalm Research Center (MRC) and other sites in Michigan and throughout the nation that are designed to evaluate the marketable maturity and adaptability of advanced selections and new releases with emphasis upon yield, chip-processing, general appearance, dry matter, and blackspot bruise resistance, external and internal defects that affect specific markets. For the 2016 field season, progeny from about 500 crosses were planted and evaluated. Of those, the majority were crosses to select for round whites (chip-processing and tablestock), with the remainder to select for yellow flesh, long/russet types, red skin, and novelty market classes. During the 2016 harvest, over 1,000 selections were made from the 60,000 seedlings produced. In addition, about 200 first year selections from elite chip-processing crosses segregating for PVY resistance were made in a commercial field with high scab pressure. All potential chip-processing selections will be tested in January and April 2017 directly out of 45°F (7.2°C) and 50°F (10°C) storages. Atlantic, Pike (50°F chipper) and Snowden (45°F chipper) are chip-processed as check cultivars. Selections have been identified at each stage of the selection cycle that have desirable agronomic characteristics and chip-processing potential. At the 12-hill and 30-hill evaluation state, about 200 and 100 selections were made, respectively; based upon chip quality, specific gravity, scab resistance, late blight resistance and DNA markers for PVY and Golden nematode resistance. Selection in the early generation stages has been enhanced by the incorporation of the scab and late blight evaluations of the early generation material. 2. Conduct screening procedures (in the field and lab) to evaluate early generation breeding material and advanced selections for chip-processing from storage, resistance to Colorado potato beetle and diseases such as late blight, scab, PVY, PLRV and golden nematode. In 2016 we had two locations to evaluate scab resistance: a commercial field with a history of severe scab infection (Sackett Potatoes) and a highly infected site at the Montcalm Research Center in the commercial production area. The commercial site and the Montcalm Research Center both gave us high infection levels. The susceptible checks of Snowden and Atlantic were highly infected with pitted scab. Promising resistant selections were MSR127-2, MSU383-A, MST252-1Y, MSV179-1, MSW474-01, MSV383-B, MSZ219-1, MSZ219-14, MSU379-1, MSW509-5, MSZ222-19 as well as the Z-series selections from the commercial scab site. The high level of scab infection at the on-farm site with a history of scab infection and MRC has significantly helped with our discrimination of resistance and susceptibility of our lines. The MRC scab site was used for assessing scab susceptibility in our advanced breeding lines and early generation material and is summarized below. In 2016 we conducted late blight trials at the Clarksville Research Center. We inoculated with the US23 genotype. Over fourteen sources of resistance can be traced in the pedigrees of these resistant lines. This data infers that we have a broad genetic base to combine resistance genes and also should be able to respond to changes in the pathogen.We are using PCR-based DNA markers to select potatoes resistant to PVY. The gene is located on Chromosome 11. In our first round we made crosses in 2013 to generate over 7,000 progeny segregating for PVY resistance. These crosses were planted in 2014 and 715 progeny were selected in the fall. DNA was isolated from those lines in the winter and 45% of the lines were positive for the DNA marker. In 2015 we planted these lines and selected 105 for further study. Each year since 2013 we are making new crosses, making selections and expanding the germplasm base that has PVY resistance. We are also using DNA markers to also screen for PVX resistance, PLRV resistance, late blight resistance and Golden nematode resistance. 3. Integrate transformation techniques into the breeding program to introduce genes for insect (Bt-cry3A), late blight resistance (RB), abiotic stress (IPT, Xerico, mannose-6-phosphate and alanine amino transferase), low reducing sugars (acid invertase silencing, invertase inhibitor), tuber quality (starch ratio and carotenoids) and PVY resistance. PVY resistance to three PVY strains (O, N and NTN) of the MSE149-5Y, Classic Russet, Silverton Russet and Russet Norkotah lines were initially evaluated by Jonathan Whitworth in GH screening. A number of lines with PVY resistance were identified, seed produced and in 2015 and 2016 we conducted a PVY resistance field test. In the inoculated field test at MSU the MSE149-5Y line was resistant to PVY as well as the Classic Russet line (Figures below). We identified a number of Silverton Russet lines with increased PVY resistance but none with complete resistance to all three PVY strains. The Russet Norkotah lines were not highly resistant. 4. Conduct breeding studies to improve early generation selection (EGS) strategies and develop novel technologies to enhance cultivar commercialization. We are using marker-assisted selection for PVY, PVX, golden nematode and late blight resistance. This effort reduces the material we evaluate in the field earlier in the program and make better selections. 5.Combine the phenotypic evaluation of mapping populations with the genome-wide SNP genotype data to identify marker-trait associations for genes with large effects for market-limiting traits. We have mapping populations for Colorado potato beetle resistance and late blight resistance. We will use this mapping work to introgress these new reisstance traits. 6.Continue to name, commercially release, and intellectually protect new potato varieties that are of value to the potato industry. Using cryotherapy to generate a) virus-free seed for the testing of advanced selections that will be evaluated in production management studies and grower industry trials, and b) virus-free tissue culture plantlets of the superior advanced selections from the MSU breeding program for the industry. We named and released MSR127-2 as Spartan Chipper We are also using a hydroponic seed production method to produce commercial seed for testing our new varieties and advanced selections.

Publications

Type: Journal Articles Status: Published Year Published: 2016 Citation: Hardigan, M. A., Crisovan, E., Hamiltion, J. P., Kim, J., Laimbeer, P., Leisner, C. P., ... & Yang, X. (2016). Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. The Plant Cell, 28 (2), 388-405.
Type: Journal Articles Status: Published Year Published: 2016 Citation: Butler, N. M., Baltes, N. J., Voytas, D. F., & Douches, D. S. (2016). Geminivirus-mediated genome editing in potato (Solanum tuberosum L.) using sequence-specific nucleases. Frontiers in plant science, 7.
Type: Journal Articles Status: Published Year Published: 2016 Citation: Butler, N. M., & Douches, D. S. (2016). Sequence-Specific Nucleases for Genetic Improvement of Potato. American Journal of Potato Research, 93(4), 303-320.