Source: CORNELL UNIVERSITY submitted to
BREEDING AND GENETICS OF THE SMALL GRAIN CEREALS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0223379
Grant No.
(N/A)
Project No.
NYC-149449
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Oct 1, 2010
Project End Date
Sep 30, 2013
Grant Year
(N/A)
Project Director
Sorrells, MA.
Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853
Performing Department
Plant Breeding
Non Technical Summary
New York agriculture depends on small grains production to provide essential food and feed for the state and the surrounding region. Cornell has the only active small grains breeding program, public or private, located in the northeastern U.S. and our research contributes directly to multiple goals of Cornell Cooperative Extension. Small grains production requires minimal inputs, is environmentally friendly, adaptable to organic production and outputs contribute directly to the economic and nutritional well-being of rural communities. Since 1907, this research project has produced more than 70 small grains cultivars. An effective plant breeding research program contributes to enhancing the productivity of small grains varieties and to meeting the changing needs that are specific to northeast agriculture. Improved small grains cultivars are required for farmers, businesses, processors, and food companies to remain competitive. Improved oat and barley cultivars are critical to the NY dairy industry and NY wheat is marketed as a cash crop for processing into grocery products. Small grains production is also important to crop rotation systems, distribution of labor, and soil and water conservation. Variety development is a long-term activity that requires sustained effort over many years. Farmers depend almost entirely on our public, state-wide variety testing programs for unbiased information about varieties of wheat, oats, and barley. Season-long requirements for seed production and evaluation over multiple years and locations are required to assess adaptation and performance. The NY small grains markets are constantly changing. Consumers' increased preference for healthy food products has increased demand for foods that not only taste good but also help to prevent heart disease and cancer. Specialty markets for spelt, triticale, organically grown cereals, and hard wheat have skyrocketed in recent years and new markets are likely. Locally produced farm products can result in substantial savings to the industry and to New York and help maintain local economic vitality. Without this project, there would be no mechanism for developing or testing small grains varieties in this region. New York farmers would have to depend on varieties and recommendations from other regions that do not accurately reflect New York growing conditions. Disease resistant varieties reduce the use of pesticides and cost to the producer. Winter grains prevent erosion of barren soils and redistribute labor requirements. Crop rotations with vegetables and other field crops reduce incidence of disease and insects resulting in higher yields and the use of fewer pesticides. Consumers are the ultimate beneficiaries of the outputs of this project because the results of this project are healthier, cheaper food products that are produced locally. A healthy farm economy depends on locally adapted, competitive varieties of all crops that in turn contribute to the New York state economy. Outputs link to field crops extension activities around the state. Information from this project is presented annually at field days, agent training schools and seed conferences.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011599106010%
2011599108010%
2011599209010%
2021599106010%
2021599108010%
2021599209010%
2041599106010%
2041599108110%
2041599209010%
2121599108110%
Knowledge Area
202 - Plant Genetic Resources; 204 - Plant Product Quality and Utility (Preharvest); 212 - Pathogens and Nematodes Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1599 - Grain crops, general/other;

Field Of Science
1080 - Genetics; 1060 - Biology (whole systems); 2090 - Statistics, econometrics, and biometrics; 1081 - Breeding;
Goals / Objectives
OBJECTIVES: 1. To develop, introduce, and evaluate new cultivars of small grains having improved yield, grain quality, disease resistance, and other characteristics that increase the crop value, safety, production efficiency, and stability for stakeholders in New York and the northeastern US. This objective includes the development of our own new varieties as well as regional evaluation of private and public varieties from other programs. 2. To devise and evaluate novel breeding methods that effectively manipulate genetic variability for desirable agronomic traits and contribute to breeding theory and graduate student training. Advances in breeding methodologies are driven by new knowledge and technologies. Optimum strategies are constantly changing and this research area is rarely explored in the public sector. This objective is critical for implementing molecular breeding methods in our breeding program. 3. To elucidate the inheritance, chromosomal location, and expression of genes controlling relevant agronomic plant characteristics. Specifically, this project is targeting preharvest sprouting, fusarium head blight and nutritional quality in grains. Outputs: Annual Regional Trial Summaries - Our winter grains are planted in September/October and harvested in July. Spring grains are planted in April/May and harvested in August. The results of our wheat, oat and barley trials are summarized and distributed each year in November. Publications - Refereed journal articles that report our research are produced each year and always cite Federal Hatch support. Varieties and Germplasm - New varieties from this project are released for commercial production when justified by our trial results. Also based on our regional trial results, we recommend varieties from companies and other public breeding programs. Germplasm lines with special attributes are sometimes developed and released.
Project Methods
This project emphasizes the development of novel breeding methods that improve the efficiency of variety development and advance the science of plant breeding. Currently our research is focused on the integration of molecular and conventional breeding methods and development of soft winter wheat varieties with resistance to wheat spindle streak mosaic virus, FHB, and PHS. Selection methods include both conventional and molecular selection for resistance to lodging and major diseases (especially FHB), acceptable milling and baking quality, PHS resistance, and improved grain yield. For PHS, markers wmc453c, barc055, and wmc474 will be used to survey for polymorphism with recurrent parents, Caledonia and Richland, Whatford, and Superior. Those that are polymorphic will be used to select PHS resistance alleles in backcross populations. Selection for FHB will be practiced using microsatellite markers Xgwm533 and Xgwm493 and is expected to reduce FHB severity by up to 20-40%. Marker assisted selection will also be applied to the 5AS FHB QTL to introgress that gene into our program to reduce DON levels and contribute to Type II resistance. Mapping for inulin content is in progress and markers linked to QTL for that trait will be used for MAS. Selections from early generations that have acceptable maturity, height, seed quality, disease resistance, and vigor enter our regional testing program. Superior genotypes will be determined by comprehensive trial testing and released through the New York Seed Improvement Project as new cultivars for commercial production in the northeast. Unbiased performance information is required for farmers, seed companies, and extension agents to choose the varieties that maximize return on investment and stability of income. In this project we are implementing a new molecular breeding strategy that is complementary to marker-assisted selection called Genomic Selection. This methodology was originally developed by animal breeders but it shows great promise for crop improvement. Last year we received an enhancement grant to implement this method in our wheat breeding program. We have already published two methodology papers on this and a publication using the empirical data generated is in preparation. We are using our main breeding (Master) nursery as the training population to develop prediction models for various traits. Those models are being used for the first time this year to select new lines for testing based only on genotype. This new breeding method is expected to reduce phenotyping cost and enhance the rate of genetic gain in our breeding program. All results will be published in peer-reviewed journals or extension publications to ensure maximum value is realized for this project. In addition, relevant information will be delivered at training workshops and field days.

Progress 10/01/10 to 09/30/13

Outputs
Target Audience: Our target audiences are farmers, extension agents and administrators, seed industry representatives, agronomists, economists, students, USDA researchers and technical support people. In addition, I give many presentations and seminars around the world on our molecular breeding research. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Participants: David Benscher - Research Support Specialist James Tanaka - Lab Manager Technical assistant - John Shiffer Graduate students - Elliot Heffner, Keith Williams, Jessica Rutkoski, Nicolas Heslot, Philomin Juliana, Siman Peng, Julio Isidro Sanchez, Lynn Veenstra Undergraduate - Jeff Neyhart, Anna Vue Visiting Scientists – Sanjay Kumar, Goro Ishikawa, Pawan Kulwal, Murugasamy Sivasamy, Yong-Gu Cho, Ranganathan Chandra Babu Post Docs – Julie Dawson, Jeff Endelman, Deniz Akdemir, Vahid Edriss, Hugues Barbier All of our students, post docs, and visiting scientists receive training in state of the art plant breeding methods including lab and fieldwork. We collaborate with many researchers both nationally and internationally. The breeding program provides indispensable training for students and post docs. There is a nationwide shortage of trained plant breeders and this project provides invaluable experience. How have the results been disseminated to communities of interest? Our results are presented at field days and training workshops where we explain to extension agents, growers and wheat end users the importance and impacts of our research. In addition, our breeding project is critically important for training the next generation of plant breeders because it provides them with hands-on experience in a modern plant breeding program that integrates conventional and modern molecular technologies. Our performance trials are published in an annual report that is mailed or emailed to approximately 200 individuals and agencies. It is also available on our web site (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/smallgrains/index.cfm). Our research results are published in peer-reviewed scientific journals. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Outcomes/Impact The Cornell small grains breeding and genetics research program has used the latest information and state-of-the-art technologies to develop new wheat varieties and more efficient breeding methods. Our genomic selection methods research has been widely cited and represents a revolutionary new approach to improving crops. We continue to evaluate preharvest sprouting (PHS) in all of our breeding nurseries. We have published many high quality research studies on the inheritance and mapping of PHS and fusarium head blight (FHB) resistance. These research projects have provided important information on the location of genes controlling complex agronomic traits in wheat and have resulted in more efficient crop improvement methods widely used by breeders around the world. Our recent winter wheat variety releases have moderate to good resistance to both FHB and PHS, the two most important problems facing New York farmers. In our regional testing program we evaluate both public and private varieties for resistance to FHB and PHS. We only recommend varieties that show at least moderate resistance to both FHB and PHS for production in New York. Our QTL mapping studies have enabled the widespread use of molecular markers for efficiently developing new wheat varieties with desirable traits. Marker-assisted selection for FHB resistance genes in adapted varieties benefits farmers by reducing the use of pesticides. Resistance to PHS will minimize the negative impact of our changing climate on wheat quality. Marker assisted selection for genes that improve milling quality increases the value of the New York wheat crop and the competitiveness of the New York farmers. These improved varieties help to stabilize small grains production and improve the rural economy of this region. In addition, varieties that are resistant to biotic stress are very attractive to farmers who use organic production methods for the same reasons. Our current work to evaluate of specialty grains under organic management fills a huge void in our knowledge base for this management system and provides organic farmers with options for crop rotation with high value grains. Our results are presented at field days and training workshops where we explain to extension agents, growers and wheat end users the importance and impacts of our research. In addition, our breeding project is critically important for training the next generation of plant breeders because it provides them with hands-on experience in a modern plant breeding program that integrates conventional and modern molecular technologies. Our performance trials are published in an annual report that is distributed to approximately 200 individuals and agencies and on our web site (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/smallgrains/index.cfm). Outcomes/accomplishments: During this project, we continued our regional trial evaluation of both public and private varieties of small grains including winter and spring wheat, winter and spring barley, spring oats, triticale, and rye. We collected data on yield, disease and lodging resistance, quality characteristics and traits that are specific to each crop. In addition, for the past two years we have been evaluating heritage winter and spring wheat, spring and winter spelt, spring emmer and einkorn under organic management. During this project, we released Bridgeport, Hopkins, and Medina soft white winter (SWW) wheat varieties and Otsego soft red winter (SRW) wheat for production in New York. Medina has excellent resistance to fusarium head blight, preharvest sprouting and soil borne viruses. Otsego is in its second production year and continues to perform well. Although Emmit SRW (W.G. Thompson, Inc.) has slightly higher yield, it is more susceptible to Wheat Spindle Streak Mosaic Virus. Also, Otsego is moderately resistant to powdery mildew and septoria leaf spot, septoria nodorum, FHB, Wheat Soil Borne Mosaic Virus, and leaf rust. This year we plan to release an Ohio line designated OH02-12686. Throughout this project we continued our work on mapping QTL for PHS resistance in two populations with NY91017-8080 as a parent that is potentially a novel source of PHS resistance. We completed our project on fine mapping a PHS QTL identified in a white winter wheat population from a cross between PHS resistant, Cayuga, and PHS susceptible, Caledonia. We have expanded the genotyping to verify that there are two QTLs closely linked in coupling on chromosome 2B. We completed a fifth year of evaluation of the Langdon/ Triticum dicoccoides substitution lines for resistance to PHS and initiated a fine mapping study in four RSL populations. We also mapped these markers in a durum wheat recombinant substitution line population that is segregating for a seed dormancy QTL on 2B. Based on corresponding rice genes, it was concluded that the PHS QTLs on 2B in common wheat were different from the seed dormancy QTL in the durum wheat. Testing of the Foster x KanQueen DH population for mapping milling quality traits was published. In our FHB research supported in part by the USWBSI, we collaborated with breeders in seven other states on three sub-projects. Over the past three years, we continued our FHB recurrent selection dominant male-sterile project that involves selection within and among 200 half-sib families. In this last year, we continued this project with MS FHB resistant half sibs planted in two replicates for selection again in 2014. The third sub-project was mapping native FHB resistance from in the same breeding line NY91017-8080 mentioned above for PHS resistance mapping. The native FHB resistance in this line is being combined with Chinese sources of FHB resistance. For spring oats, we co-released a new Illinois line and named it “Corral”. Corral ranked first in the New York Variety Trial five consecutive years from 2007 to 2011 and is still the highest yielding oat line in our trials by a wide margin. Corral saw limited first year production. During this project, the New York State Legislature passed a Farm Brewery Bill that provides tax incentives to small breweries that use New York grown ingredients. Consequently, we have switched our regional testing from feed barley to malting barley because there was essentially no information available on suitable malting barley varieties for this region. Over two years, KWS Scala and Sytepee winter barley had the highest yield and acceptable malting quality. For spring malting barley, AAC Synergy and the University of Minnesota lines were the highest yielding in this first year of testing. Because of the extensive rainfall in 2013, foliar diseases and FHB were severe. We continued to expand our research on genomic selection. The results of this work have been groundbreaking and have resulted in several publications. 2013 was the first year we evaluated Hybrid Rye varieties from the German company KWS. The results were astounding! The better hybrids outyielded Medina SWW wheat by 80% and outyielded Aroostok Rye by 2.5 fold. If we can get seed into NY, hybrid rye could revolutionize rye production in this region. In 2013 we conducted our second year of evaluation of winter and spring grains under organic management conditions at the Freeville Farm as a part of a USDA grant under the Organic Research and Extension Program. Each year we distributed the results of our New York State variety-testing program for spring and winter grains to extension agents, seed companies and farmers in the northeast and were also published on the web (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/smallgrains/index.cfm).

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Heslot, N., D. Akdemir, � M.E. Sorrells, J-L. Jannink. 2013. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions. Theor. Appl. Genet. DOI 10.1007/s00122-013-2231-5.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Kulwal, P., Ishikawa, G., Benscher, D., Feng, Z., Yu, L-X., Jadhav, A., Mehetre, S., and Sorrells, M.E. (2012). Association Mapping for Pre-harvest Sprouting Resistance in White Winter Wheat. Theor Appl Genet., DOI 10.1007/s00122-012-1872-0.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Poland, J.A., Brown, P.J., Sorrells, M.E, and Jannink, J-L. (2012). Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE, 7: e32253. doi:10.1371/journal.pone.0032253.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Heslot, N., J. Rutkoski, J. Poland, J-L. Jannink, and M.E. Sorrells. 2013. Impact of ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLoS One 8(9): e74612. doi:10.1371/journal.pone.0074612.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Munkvold, J.D., D. Laudencia-Chingcuanco, and M.E. Sorrells. 2013. Systems genetics of environmental response in the mature wheat embryo. Genetics 194:265277.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Williams, K.R., J.D. Munkvold, and M.E. Sorrells. 2013. Comparison of digital image analysis using elliptic Fourier descriptors and major dimensions to phenotype seed shape in hexaploid wheat (Triticum aestivum L.). Euphytica. 190:99-116.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Williams, K.R. and M.E. Sorrells. 2013. Three dimensional seed size and shape QTL in hexaploid wheat (Triticum aestivum L.) populations. Crop Sci. doi: 10.2135/cropsci2012.10.0609; Posted online 20 Aug. 2013.
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Chao, S., J. Dubcovsky, J. Dvorak, M.C. Luo, P.S. Baenziger, R. Matnyazov, D.R. Clark, L. Talbert, J.A. Anderson, S. Dreisigacker, K. Glover, .J Chen, K. Campbell, P.L. Bruckner, J.C. Rudd, S. Haley, B.F. Carver, R. Sims15, S. Perry, M.E. Sorrells, and E. Akhunov, E. 2010. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat. BMC Genomics 11:727. doi:10.1186/1471-2164-11-727.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Gauch, Jr., H.G, P.C. Rodrigues, J.D. Munkvold, E.L. Heffner, and M.E. Sorrells. 2011. Two new strategies for detecting and understanding QTL by environment Interactions. Crop Sci. 51: 96-113.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Heffner, E.L., J.L. Jannink, and M. E. Sorrells. 2011. Genomic selection accuracy using multi-family prediction models in a wheat breeding program. The Plant Genome. 4:65-75.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Heffner, E.L., J.L. Jannink, H. Iwata, E. Souza, and M.E. Sorrells. 2011. Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci. doi: 10.2135/cropsci2011.05.0253.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Smith, N., M. Guttieri, E. Souza, J. Shoots, M.E. Sorrells, and C. Sneller. 2011. Identification and Validation of QTL for Grain Quality Traits in a Cross of Soft Wheat Cultivars Pioneer Brand 25R26 and Foster. Crop Science 51:1424-1436.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Somyong, S., J.D. Munkvold, J. Tanaka, D. Benscher, and M.E. Sorrells. 2011. Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling. Funct Integr Genomics 11:479-490.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Sorrells, M.E., J.P. Gustafson, D. Somers, S. Chao, D. Benscher, G. Guedira-Brown, E. Huttner, A. Kilian, P.E. McGuire, K. Ross, J. Tanaka, P. Wenzl, K. Williams, and C.O. Qualset. 2011. Reconstruction of the synthetic W9784 x Opata M85 wheat reference population. Genome 54:875-882.
  • Type: Journal Articles Status: Published Year Published: 2011 Citation: Yu, L-X, A. Lorenz, J. Rutkoski, R.P. Singh, S. Bhavani, J. Huerta-Espino, and M.E. Sorrells. 2011. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor. Appl. Genet. DOI 10.1007/s00122-011-1664-y
  • Type: Journal Articles Status: Published Year Published: 2010 Citation: Zeid, M., J.K. Yu, I. Goldowitz, M.E. Denton, Denise E. Costich, C.T. Jayasuriya, M. Saha, R. Elshire, D. Benscher, F. Breseghello, J. Munkvold, R.K. Varshney, G. Belay, M.E. Sorrells. 2010. Cross-amplification of EST-derived markers among 16 grass species. Field Crops Res. 118:28-35.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Heslot, N., Yang, H-P., Sorrells, M.E, and Jannink, J-L. (2012). Genomic selection in plant breeding : A comparison of models. Crop Sci., 52: 146-160.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Poland, J., Endelman, J. Dawson, J., Rutkoski, J., Wu, S., Manes, Y., Dreisigacker, S., Crossa, J., Sanchez-Villeda, H., Sorrells, M.E, Jannink, J-L. (2012). Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing. The Plant Genome, In press.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Rutkoski, J., J. Benson, Y. Jia, G. Brown-Guedira, Jannink, J-L, and Sorrells, M.E. (2012). Evaluation of genomic prediction methods for fusarium head blight resistance in wheat. The Plant Genome, 5:51-61.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Yu, L-X, Morgounov, A., Wanyera, R., Keser, M., Kumar Singh, S., and Sorrells, M.E. (2012). Identification of Ug99 Stem Rust Resistance loci in Winter Wheat Germplasm Using Genome-Wide Association Analysis. Theor. Appl. Genet., DOI 10.1007/s00122-012-1867-x.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Heslot, N., J-L. Jannink, and M.E. Sorrells. 2013. Using genomic prediction to characterize environments and optimize prediction accuracy in applied breeding data. Crop Sci. 53: 921-933.


Progress 10/01/11 to 09/30/12

Outputs
OUTPUTS: Otsego soft red winter wheat was released last year and continues to perform well. Over 4 years of testing, Otsego is equal or better than all other wheat varieties in NY. Otsego is moderately resistant to powdery mildew and septoria leaf spot, septoria nodorum, fusarium head blight, wheat spindle streak mosaic virus, wheat soil borne mosaic virus and leaf rust. This year we completed a 3 year project on mapping QTL for preharvest sprouting (PHS) resistance in two populations with NY91017-8080 as a parent. This study is expected to reveal a novel source of PHS resistance. We continued our research to fine map and clone a PHS QTL that was mapped in a white winter wheat population from a cross between PHS resistant, Cayuga, and PHS susceptible, Caledonia. Recent fine mapping revealed that there are 2 QTLs closely linked in coupling and one of the QTL intervals was 4.2 cM and located between Wmc453c and Barc55. We mapped the same markers in a durum wheat recombinant substitution line (RSL) population that is segregating for a seed dormancy QTL on 2B. Based on corresponding rice genes, it was concluded that the PHS QTLs on 2B in common wheat were different from the seed dormancy QTL in the durum wheat. In our FHB research, we collaborate with breeders in 7 other states on 3 sub-projects. For our FHB recurrent selection project we tagged 2-5 MS spikes at anthesis in each of 200 half-sib families. Selection was applied both among and within families for absence of symptoms on spikes and seed. This fall, MS FHB resistant half sibs were planted in two replicates for selection again in 2013. We completed the evaluation of genomic selection for FHB resistance and published the results. The third project is mapping native FHB resistance from a breeding line NY91017-8080. The phenotyping has been competed and it will be genotyped this winter. The native FHB resistance in this line is being combined with Chinese sources of resistance. We repeated the evaluation of the Langdon/ Triticum dicoccoides recombinant substitution lines (RSL) for resistance to PHS that will allow the fine mapping of the resistance loci. For spring oats, a seed increase of the new variety, Corral was produced. Corral ranked first in the New York Variety Trial four consecutive years from 2007 to 2010 and is still the highest yielding variety in our trials. Our spring barley variety testing program has identified HY101-6R as the best variety. RB07 and Stoa spring wheat varieties have the best performance in NY. We have expanded our research on genomic selection. The results of this work have been ground-breaking and has resulted in several publications. This year we planted spring grains under organic management conditions at the Freeville Farm as a part of a USDA grant under the Organic Research and Extension Program. The results of our New York State variety testing program for spring and winter grains are distributed to extension agents, seed companies and farmers in the northeast and are published on the web (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/small grains/index.cfm). PARTICIPANTS: David Benscher - Research Support Specialist James Tanaka - Lab Manager Technical assistant - John Shiffer Graduate students - Keith Williams, Jessica Rutkoski, Nicolas Heslot, Philomin Juliana, Siman Peng, Julio Sanchez, Lynn Veenstra Undergraduate - Jeff Neyhart, Anna Vue Visiting Scientists -Goro Ishikawa, Pawan Kulwal, Murugasamy Sivasamy, Yong-Gu Cho Post Docs - Julie Dawson, Jeff Endelman, Deniz Akdemir Research Associate - Long Xi Yu All of our students, post docs, and visiting scientists receive training in state of the art plant breeding methods including lab and field work. We collaborate with many researchers both nationally and internationally. The breeding program provides indispensable training for students and research associates. There is a nation wide shortage of trained plant breeders and this project provides invaluable experience. TARGET AUDIENCES: Our target audiences are farmers, extension agents and administrators, seed industry representatives, agronomists, economists, students, USDA researchers and technical support people. In addition, I give many presentations and seminars around the world on our molecular breeding research. PROJECT MODIFICATIONS: None

Impacts
Our Cornell small grains breeding and genetics research program uses state-of-the-art technologies to develop new wheat varieties and more efficient breeding methods. Our research on genomic selection methods is widely cited and represents a revolutionary new approach to improving crops. We have published several high quality research studies on the inheritance and mapping of preharvest sprouting and fusarium head blight resistance. The information from these research projects has provided critical information on the location of genes affecting complex agronomic traits in wheat and resulted in more efficient crop improvement methods. All of our recent winter wheat variety releases have moderate to good resistance to both FHB and PHS, the two most important problems facing New York farmers. In our regional testing program we evaluate both public and private varieties for resistance to FHB and PHS. Varieties that do not show at least moderate resistance to both FHB and PHS are not recommended for production in New York. Our QTL mapping studies have enabled the use of molecular markers for efficiently developing new wheat varieties with these characteristics. The incorporation of FHB resistance genes into adapted varieties benefits farmers by reducing the use of pesticides, and resistance to preharvest sprouting will minimize the negative impact of the environment on wheat quality. Marker assisted selection for genes that improve milling quality increases the value of the New York wheat crop and the competitiveness of the New York farmers. These benefits help to stabilize wheat production and improve the rural economy of this region. In addition, these new varieties are very attractive to farmers who use organic production methods for the same reasons. Currently, we are expanding our evaluation of specialty grains under organic management. We present our results at field days and training workshops to explain to extension agents, growers and wheat end users the importance and impacts of our research. In addition, our breeding project is important for training the next generation of plant breeders by providing hands-on experience in a modern plant breeding program that integrates conventional and modern molecular technologies. All of our performance trials are published in an annual report that is mailed or emailed to approximately 200 individuals and agencies. It is also made available on our web site (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/small grains/index.cfm).

Publications

  • Heslot, N., Yang, H-P., Sorrells, M.E, and Jannink, J-L. (2012). Genomic selection in plant breeding : A comparison of models. Crop Sci., 52: 146-160.
  • Kulwal, P., Ishikawa, G., Benscher, D., Feng, Z., Yu, L-X., Jadhav, A., Mehetre, S., and Sorrells, M.E. (2012). Association Mapping for Pre-harvest Sprouting Resistance in White Winter Wheat. Theor Appl Genet., DOI 10.1007/s00122-012-1872-0.
  • Poland, J.A., Brown, P.J., Sorrells, M.E, and Jannink, J-L. (2012). Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE, 7: e32253. doi:10.1371/journal.pone.0032253.
  • Poland, J., Endelman, J. Dawson, J., Rutkoski, J., Wu, S., Manes, Y., Dreisigacker, S., Crossa, J., Sanchez-Villeda, H., Sorrells, M.E, Jannink, J-L. (2012). Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing. The Plant Genome, In press.
  • Rutkoski, J., J. Benson, Y. Jia, G. Brown-Guedira, Jannink, J-L, and Sorrells, M.E. (2012). Evaluation of genomic prediction methods for fusarium head blight resistance in wheat. The Plant Genome, 5:51-61.
  • Yu, L-X, Morgounov, A., Wanyera, R., Keser, M., Kumar Singh, S., and Sorrells, M.E. (2012). Identification of Ug99 Stem Rust Resistance loci in Winter Wheat Germplasm Using Genome-Wide Association Analysis. Theor. Appl. Genet., DOI 10.1007/s00122-012-1867-x.
  • Williams, K.R., Munkvold, J.D., and Sorrells, M.E. (2012). Comparison of digital image analysis using elliptic Fourier descriptors and major dimensions to phenotype seed shape in hexaploid wheat (Triticum aestivum L.). Euphytica, In press.


Progress 10/01/10 to 09/30/11

Outputs
OUTPUTS: We released a new soft red winter wheat variety named Otsego originating at the Ohio Agriculture Research and Development Center but was not released in Ohio. Over 5 years of testing, Otsego was the highest yielding cultivar in NY. Otsego is moderately resistant to powdery mildew and septoria leaf spot, septoria nodorum, fusarium head blight, wheat spindle streak mosaic virus, wheat soil borne mosaic virus and leaf rust. This year we completed a 4 year project on association mapping QTL for preharvest sprouting (PHS) resistance and a publication is in review. This study revealed 8 QTLs on 7 chromosomes. We continued our research to fine map and clone a PHS QTL that was mapped in a white winter wheat population from a cross between PHS resistant, Cayuga, and PHS susceptible, Caledonia. Recent fine mapping revealed that there are 2 QTLs closely linked in coupling and one of the QTL intervals was 4.2 cM and located between Wmc453c and Barc55. We also mapped these markers in a durum wheat recombinant substitution line (RSL) population that is segregating for a seed dormancy QTL on 2B. Based on corresponding rice genes, it was concluded that the PHS QTLs on 2B in common wheat were different from the seed dormancy QTL in the durum wheat. In the FHB research, we collaborate with breeders in 7 other states on 3 mini-projects. For the FHB recurrent selection project we tagged 649 MS spikes at anthesis. Selection for absence of symptoms on spikes and seed left 164 MS FHB resistant half sibs. In another experiment we are evaluating genomic selection for FHB resistance and was planted for a second year of evaluation. The third project is mapping native FHB resistance from a breeding line NY91017-8080. This population has been phenotyped and will be genotyped this spring. The native FHB resistance in this line is being combined with Chinese sources of resistance. We completed a fifth year of evaluation of the Langdon/ Triticum dicoccoides substitution lines for resistance to PHS and initiated a fine mapping study in 4 RSL populations. Testing of the Foster x KanQueen DH population for mapping milling quality traits was published. For spring oats, we co-released a new Illinois line and named it "Corral". Corral ranked first in the New York Variety Trial four consecutive years from 2007 to 2010. Our spring barley variety testing program has identified Benefit and AC Kawartha as the best varieties although the test weight for AC Kawartha is marginal. We have expanded our research on genomic selection. The results of this work have been ground-breaking and has resulted in several publications. Finally, for the first time we planted spring grains under organic management conditions at the Freeville Farm. We were awarded a USDA grant under the Organic Research and Extension Program. The results of our New York State variety testing program for spring and winter grains are distributed to extension agents, seed companies and farmers in the northeast and are published on the web (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/small grains/small-grains-cultivar-testing.cfm). PARTICIPANTS: David Benscher - Research Support Specialist James Tanaka - Lab Manager Technical assistant - John Shiffer Graduate students - Elliot Heffner,, Keith Williams, Jessica Rutkoski, Nicolas Heslot, Kaileigh Ahlquist, Philomin Juliana, Siman Peng Undergraduate - Celeste Falcon, Jeff Neyhart, Lo Him Tsz Visiting Scientists - Sanjay Kumar, Goro Ishikawa, Pawan Kulwal, Murugasamy Sivasamy, Yong-Gu Cho Post Docs - Julie Dawson, Jeff Endelman, Deniz Akdemir Research Associate - Long Xi Yu All of our students, post docs, and visiting scientists receive training in state of the art plant breeding methods including lab and field work. We collaborate with many researchers both nationally and internationally. The breeding program provides indispensable training for students and research associates. There is a nation wide shortage of trained plant breeders and this project provides invaluable experience. TARGET AUDIENCES: Our target audiences are farmers, extension agents and administrators, seed industry representatives, agronomists, economists, students, USDA researchers and technical support people. In addition, I give many presentations and seminars around the world on our molecular breeding research. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The Cornell small grains breeding and genetics program uses state of the art technologies to develop new wheat varieties and more efficient breeding methods. Our work on genomic selection methods is ground breaking and is ushering in a revolutionary new plant breeding methodology. We published high quality research on the inheritance and mapping of preharvest sprouting and fusarium head blight resistance. The information from this research has provided critical information on the location of genes affecting complex agronomic traits in wheat and resulted in more efficient crop improvement methods. All of our winter wheat variety releases have moderate to good resistance to both FHB and PHS, the two most important problems facing New York farmers. Our QTL mapping studies have enabled the use of molecular markers for efficiently developing new wheat varieties with these characteristics. The incorporation of fusarium resistance genes into adapted varieties benefits farmers by reducing the use of pesticides and resistance to preharvest sprouting will minimize the negative impact of the environment on wheat quality. Marker assisted selection for genes that improve milling quality increases the value of the New York wheat crop and the competitiveness of the New York farmers. These benefits help to stabilize wheat production and improve the rural economy of this region. In addition, these new varieties are very attractive to farmers who use organic production methods for the same reasons. Currently, we are expanding our evaluation of specialty grains under organic management. We present our results at field days and training workshops to explain to extension agents, growers and wheat end users the importance and impacts of our research. In addition, our breeding project is important for training the next generation of plant breeders by providing hands-on experience in a modern plant breeding program that integrates conventional and modern molecular technologies. All of our performance trials are published in an annual report that is mailed or emailed to approximately 200 individuals and agencies. It is also made available on our web site (http://plbrgen.cals.cornell.edu/cals/pbg/programs/departmental/small grains/small-grains-cultivar-testing.cfm).

Publications

  • Chao, S., J. Dubcovsky, J. Dvorak, M.C. Luo, P.S. Baenziger, R. Matnyazov, D.R. Clark, L. Talbert, J.A. Anderson, S. Dreisigacker, K. Glover, .J Chen, K. Campbell, P.L. Bruckner, J.C. Rudd, S. Haley, B.F. Carver, R. Sims15, S. Perry, M.E. Sorrells, and E. Akhunov, E. 2010. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat. BMC Genomics 11:727. doi:10.1186/1471-2164-11-727.
  • Gauch, Jr., H.G, P.C. Rodrigues, J.D. Munkvold, E.L. Heffner, and M.E. Sorrells. 2011. Two new strategies for detecting and understanding QTL by environment Interactions. Crop Sci. 51: 96-113.
  • Heffner, E.L., J.L. Jannink, and M. E. Sorrells. 2011. Genomic selection accuracy using multi-family prediction models in a wheat breeding program. The Plant Genome. 4:65-75.
  • Heffner, E.L., J.L. Jannink, H. Iwata, E. Souza, and M.E. Sorrells. 2011. Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci. doi: 10.2135/cropsci2011.05.0253.
  • Smith, N., M. Guttieri, E. Souza, J. Shoots, M.E. Sorrells, and C. Sneller. 2011. Identification and Validation of QTL for Grain Quality Traits in a Cross of Soft Wheat Cultivars Pioneer Brand 25R26 and Foster. Crop Science 51:1424-1436.
  • Somyong, S., J.D. Munkvold, J. Tanaka, D. Benscher, and M.E. Sorrells. 2011. Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling. Funct Integr Genomics 11:479-490.
  • Sorrells, M.E., J.P. Gustafson, D. Somers, S. Chao, D. Benscher, G. Guedira-Brown, E. Huttner, A. Kilian, P.E. McGuire, K. Ross, J. Tanaka, P. Wenzl, K. Williams, and C.O. Qualset. 2011. Reconstruction of the synthetic W9784 x Opata M85 wheat reference population. Genome 54:875-882.
  • Yu, L-X, A. Lorenz, J. Rutkoski, R.P. Singh, S. Bhavani, J. Huerta-Espino, and M.E. Sorrells. 2011. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor. Appl. Genet. DOI 10.1007/s00122-011-1664-y
  • Zeid, M., J.K. Yu, I. Goldowitz, M.E. Denton, Denise E. Costich, C.T. Jayasuriya, M. Saha, R. Elshire, D. Benscher, F. Breseghello, J. Munkvold, R.K. Varshney, G. Belay, M.E. Sorrells. 2010. Cross-amplification of EST-derived markers among 16 grass species. Field Crops Res. 118:28-35.