Accomplishments Report for 2012

Triticeae CAP: “Improving barley and wheat germplasm for changing environments”

 Project Director: J. Dubcovsky, University of California, Davis; jdubcovsky@ucdavis.edu

 Co-Director: G. Muehlbauer, University of Minnesota; muehl003@umn.edu

Co-PDs:

Akhunov Eduard, eakhunov@ksu.eduAnderson Jim, ander319@umn.edu Arnall Brian, b.arnall@okstate.edu Baenziger Steve, agro104@unlnotes.unl.edu Bai Guihua, gbai@ksu.edu Blake Tom, blake@montana.edu Bockelman Harold, hbockelman@ars-grin.gov Bonman Mike, mike.bonman@ars.usda.gov Bowden Bob, rbowden@ksu.edu Bradbury Peter, pjb39@cornell.edu Brakke Mary, brakk001@umn.edu Brown-Guedira G.  Gina_Brown-Guedira@ncsu.edu Brueggeman R.t, robert.brueggeman@ndsu.edu Byrne Patrick, Patrick.Byrne@ColoState.edu Campbell Kim, kgcamp@wsu.edu Carter Arron, ahcarter@wsu.edu Carver Brett, bfc@mail.pss.okstate.edu Chao Shiaoman, chaos@fargo.ars.usda.gov Chen Jianli, jchen@uidaho.edu Chen Xianming, xianming@mail.wsu.edu Close Timothy J., timothy.close@ucr.edu Costa   Jose M., costaj@umd.edu Friesen Timothy, timothy.friesen@ars.USDA.gov Fritz Allan, akf@ksu.edu Gill Bikram, bsg@ksu.edu Glover Karl, karl_glover@sdstate.edu Griffey Carl, cgriffey@vt.edu Haley Scott, shaley@lamar.colostate.edu Hayes, Patrick, Patrick.m.hayes@oregonstate.edu

Hole David, david.hole@usu.eduHorsley Rich, Richard.Horsley@ndsu.edu Ibrahim Amir, aibrahim@ag.tamu.edu Jannink Jean-Luc, jj332@cornell.edu Jin Yue, yuejin@umn.edu Kolmer James, jkolmer@umn.edu Lee Donald J., djlee@unlnotes.unl.edu Matthews D., matthews@greengenes.cit.cornell.edu Mckendry Ann, mckendrya@missouri.edu Morrell Peter, pmorrell@umn.edu Mullen Robert, mullen.91@osu.edu Namuth Covert D.M., dcovert2@unlnotes.unl.edu Poland Jesse, jpoland@ksu.edu Pumphrey Mike, m.pumphrey@wsu.edu Regassa   T. H., tregassa2@unlnotes.unl.edu See Deven, deven_see@wsu.edu Sherman Jamie, JSherman@Montana.edu Smith Kevin, smith376@UMN.EDU Sneller Clay, sneller.5@osu.edu Sorrells Mark, mes12@cornell.edu Souza Ed, souza.6@osu.edu Steffenson Brian J., bsteffen@umn.edu Talbert Luther, usslt@montana.edu Van Sanford Dave, dvs@uky.edu Vara   Prasad Pagadala V., vara@ksu.edu Waters Brian M., bwaters2@unl.edu Yan Liuling, lyan@mail.pss.okstate.edu Zhong Shaobin, shaobin.zhong@ndsu.edu

Project website (URL): https://triticeaecap.org/

 The purpose of the project: Human population growth and increasing climate variability require faster rates of improvement in wheat and barley production. The TCAP project is contributing to the mitigation of and adaptation to climate change effects by developing nationally coordinated high-throughput phenotyping and genotyping platforms, establishing a central database that integrates both types of data (T3), and testing innovative marker-based breeding strategies to accelerate breeding cycles. The project has also developed an integrated plant breeding education network that is training the next generation of modern plant breeders. The TCAP integrated approaches and web-based communication network has allowed barley and wheat breeders to tackle complex traits, such as water and nitrogen use efficiency and to adopt new complex technologies faster (e.g. canopy spectral reflectance). The new genotyping and phenotyping tools have already resulted in a comprehensive characterization of the natural variation available in the wheat and barley core germplasm collections at the USDA-ARS National Small Grain Collection (NSGC).

Objectives and Accomplishments:

Genotyping: SNP Genotyping: The barley iSelect 9,000 SNP barley chip was cross-referenced with previous chips, automatic SNP calling procedures were implemented and the SNP metadata was expanded. The TCAP wheat group mapped 7,517 SNPs from the 9,000 SNP wheat chip and that information was used to identify regions of the genome that were subjected to selection. The TCAP project played a key role in the development of a new 90,000 SNP wheat chip that has already been used to genotype approximately 2,500 US accessions. Genotyping of the barley and wheat association mapping panels, elite breeding, and genomic selection populations is on target.

New genotyping technologies: The Nimblegen whole exome capture assays targeting 110 Mb of sequence in the wheat genome and 90 Mb of sequence in the barley genome have been designed and tested with promising results (77% of sequence reads mapped to the references and more than 90% of targeted exonic regions were represented). Many of the NAM population parental lines have been characterized and 300,000 SNPs have been identified. Genotyping by sequencing was expanded into new mapping populations generating thousands of polymorphic GBS tags and high density maps.

The Triticeae toolbox database (T3): The user interface was improved to enable more intuitive searching of the data in T3 and the integration of multiple datasets. We incorporated into T3 several new phenotypic and genotypic datasets. Three online tutorials explaining data submission to T3 have been developed for submitting line names and properties, experiment annotations, and genotype data. Hyperlinks to other databases were created to facilitate users tracking down information about lines or markers. T3 now uses two-dimensional “materialized view” tables to access genotype data. This approach provides quicker access to large blocks of data as well as more compact storage.

Phenotyping: During this period, we made significant improvements in the canopy spectral reflectance protocols: improved equipment configurations, developed a more precise measurement protocol and implemented scripts to facilitate the management and analysis of data. This technology is being used to evaluate the NSGC core collections of barley (500 six-row spring accessions) and wheat (540 spring wheat accessions). The best drought resistant lines from the NSGC screen from 2011 have been incorporated into the breeding programs.

Water use efficiency (WUE): In barley, four association mapping populations have been planted in six locations for WUE evaluation and one has
been planted for seed increase. In wheat, two association mapping panels have been planted in five (spring) and three (winter) locations and are being evaluated for CSR and other physiological traits. Eight additional specialized mapping populations have been phenotyped for root characteristics, physiological traits associated to WUE, heat stress, and agronomic performance. The chromosome region defining drought tolerance in the 1RS translocation was identified and the beneficial effect of photoperiod sensitivity in early planting rain-fed northern latitudes was validated.

Nitrogen use efficiency (NUE): In barley, NUE is being evaluated using the spring six-row (SP6), spring two-row (SP2), and winter six-row (WN6) association mapping panels in low (70%) nitrogen and normal (100%) nitrogen in three environments. Results from 2011 are being analyzed and incorporated into T3. In wheat, both the hard and soft winter wheat panels are being evaluated for NUE at two locations (at different N levels) and in four additional locations for yield. All lines have been genotyped with the iSelect 90,000 SNP wheat chip.

Disease resistance: In barley, the NSGC was evaluated for resistance to stripe rust, stem rust, spot blotch and spot form net blotch. Putative new sources of resistance have been identified to each disease and are being genetically characterized. In wheat, the analyses of the 2011 data for leaf, stem and stripe rust (1000 spring lines) yielded 35 significant resistance loci. New sources of resistance to the three rust species were identified and are being validated experimentally. Seedling screening of the complete core collection for the three rusts has been completed.

Population development: Nested association mapping populations for barley and wheat were advanced two generations. Seed increases have been planted for the first 1000 complete NAM lines. The development of the wild barley introgression population was completed and has been genotypes with 384 SNP markers.

Education: Fifty-nine graduate students have participated in TCAP activities. Thirty-three of these students are funded by TCAP. Twenty undergraduate students are being mentored by TCAP PIs and graduate students, while 15 minority students are being mentored by eight Minority Serving Institution (MSI) faculty.

Plant Breeding Training Network (PBTN): The online environment was used to deliver and archive four courses, including Plant Breeding Strategies, Entering Mentoring, Quantitative Genetics and Association Mapping and Genomic Selection. To insure sustainability of course offerings, development of an online Plant Breeding Program through Ag*Idea continues with a letter of intent approved, a business plan developed and an Ag*Idea conference planned. Undergraduate students have been supported in their development through three online meetings with industry representatives and TCAP PIs. The development of three undergraduate educational tools has continued and one tool was submitted to an education journal. The PBTN also has been used as a communication tool for project management both for the TCAP, Ag*Idea Executive Committee, and the NAPB graduate student committee.

Newsletters, films and other communication resources: Information about research and education was shared both internally and externally through six meetings of the TCAP seminar series. Other communication tools include the quarterly newsletters and the face to face meetings at PAG. The TCAP produced film “Holding the future in the palm of your hand” was shown during three recruiting trips to about 200 students. Two of these students applied to TCAP graduate schools. Minority students have been attracted to several internships. Two other films have been created and posted online. The first year evaluation report was received and used to guide second year planning. Evaluation tools were also refined.  

Publications and germplasm releases: TCAP participants generated 35 peer reviewed publications during 2012. In addition, eight new wheat and barley varieties and germplasm were released.

Deliverables

Publications:  

1.- Anderson, J.A., J.J. Wiersma, G.L. Linkert, J.A. Kolmer, Y. Jin, R. Dill-Macky, J.V. Wiersma, G.A. Hareland, and R. H. Busch. 2012. Registration of ‘Tom’ Wheat. J. Plant Registrations. 6: 2: 180-185

2.- Anderson, J.A., J.J. Wiersma, G.L. Linkert, J.A. Kolmer, Y. Jin, R. Dill-Macky, J.V. Wiersma, G.A. Hareland, and R. H. Busch. 2012. Registration of ‘Sabin’ Wheat. J. Plant Registrations. 6: 2: 174-179

3.- Baenziger, P.S., R. A. Graybosch, t. Regassa, L.A. Nelson, R. N. Klein, D. K. Santra, D.D. Baltensperger, L. Xu, S. N. Wegulo, Y. Jin, J. Kolmer, Ming-shun Chen, and Guihua Bai. 2012. Registration of ‘NE01481’ hard red winter wheat. J. Plant Reg. 6:49-53.

4.- Baenziger, P.S., R. A. Graybosch, T. Regassa, L.A. Nelson, R. N. Klein, D. K. Santra, D.D. Baltensperger, J. M. Krall, S. N. Wegulo, Y. Jin, J. Kolmer, Ming-shun Chen, and Guihua Bai. 2012. Registration of ‘NI04421’ hard red winter wheat. J. Plant Reg. 6:54-59.

5.- Bernardo A. N., H. Ma, D. Zhang, and G. Bai. 2012. Single Nucleotide Polymorphism in wheat chromosome region harboring Fhb1 for Fusarium Head Blight resistance. Mol Breed. 29:477–488.

6.-Blake, V.C., J.G. Kling, P.M. Hayes, J.-L. Jannink, S.R. Jillella, J. Lee, D.E. Matthews, S. Chao, T.J. Close, G.J. Muehlbauer, K.P. Smith, R.P. Wise and J.A. Dickerson.  2012.  The Hordeum Toolbox – The barley coordinated agricultural project genotype and phenotype resource. The Plant Genome 5:81-91.

7.- Chen, J. L. ; C. G. Chu; E. J. Souza; M. J. Guttieri; X.M. Chen; S. Xu; D. Hole; R. Zemetra. 2012. Genome-wide identification of QTL conferring high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici) in wheat. Mol. Breeding 3:791-800.

8.- Edwards, J.T., R.M. Hunger, E.L. Smith, G.W. Horn, M.-S. Chen, L. Yan, G. Bai, R.L. Bowden, A.R. Klatt, P. Rayas-Duarte, R.A. Osburn, J.A. Kolmer, Y. Jin, D.R. Porter, K.L. Giles, B.W. Seabourn, M.B. Bayles, and B.F. Carver. 2012. ‘Duster’ wheat: A durable, dual-purpose cultivar adapted to the southern Great Plains of the USA. J. Plant Reg. 6:1-12.

9.- Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of ‘Byrd’ wheat. Journal of Plant Registrations. 6:302-305.

10.- Haley, S.D., Johnson, J., Westra, P., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of ‘Brawl CL Plus’ wheat. Journal of Plant Registrations. 6:306-310.

11.- Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Martin, T.J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of ‘Denali’ wheat. Journal of Plant Registrations. 6:311-314.

12.- Hazard B., X. Zhang, P. Colasuonno, C. Uauy, D.M. Beckles, and J. Dubcovsky. 2012. Induced mutations in the Starch Branching Enzyme II (SBEII) genes increase amylose and resistant starch content in pasta wheat. Crop Sci. 52: 1754-1766.

13.- Heslot, N., H.-P. Yang, M.E. Sorrells, and J-L. Jannink. 2012. Genomic selection in plant breeding: A comparison of models. Crop Sci. 52:146-160.

14.- Lanning, S. P., P. Hucl, M. Pumphrey, A. H. Carter, P. F. Lamb, G. R. Carlson, D. M. Wichman, K. D. Kephart, D. Spaner, J. M. Martin and L. E. Talbert.  2012.  Agronomic performance of spring wheat as related to planting date and photoperiod response.  Crop Sci. 52:1633-1639.

15.- Lanning, S. P.,  J. M. Martin, R. N. Stougaard, F. R. Guillen-Portal, N. K. Blake, J. D. Sherman, A. M. Robbins, K. D. Kephart, P. Lamb, G. R. Carlson, M. Pumphrey, and L. E. Talbert.  2012.  Evaluation of near-isogenic lines for three height-reducing genes in hard red spring wheat.  Crop Sci. 52:1145-1152.

16.- Leng, Y. and S. Zhong. 2012, Sfp-type 4′-phosphopantetheinyl transferase is required for lysine synthesis, tolerance to oxidative stress and virulence in the plant pathogenic fungus Cochliobolus sativus. Mol. Plant Path. 13: 375–387.

17.- Liu, Z.-H., Zhong, S., Edwards, M.C., and Friesen, T.L. 2012. Virulence profile and genetic structure of a North Dakota population of Pyrenophora teres f. teres, the causal agent of net form net blotch of barley. Phytopath. 102:539-546.

18.- Lorenz, A.J., K.P. Smith, and J.-L. Jannink. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci. Vol. 52 No. 4, p. 1609-1621.

19.- Mengistu, N., P. S. Baenziger, K. M. Eskridge, I. Dweikat, S. N. Wegulo, K. S. Gill, and A. Mujeeb-Kazi. 2012. Validation of QTL for grain yield-related traits on wheat chromosome 3A using recombinant inbred chromosome lines. Crop Sci.: 52:1622-1632.

20.- Morrell, P.L., Buckler, E.S., Ross-Ibarra, J. 2012. Crop genomes: advances and applications. Nat. Rev. Genet. 13:85-96

21.- Naruoka, Y., J. D. Sherman, S. P. Lanning, N. K. Blake, J. M. Martin, and L. E. Talbert. 2012. Genetic analysis of long green leaf duration in spring wheat. Crop Sci. 52: 1: 99-109.

22.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. Response of Aegilops species to drought stress during reproductive stages of development. Functional Plant Biology. 39:51-59.

23.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. Effect of drought and high temperature stress on synthetic hexaploid wheat. Functional Plant Biology. 39:190-198.

24.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. High temperature tolerance in Aegilops species and its potential transfer to wheat. Crop Sci. 52: 292-304.

25.- Poland J.A., P.J. Brown, M.E. Sorrells, and J.-L. Jannink. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS ONE 7:e32253.

26.- Yu, L-X, A. Morgounov, R. Wanyera, M. Keser, S. Kumar Singh, and M.E. Sorrells. 2012. Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis. Theor. Appl. Genet. 125:495-502.

27.- Zhang X.H., H.Y. Pan and G.H. Bai. 2012. Quantitative trait loci for fusarium head blight resistance in U.S. hard winter wheat cultivar ‘Heyne’. Crop Sci. 52:1187–1194.

Published on line

28.- Kulwal, P., G. Ishikawa, D. Benscher, Z. Feng, L-X Yu, A. Jadhav, S. Mehetre, and M. E. Sorrells. 2012. Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet. DOI 10.1007/s00122-012-1872-0

29.- Kumar S., S.K. Sehgal, U. Kumar, P.V.V. Prasad, A.K. Joshi, B.S. Gill. 2012. Genomic characterization of drought tolerance-related traits in spring wheat. Euphytica. DOI:10.1007/s10681-012-0675-3

30.- Rutkoski, J., J. Benson, Y. Jia, G. Brown-Guedira, J.-L. Jannink, and M.E. Sorrells. 2012. Evaluation of genomic prediction methods for Fusarium head blight resistance in wheat. The Plant Genome. DOI: 10.3835/plantgenome2012.02.0001

31.- Tao Li, Guihua Bai, Shuangye Wu and Shiliang Gu. 2012. Quantitative trait loci for resistance to fusarium head blight in a Chinese wheat landrace Huangfangzhu. Euphytica. DOI 10.1007/s10681-012-0631-2

32.- Zhang X.H., H.Y. Pan and G.H. Bai. 2012. Quantitative trait loci responsible for fusarium head blight resistance in Chinese wheat landrace Baishanyuehuang. Theor. Appl. Genet. DOI: 10.1007/s00122-012-1848-0

33.- Neelam K.,  G. Brown-Guedira, L. Haung. 2012. Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21. Mol Breeding DOI 10.1007/s11032-012-9773-0

34.- Hale I., X. Zhang, D. Fu, and J. Dubcovsky. 2012. Registration of wheat lines carrying the partial stripe rust resistance gene Yr36 without the Gpc-B1 high grain protein content allele. J. Plant Reg. doi:10.3198/jpr2012.03.0150crg

35.- X. Wang, J. Richards, T. Gross, A. Druka, A. Kleinhofs, B. Steffenson, M. Acevedo and R. Brueggeman (2012) The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene and an actin depolymerization factor. MPMI. In Press.

Community Resources Generated:

• 9,000 and 90,000 SNP iSELECT Illumina chips for wheat, and improved metadata for the 9,000 SNP chip for barley.
• Gene capture platforms for wheat and barley.
• High density barley and wheat genetic maps integrating SNPs and genotyping by sequencing.
• Genotyped core germplasm collections for barley and wheat.
• An integrated genotyping-phenotyping database (T3).
• Association mapping and nested association mapping populations for WUE, NUE and disease resistance genes.
• A plant breeding training network that provides access to 59 graduate and 20 undergraduate students across the US to the best teachers and scientists.
• Three workshops, six seminars, four online courses and three educational films.

 

Other Products/ Outcomes: Improved varieties and gemplasm  

• UI Stone (IDO599) soft white spring wheat with high yield potential under both irrigation and water limited conditions as well as excellent end-use quality. Selected with markers for FHB.  IDO671 (SWS), IDO694 (HWS) are also being released
• Hard red spring variety ‘Rollag’ combines highest resistance to Fusarium head blight and strong straw.  Rollag contains the Fhb1 QTL for Fusarium head blight resistance and Lr34.
• Hard red spring variety ‘Norden’ is a competitive yielder with high test weight, good straw strength and includes resistance genes Lr21, Fhb1 and Lr34.
• WB9879CLP is a variety with resistance to imidazolinone herbicides developed by Montana State University for areas with wheat stem sawfly pressure.
• Patwin-515 HWS wheat including stripe rust resistance genes Yr5, Yr15, and Yr17.
• SRW wheat cultivars 5187J (Sr24 + 1A.1R translocation conferring resistance to Ug99) and 12V51 (resistant to S. nodorum and has Lr9).
• Recombinant inbreed lines with Yr36 but without the closely linked gene GPC-B1 in both tetraploid (PI 656793) and hexaploid wheat (PI 664549). The hexaploid recombinant line is particularly useful for soft wheat breeding programs.

 

 

 

Extension and/or education activities completed or upcoming:

• 59 graduate students participated in the PBTN and 33 were supported by TCAP funding
• 20 undergraduate students were mentored by graduate students and faculty
• 15 students from Minority Serving Institutions participated in TCAP activities
• Undergraduate students have been supported in their development through three online meetings with industry representatives and TCAP PIs.
• The online environment was used to deliver and archive 4 courses and 6 seminars.
• Other communication tools include the quarterly newsletters and films “Holding the future in the palm of your hand”, “Seeds of Hope”, and “Everything is local: Fighting the Wheat Stem Sawfly” with related handouts.

Collaborations: The TCAP funding was essential to integrate the US into international wheat and barley consortia:

• International consortia for barley and wheat SNP development.
• International consortia for barley and wheat gene capture.
• Collaborations with breeding database teams around the world.
• Contribution of transcriptome data of tetraploid wheat to the International Wheat Sequencing Consortium

The significance of TCAP findings to Food and Agriculture

The TCAP project has integrated the barley and wheat research and breeding activities across the country into a single collaborative community. This integration has facilitated the implementation of common high-throughput genotyping and phenotyping platforms and the integration of all the information in a centralized database. These new tools were used to characterize the complete germplasm core collections for barley and wheat and to discover new gene variants for improved water and nitrogen use efficiency and for disease resistance. Marker-assisted selection and genomic selection strategies are being implemented in the public barley and wheat breeding programs to deploy these valuable genes into commercial varieties and to accelerate breeding cycles. The TCAP is revitalizing training in plant breeding in the US. Fifty-six graduate students and 35 undergraduate students are getting hands-on training in plant breeding and have now access to the best teachers and scientists in plant breeding and related disciplines through the Plant Breeding Training Network (PBTN). This online environment and the large student cohort have reduced the isolation of plant breeding students and better prepare them for the collaborative enterprise of plant breeding. Plant breeders from industry and other countries are making use of the materials we are creating. The collaborations with faculty at minority serving institutions have established a bridge that has been already used by MSI students to reach TCAP barley and wheat breeding programs.

 

Other comments or recommendations for future work

We appreciate the generous support of USDA and NIFA that has made this ambitious project possible.