SOYBEAN BREEDING AND GENETICS

• Sponsoring Institution: State Agricultural Experiment Station
• Project Status: TERMINATED
• Funding Source: STATE
• Reporting Frequency: Annual
• Accession No.: 1009950
• Project No.: MIN-13-110
• Project Start Date: Jul 1, 2016
• Project End Date: Jun 30, 2020

Project Director
Lorenz, AA, J..

Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108

Performing Department
Agronomy & Plant Genetics

Non Technical Summary
Soybean (Glycine max) was grown on over 7.5 million acres in Minnesota and produces 3.2 billion dollars in cash receipts, accounting for 30% of the total crop cash receipts received by Minnesota farmers in 2015. Soybean breeding is an important activity that results in the development of new varieties improved for yield, time to maturity, disease resistance, insect resistance and quality. Soybean yields have increased from ~20 bu/ac in the early 1940s to near 50 bu/ac in 2015. Approximately 67% of this increase has been attributed to genetic gain, or in other words, the development of better varieties through breeding. Soybean breeding programs are constantly changing methodology in response to advances in knowledge of the underlying trait genetics and advancing technology. The objectives of this MAES project proposal are: 1) Develop superior general purpose, food type, and specialty type soybean varieties adapted to Minnesota. 2) Develop new traits, sources of pest resistance, and germplasm for new cropping systems and conventional cropping systems. 3) Research new methods for improving the effectiveness and efficiency of soybean breeding programs. 4) Educate and train graduate students. Two examples of activities are provided for each of the first three objectives. The development of specialty varieties, such as the Triple Null variety and high oleic - low linolenic soybean varieties will open up market opportunities for MN farmers. New sources of soybean aphid and soybean cyst nematode resistance will be developed and incorporated into MN-adapted varieties. Research on genomic selection and high-throughput phenotyping will be conducted in order to improve the effectiveness and efficiency of soybean breeding. Training and education of graduate students is an ongoing activity of the breeding program.

Animal Health Component

0%

Research Effort Categories

Basic

15%

Applied

70%

Developmental

15%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
202	1820	1081	100%

Knowledge Area
202 - Plant Genetic Resources;

Subject Of Investigation
1820 - Soybean;

Field Of Science
1081 - Breeding;

Keywords

soybean

breeding

Goals / Objectives
Develop superior general purpose, food type, and specialty type soybean varieties adapted to Minnesota.Develop new traits, sources of pest resistance, and germplasm for new cropping systems and conventional cropping systems.Research new methods for improving the effectiveness and efficiency of soybean breeding programs.Educate and train graduate students.

Project Methods
Objective 1: Develop superior general purpose, food type, and specialty type soybean varieties adapted to Minnesota. Soybean varieties are developed using a modified single-seed descent method as outlined in Table 1 in attached document. Parents of new breeding populations are chosen for a variety of reasons related to producer demand and objectives of sponsored projects. Reasons include yield, earliness, protein, disease/insect resistance, seed size, etc. Selections are made on the basis of yield, appropriate maturity, quality, disease/insect resistance, and value for specialty traits. The development of two specific types of varieties are highlighted: A"Triple Null" soybean variety and high oleic - low linolenic soybean varieties.Triple Null: The goal of this project is to introgress these three alleles into elite varieties adapted to Minnesota. Two avenues will be taken to accomplish this: 1) Use the Williams82-Triple Null as a source of alleles for backcrossing into a MN-adapted variety. 2) Recovery of the lectin and KTI null alleles from an Amsoy double null source, and combine those alleles with a null allele for P34 already present in a MN-adapted variety. Crosses will be made in a growth chamber, and backcrossing (avenue 1) or segregating populations will be developed in hopes of recovering individuals homozygous for all three null alleles (avenue 2). Selections for null alleles will be made on the basis of SNP markers and individuals carrying the null alleles will be tested according to the scheme outlined in Table 1. Seed from any tested progeny will also be screened for the presence of the anti-nutritional factors using protein gel assays.High oleic - low linolenic varieties: A project funded by the United Soybean Board has established a year-round backcrossing program in Puerto Rico to introgress four genes affecting the fatty acid profile (two for oleic and two for linolenic). Elite parents (~8) adapted to MN will be nominated for the backcrossing program and varieties converted to high oleic and low linolenic will be returned to MN within 2.5 years. These converted varieties will be tested for yield, maturity, and pest resistance according to the scheme outlined in Table 1. Additionally, forward breeding will be carried out by crossing MN elite varieties to sources of the high oleic and low linolenic alleles.Objective 2: Develop new traits, sources of pest resistance, and germplasm for new and conventional cropping systems.Soybean aphid resistance: To accomplish this, sources of Rag1, Rag2, rag3, and rag4 will be crossed together to obtain F1s heterozygous for two of the four genes. Complimentary F1s will be crossed together, and a large F2 population will be created in hopes of identifying individuals homozygous, or at least heterozygous, for all four Rag genes. Progenies carrying the Rag genes will be tested for yield, maturity, and other important traits using the schemes outlined in Table 1. Because obtaining all four Rag genes in a single progeny is a matter of probability and seed numbers, contingency plans will be followed using the F2 populations obtained from flowers not used for crossing on F1 plants. A contingency plan includes identifying pairs of F2s carrying two Rag genes and attempting the cross again.New sources of resistance to soybean cyst nematode: Previous work by Drs. Nevin Young, James Orf, and Senyu Chen identified PI 567516C as a new source of resistance and found it to be resistant to all races tested (Lian Lian, 2012). The QTL contributing resistance from this source appears to be on chromosome 10. Senyu Chen and James Orf crossed this source into MN-adapted varieties starting in 2009. Progenies developed from these crosses were recently entered into the SCN Northern Regional Trials, and one soybean line resulting from these crosses was the best in the trial in terms of seed yield. This exciting result indicates that there is little, if any, yield drag from this new source of SCN resistance. This new source will be heavily used in crosses to continue the development of this new source and introgress it into the background of additional varieties adapted to Minnesota. Genetic resources will be developed using this source of resistance as well as others. Near isogenic lines carrying the 88788, 567516C, Peking, and 438489B will be developed to better understand their impacts on yield and maturity, as well as characterize modes of action.Objective 3: Research new methods for improving the effectiveness and efficiency of soybean breeding programs.Genomic selection: Genomic selection involves the creation of a training population, or calibration set, for the development of statistical models aimed at predicting performance for traits such as seed yield. A training population consists of individuals that have been genotyped and phenotyped. One source of data that could be used is data from USDA-coordinated Uniform Soybean Tests. These are regional trials that have been conducted since 1939 and include the best performing varieties from each public breeding program. Phenotypic data from these trials will be compiled into an analyzable format for the development of statistical models. Genotype data in the form of SNPs collected using "genotyping by sequencing" will be generated on as many lines as possible going back 10 years. Environmental data for each testing location and year will be collected using the National Climatic Data Center. Pedigrees going back to 1939 will be compiled and analyzed in order to leverage information coming from relatives. A training data set comprised of the aforementioned items will be developed, optimized and tested within the UMN Soybean Breeding program by making predictions and comparing the predictions to actual yield data collected on breeding candidates over 2-3 years.High-throughput phenotyping: One obvious application of high-throughput phenotyping is the evaluation of iron deficiency chlorosis (IDC). All lines in the NEL stage of the program and beyond (Table 1) will be screened for IDC resistance in a nursery in western MN. Nursery plots will be rated using the traditional method of visual ratings and a 1-5 rating scale. A subset of nursery plots will also be imaged using a handheld digital camera. Images will be adjusted for incident solar radiation, masked to remove background components, and pixels will be extracted. Pixel colors and intensity will be computationally compared with visual ratings to develop an index, which will then be applied to all images to generate digital ratings. While the use of a hand-held camera may be more sensitive and accurate compared to visual ratings, it is more time consuming. To increase throughput, a camera will be attached to the bottom of a UAV, which will be flown to capture large images of the field. Images will be digitally stitched together using georeferencing, and pixels will be extracted for each individual plot and used to create an IDC index as described for the handheld camera. The ability of fly a UAV has been made much easier through the U of M's COA from the FAA.Objective 4: Educate and train graduate students. Graduate students will participate in the UMN Applied Plant Sciences program. Each student will have a thesis project that relates to soybean breeding and genetics. Additionally, each student will be tasked with managing the breeding of a specific trait that is of interest to the program. For example, a current student is tasked with the management of a sponsored project aimed at developing black food-type soybeans for Asian specialty projects. Between four and six graduate students are expected to be on the project at any given time.

Progress 07/01/16 to 06/30/20

Outputs
Target Audience:Farmers and seed companies Changes/Problems:None What opportunities for training and professional development has the project provided?Two workshops on genomic selection for plant breeding given. How have the results been disseminated to communities of interest?Yes 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. Three public varieties released and 11 invention disclosures on new varieties facilitating transfer to seed companies. 2. Numerous variety candidates in breeding pipeline with new forms of resistance for common soybean pests such as aphid and SCN. 3. Seven articles published on breeding methods. 4. Three M.S. students graduated, two PhD students graduated, three postdocs mentored and moved onto permanent positions. Three visiting scholars advised.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Jarquin, D., J.E. Specht, A.J. Lorenz*. 2016. Prospects of genomic prediction in the USDA Soybean Germplasm Collection: Historical data creates robust models for enhancing selection of accessions. G3: Genes, Genomes, Genetics doi: 10.1534/g3.116.031443.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Bandillo, N., A.J. Lorenz, G.G. Graef, D. Jarquin, D. Hyten, R. Nelson, J.E. Specht. 2016. Genome-wide association mapping of qualitatively inherited traits in a germplasm collection. Plant Genome doi:10.3835/plantgenome2016.06.0054.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Bandillo, N., J.E. Anderson, M.B. Kantar, R.M. Stupar, J.E. Specht, G.L. Graef, A.J. Lorenz*. 2017. Dissecting the genetic basis of local adaptation in soybean. Sci. Reports 7:17195.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Xavier, A., D. Jarquin, R. Howard, V. Ramasubramanian, J.E. Specht, G.L. Graef, W.D. Beavis, Q. Song, P. Cregan, R. Nelson, R. Mian, J.G. Shannon, L. McHale, D. Wang, W. Schapaugh, A.J. Lorenz, W.M. Muir, K.M. Rainey. 2017. Genome-wide analysis of grain yield stability and environmental interactions in a multi-parental soybean population. G3: Genes, Genomes, and Genetics doi: 10.1534/g3.117.300300.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Hanson, A.A., A.J. Lorenz*, L.S. Hesler, S.J. Bhusal, R. Bansal, A.P. Michel, G-L. Jiang, R.L. Koch*. 2018. Genome-wide association mapping of host-plant resistance to soybean aphid. Plant Genome doi:10.3835/plantgenome2018.02.0011.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Jo, H., A.J. Lorenz, K.M. Rainey, J.G. Shannon, P. Chen, K.D. Bilyeu. 2019. Environmental stability study of soybeans with modified carbohydrate profiles in maturity groups 0 to V. Crop Sci. 59:1531-1543.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Merry, R., K. Butenhoff, B.W. Campbell, J-M. Michno, D. Wang, J.H. Orf, A.J. Lorenz*, R.M. Stupar*. 2019. Identification and fine-mapping of a soybean QTL on chromosome 5 conferring tolerance to iron deficiency chlorosis. Plant Genome doi:10.3835/plantgenome2019.01.0007.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Dobbels, A.D., and A.J. Lorenz*. 2019. Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system. Plant Methods doi:10.1186/s13007-019-0478-9.
• Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Volpato, L., A. Dobbels, L. Borem, A.J. Lorenz*. 2021. Optimization of Temporal UAS-based imagery analysis to estimate plant maturity date for soybean breeding. The Plant Phenome J. (accepted pending revision). Bhusal, S., R. Koch, A.J. Lorenz*. 2021. Variation in soybean aphid

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

Outputs
Target Audience:Farmers, seed companies, and professional plant breeders. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Young Leaders of Japanese Natto Manufacturing. Sept. 7, 2019. St. Paul, MN. (Presented to and led tour for visiting group of Japanese natto professionals) Crop Pest Management Workshop. 2019. Fundamentals of and current trends in soybean variety development. Dec. 11. Minneapolis, MN. How have the results been disseminated to communities of interest?Yes What do you plan to do during the next reporting period to accomplish the goals?Research Method and Plan Develop commodity and food-type soybean varieties adapted to Minnesota Variety development is a multi-step process involving crossing between promising parents, inbreeding to create true breeding lines, visual assessment to assess plant health and maturity, and yield and quality trials to generate data that can be used to make selections and identify superior new varieties. Yield trials are classified into preliminary yield trials, new experimental line trials (i.e., advanced yield trials), and regional trials. Regional trials consist of the best lines and are conducted across different states in a cooperative fashion between breeders. Crossing blocks, observation rows, and yield trials are organized based on the intent of the cross (commodity type, SCN resistance, food type, etc.). Planting at over 15 locations is conducted in May. Trials are designed using a randomized complete block design with less than 50 entries to reduce spatial variation within trials. Notes on stand establishment are recorded in June. Crossing and notes on iron deficiency chlorosis are recorded in July. Greenhouse screening of Phytophthora begins in July. Rogueing off-type plants begins in August. Harvest and notes on maturity begin in September. Visual selections on observation rows occur during October. Samples are collected from each plot and measured for protein, oil, and carbohydrate and fatty acid composition during November through March. Data is analysed for purposes of making selections during November through February. Decisions on variety releases occur in December. A new goal this year is to increased efficiencies and decreased workload under reduced budgets. We will minimize the number of preliminary yield trials in northern MN, remove smaller sites from our northern region, and cooperate more with private partners to grow and manage plots. Conduct public and private variety soybean trials Each year, the UMN Soybean Breeding program organizes and conducts the Minnesota State Variety trials. Both companies and public institutions are eligible to enter varieties into this trial. The trials consist of two different types: 1) General purpose trial; 2) Special purpose/Food-type trial. The trials are conducted in four zones: far northern, northern, central, and southern. Three locations are planted within each zone. Trials are planted and harvested according to standard practices. Quality and SCN resistance (in the SCN trials) are measured. Results are distributed to the farmers through www.soybeans.umn.edu as well as through MSRPC. Discover and develop new sources of resistance to soybean pests and diseases. Close collaboration with fellow researchers in plant pathology and entomology creates a dynamic that ties discovery of novel sources of resistance directly with variety development. As soon as putative new sources of resistance are discovered, those sources are included in the UMN Soybean Breeding crossing block. New crosses carrying the new sources of resistance are advanced in the breeding pipeline as described under Objective 1. Develop molecular markers for in-house genotyping to conduct marker-assisted selection on Phytophthora resistance. Each year our program attempts to find places where use can use various technologies, including genotyping technologies, to enhance efficiency. One area where a fair amount of resources is spent is on the evaluation of Phytophthora resistance in the greenhouse. The location of these genes is known, but robust and broadly applicable molecular markers are not available. To develop molecular markers for our own program, we will first perform a genome-wide association analysis using currently available genotype and phenotype data on breeding lines. Molecular markers showing an association with resistance to Phytophthora will be identified and tested on known common parents in the Minnesota breeding program. Progenies from crosses among these parents and susceptible parents will be both genotyped and phenotyped, allowing us to determine if the markers co-segregate with resistance. This capability will allow us to select for Phytophthora resistance in the early generations of the breeding pipeline. Timeline The timeline for objective 1 is outlined in the methods under objective 1. The timeline for objective 2 is largely the same and follows standard planting and harvesting practices. The invitation letter goes out to participants in January, seed is received by April 10, and the report of results is generated in early November. The timeline for objective 3 varies on a case by case basis. The timeline for objective 4 is as follows: candidate molecular markers will be sent in for design in June. Populations segregating for Rps genes will be phenotyped from July to Sept. Markers will be associated with resistance in November. Markers not associating with resistance will be re-designed over the winter.

Impacts
What was accomplished under these goals? Objective 1. Because the main outputs from this project are varieties and improved germplasm, we will focus on that and refer the reader to the progress reports for a detailed description of progress. This year we created breeder's seed of nine new candidate varieties that are being made available for companies for evaluation. Additionally, 20 lines of great promise were purified. Yield data is currently being analysed and the best of these will be advanced to purified increases to make breeder's seed in 2020. Twenty-one hundred units of foundation seed of a new 0.5 RM glyphosate tolerant (GT) variety was produced during 2019 by MCIA. This variety will be released pending approval from the UMN Variety Review Committee in December. If approval is granted, these 2100 units of foundation seed will be made available to seed growers. We know there is great interest GT public varieties so farmers can save seed costs and still have some additional herbicide tools to work with. Seed was increased for an improved high oleic variety. This variety has greater than 70% oleic acid and normal levels of linolenic acid. Yield and standability of this variety is much better than the previous version, being approximately 90-95% of the check cultivars. Approximately 75 units of foundation seed is available. The UMN Variety Review Committee meets on December 16. We have four new varieties that are candidates for public release. All of them have greater yield than available public varieties of similar maturity. Three of the four have very good SCN resistance, with the fourth one having both good yield and high protein content (but susceptible to SCN). It's difficult to document the impact of the breeding program in terms of acres planted and value of seed harvested because this information is proprietary to our licensees. One way we can document impact is through examination of seed transfers and agreements signed. Below is a summary of those signed since this time last year. The information of the requestor is kept confidential. 66 seed requests from private companies were filled. These seed requests include transferring of seed from our program to theirs for evaluation and crossing preceding possible licensure. 101 seed requests from public researchers were filled. These requests for transferring seed to public researchers for breeding, for evaluation of resistance to various pests and pathogens, and for molecular genetic studies advancing the technology of soybean improvement. 8 invention disclosures were filled out and approved for the disclosure of 20 new varieties for transfer to private companies for possible licensure. Objective 2. The 2019 State Soybean Variety Trials have been published and are available at www.soybeans.umn.edu. They have also been distributed to MSRPC. Objective 3. Specifically, we engaged in two activities this summer related to this. First, we again provided germplasm to Dean Malvick for a Rhizoctonia screening. I am a committee member on his students POS committee and actively assist her research by providing germplasm for studies. I am also working with Dean Malvick on putting together a panel of lines for a brown stem rot resistance study he will conduct in the greenhouse over the wintertime. Breeding for aphid resistance is also a major focus of the program. Through partial funding provided by the LCCMR Minnesota Invasive Pests Center, we are working with Dr. Bob Koch on new aphid-resistant varieties. Eleven advanced breeding lines with confirmed aphid resistance are being tested in regional trials, and hundreds more are in earlier stages of the pipeline. We are hoping to identify some new varieties with stacked resistance in addition to the existing Rag1 variety already available for purchase. Objective 4. For UAV-enabled ratings of IDC, our 2019 results were similar to those we obtained in 2017. For some studies, we are relying solely on the UAV-based ratings. For others, we still relied on the human visual scores, but a side-by-side comparison of variety averages for human- and UAV-based ratings are very similar. In 2019, we learned several things about how to optimally use this technology for ratings, and we plan to deploy this technology in 2020 using these lessons learned. We dove head first into using UAVs for scoring maturity date in 2019. We did not have an option for taking ground maturity notes at several northern locations. To circumvent this issue, we purchased two UAVs and hired students through Angie Peltiers to fly them. We used the data from the imagery to predict maturity date, and learned much in terms of practical implementation in the process. Using locations from which we had both good UAV data and good ground scores, we found that we could explain 80% of the variation in ground dates with UAV dates. Moreover, there were as many errors on the ground and through predicting by UAV imagery. We are hoping to using this technology in 2020 for scoring maturity date in yield trials at several sites.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Dobbels, A.D., and A.J. Lorenz*. 2019. Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system. Plant Methods doi:10.1186/s13007-019-0478-9.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Merry, R., K. Butenhoff, B.W. Campbell, J-M. Michno, D. Wang, J.H. Orf, A.J. Lorenz*, R.M. Stupar*. 2019. Identification and fine-mapping of a soybean QTL on chromosome 5 conferring tolerance to iron deficiency chlorosis. Plant Genome doi:10.3835/plantgenome2019.01.0007.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Jo, H., A.J. Lorenz, K.M. Rainey, J.G. Shannon, P. Chen, K.D. Bilyeu. 2019. Environmental stability study of soybeans with modified carbohydrate profiles in maturity groups 0 to V. Crop Sci. 59:1531-1543.

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

Outputs
Target Audience:Soybean producers Plant breeders Soybean breeders Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?7 publications (6 in scientific journals, 1one book chapter). 12 conference abstracts 5 invited presentations 5 invention disclosures on new soybean varieties 2 symposia organized at national research conferences What do you plan to do during the next reporting period to accomplish the goals?Continue to advance research and publish more than 5 resarch articles.

Impacts
What was accomplished under these goals? 7 publications (6 in scientific journals, 1one book chapter). 12 conference abstracts 5 invited presentations 5 invention disclosures on new soybean varieties 2 symposia organized at national research conferences Currently advising five graduate students, three postdocs, and serve on six graduate student program of study committees

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Elbasyoni, I.S., A.J. Lorenz, M. Guttieri, K. Frels, P.S. Baenziger, J. Poland, E. Akhunov. 2018. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction in winter wheat. Plant Sci. 270:123-130.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Coletta, R.D., C.N. Hirsch, M.N. Rouse, A. Lorenz, and D.F. Garvin. 2018. Genomic dissection of nonhost resistance to wheat stem rust in Brachypodium distachyon. Mol. Plant-Microbe In. doi/10.1094/MPMI-08-18-0220-R.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: AlKhalifah, N., D.A. Campbell, C.M. Falcon, &, A. Lorenz (24th of 44 authors), &, C.J. Lawrence-Dill. 2018. Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Research Notes 11:425.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Hanson, A.A., A.J. Lorenz*, L.S. Hesler, S.J. Bhusal, R. Bansal, A.P. Michel, G-L. Jiang, R.L. Koch*. 2018. Genome-wide association mapping of host-plant resistance to soybean aphid. Plant Genome doi:10.3835/plantgenome2018.02.0011.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Belamkar, V., M.J. Guttieri, I. El-Basyoni, W. Hussain, D. Jarquin, N. Garst, M. Wang, A. Easterly, J. Poland, A.J. Lorenz and P.S. Baenziger . 2018. Evaluation and implementation of genomic selection in preliminary yield trials in the University of Nebraska winter wheat breeding program G3: Genes, Genomes, and Genetics doi:10.1534/g3.118.200415.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2019 Citation: Kadam, D., and A.J. Lorenz*. Evaluation of nonparametric models for genomic prediction of early-stage single crosses in maize. Crop Sci. (in press).
• Type: Book Chapters Status: Published Year Published: 2018 Citation: Kadam, D.C., and A.J. Lorenz*. 2018. Towards redesigning hybrid maize breeding through genomics-assisted breeding. In J. Bennetzen, S. Flint-Garcia, C. Hirsch, and R. Tuberosa (Eds.) The Zea Mays Genome. Springer.

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

Outputs
Target Audience:Soybean producers, fellow soybean breeders, and students of plant breeding/genetics. Changes/Problems:None. What opportunities for training and professional development has the project provided? I spoke to producers at several field days about aphid resistance, SCN resistance, and the role of public soybean breeding: Lamberton (July 9), Northwest Plot Tours (Aug 30-31), Midwest Shippers (Dec 4). How have the results been disseminated to communities of interest?Yes. Peer-reviewed publications and variety trial reports have been published. What do you plan to do during the next reporting period to accomplish the goals? Goal 1: Publish five peer-reviewed articles. Goal 2: Successfully teach my first undergraduate course, PLSC 3401 (Plant Genetics and Breeding), and receive positive student evaluations. Goal 3: Lead or heavily contribute to one federal grant application in addition to successfully managing all ongoing grants. Goal 4: Release or license at least one UMN soybean variety. Goal 5: Organize all historical soybean seed inventory and integrate into Prism database. Goal 6: Continue to advance high-throughput phenotyping technologies in program by scoring iron deficiency chlorosis using drone imaging.

Impacts
What was accomplished under these goals? All breeding nurseries and yield trial plots were successfully planted across Minnesota at locations ranging from Roseau to Lamberton during May and early June. 97 unique parents were planted in the crossing block and 202 crosses were designed between breeding lines selected for high yield, early maturity, high protein, small seed (natto), large seed/high protein (tofu), aphid resistance, SCN resistance, high oleic, genetic diversity, among other traits. Most crosses were successfully made, and F1 seeds of 167 crosses were sent to the Chile winter nursery for generational advancement. The breeding nursery consisted of the following numbers for each generation during the summer of 2017: 137 F2 populations; 41 F3 populations; 98 F4 populations. Pod picks on all F2 populations were successfully conducted and populations were advanced to the F3 generation for planting in the Chile winter nursery. Selected F3 and F4 breeding populations were advanced via plant pulls for planting into plant rows in 2018. Approximately 8200 plant rows were planted in 2017 resulting from plant pulls in 2016. Visual selections were made in Oct and all selected plant rows were successfully harvested. All seed samples were scanned with the NIR to facilitate final selections based on seed composition. 1939 breeding lines were planted in preliminary yield trials (PYTs) at two locations. Lines were placed according to the maturity score in the plant row stage. Early maturing lines were planted at Crookston and Moorhead; intermediate lines were planted at Rosemount and Morris; and late lines were planted at Lamberton and Waseca. Yield, maturity, and quality data was successfully collected. Data analysis and selections were currently underway. 504 breeding lines were planted in advanced yield trials at three MN locations. Early lines were planted at Crookston, Moorhead, and Shelly; intermediate lines were planted at Rosemount, Danvers, and Becker; late lines were planted at Lamberton, Westbrook, and Waseca. Data on yield, maturity, and quality were all successfully collected. Data analysis and selections are currently under way. The 2017 regional tests were successfully conducted, including our lines and lines from regional co-operators were planted. The regional trials included 224 lines from the MN breeding program, plus many others from co-operators. Data analysis and selections are currently under way. Several levels of increases were successfully made last summer. The most advanced seed increase we perform is the purified seed increase, which results in the breeders seed that is handed over for foundation seed production. Last year, we grew 15 purified seed increases. Evaluation of these lines is currently underway to determine variety release and licensing options. One line - M08-362045 - look particularly promising. I spoke to producers at several field days about aphid resistance, SCN resistance, and the role of public soybean breeding: Lamberton (July 9), Northwest Plot Tours (Aug 30-31), Midwest Shippers (Dec 4). Beyond SCN and aphid resistance, which are the two major pests we seek resistance for, we continually work with entomologists and pathologists and provide germplasm for disease screenings to facilitate their work and help us identify susceptible and resistant germplasm. Specifically, we engaged in two activities this summer related to this. First, we provided germplasm to Dean Malvick for a Rhizoctonia screening. The screening was successful and Dr. Malvick observed large differences between elite UMN breeding lines. Secondly, we worked with Jim Kurle to introduce new Phytophthora genes into our germplasm, Rps8, discovered at Purdue. Crosses were made last spring, F1s were advanced this last summer, and F2s were sent to Chile for generational advancement. 4 graduate students are currently being trained

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Campbell, M.T., N. Bandillo, S. Sharma, F. Al-Shiblawi, K. Liu, Q. Du, A.J. Schmitz, C. Zhang, A-A. Very, A.J. Lorenz, H. Walia. 2016. Allelic variants of OsHKT1;1 underlie the divergence between Indica and Japonica subspecies of rice (Oryza sativa) for root sodium content. PLOS Genetics 13(6): e1006823.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Neyhart, J.L., T. Tiede, A.J. Lorenz, K.P. Smith. 2017. Evaluating methods of updating training data in long-term genome-wide selection. G3: Genes, Genomes, and Genetics doi: 10.1534/g3.117.040550.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Gage, J., D. Jarquin, C. Romay, A. Lorenz, [39 authors], N. de Leon. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nat. Communications doi 10.1038/s41467-017-01450-2.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Bandillo, N., J.E. Anderson, M.B. Kantar, R.M. Stupar, J.E. Specht, G.L. Graef, A.J. Lorenz*. 2017. Dissecting the genetic basis of local adaptation in soybean. Sci. Reports 7:17195.
• Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Luetchens, J., and A.J. Lorenz*. 2018. Changes in dynamic leaf traits in maize associated with year of hybrid release. Crop Sci. (in press).
• Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Kadam, D., and A.J. Lorenz*. Evaluation of nonparametric models for genomic prediction of early-stage single crosses in maize. Crop Sci. (in review).

Progress 07/01/16 to 09/30/16

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Nothing to report.

Publications