Source: COLORADO STATE UNIVERSITY submitted to
MOLECULAR-MARKER-ASSISTED ANALYSIS OF QUANTITATIVE TRAITS FOR WHEAT, DRY BEANS, AND BRASSICA SPECIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0229377
Grant No.
(N/A)
Project No.
COL00737A
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jul 1, 2012
Project End Date
Jun 30, 2017
Grant Year
(N/A)
Project Director
Byrne, PA.
Recipient Organization
COLORADO STATE UNIVERSITY
(N/A)
FORT COLLINS,CO 80523
Performing Department
Soil and Crop Science
Non Technical Summary
Drought stress is an important constraint on wheat production in Eastern Colorado. Therefore, tolerance to limited soil moisture is an important goal of CSU's wheat breeding program. Efforts to improve genetic tolerance to these stresses are limited by variability of field and weather conditions, lack of knowledge of the genes or chromosome regions controlling stress tolerance, and lack of information on the relationships among various physiological/biochemical indicators of stress and grain yield. Better end-use quality is another high priority goal for Colorado wheat varieties to maintain competitiveness in a global marketplace that places increasing importance on quality. Through a variety of approaches this project is attempting to develop germplasm and information that will assist CSU's wheat breeding program develop more drought tolerant cultivars. White mold and Fusarium wilt of common bean are serious disease problems in the High Plains region of Colorado and neighboring states, with annual yield losses reaching 30% in some areas. Exploitation of genetic resistance is considered the most feasible control method. Molecular markers closely linked with disease resistance will speed the development of resistant bean cultivars. Canola and related species are potential biofuel crops in Colorado. Research in this project will identify adapted germplasm and some of the genes responsible for good performance under Colorado conditions.
Animal Health Component
0%
Research Effort Categories
Basic
20%
Applied
80%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011540108020%
2011544108015%
2031540108010%
2031544108010%
2011541108010%
2041544108010%
2011410108015%
2011848108010%
Knowledge Area
204 - Plant Product Quality and Utility (Preharvest); 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1410 - Beans (dry); 1540 - Hard red winter wheat; 1541 - Hard red spring wheat; 1848 - Canola; 1544 - Hard white wheat;

Field Of Science
1080 - Genetics;
Goals / Objectives
The overall goal of the project is to obtain genetic information on quantitative trait inheritance that is useful to CSU's applied plant breeding programs and to the larger community of plant breeders and geneticists. Specific objectives are (1) To locate and characterize quantitative trait loci (QTL) for important quantitative traits in winter wheat, focusing specifically on drought tolerance, yield potential, and end-use quality, and including other traits as opportunities arise. (2) To locate and characterize QTL for important quantitative traits in dry beans, concentrating specifically on disease resistance, and including other traits as opportunities arise. (3) To collaborate with CSU's applied breeding programs for wheat and dry beans to incorporate marker-assisted selection into their breeding strategies. (4) To conduct genetic and phenotypic analyses in Brassica species relevant to biofuel production in Colorado. (5) To pursue additional opportunities that may arise for applying genetic analyses to problems facing Colorado agriculture and natural ecosystems.
Project Methods
For genetic analysis of stress tolerance in wheat, we have moved away from biparental mapping populations and toward association mapping with hundreds of diverse cultivars and breeding lines. One example of this is our evaluation of the Hard Winter Wheat Association Mapping Panel of 300 Great Plains cultivars and experimental lines. This study forms part of the national Triticeae Coordinated Agricultural Project. High-density molecular markers will be generated by regional USDA marker labs and analyzed together with our phenotypic data on stress tolerance and yield-related traits, evaluated under fully irrigated and drought stress conditions. Initial detection of marker-trait associations based on two years of field data will be followed by more detailed analysis to validate the associations and integrate the findings into marker-assisted breeding strategies. Another aspect of this work will be to try to elucidate the basis of differential drought tolerance by examining root systems both in greenhouse and field environments. Using a flatbed scanner and digital analysis software, we will analyze root biomass, length, and diameter of a subset of cultivars at different soil depths and compare those variables to yield performance. A second association mapping population we are studying is CIMMYT's Wheat Association Mapping Panel II, which we have evaluated under stress and non-stress conditions in Colorado and Ethiopia. Phenotypic data will be combined with marker data to identify genomic regions associated with the traits of interest. Another use of CIMMYT germplasm is the crossing of six of their synthetic hexaploid lines with the adapted Colorado cultivar Hatcher. BC1 and BC2 families of these crosses have been developed; a subset of these has been selected and will be evaluated for yield performance and stress tolerance traits in multilocation field trials. For end-use quality traits, we will attempt to validate two QTL detected in the Platte x CO940610 doubled haploid population by testing for the presence of the same QTL in a recombinant inbred line population of the same cross. We will also develop near-isogenic lines for those QTL, grow them in replicated field trials, and evaluate their end-use quality. In dry beans, our major focus will be on QTL analysis of resistance to the fungal disease Fusarium wilt. Having recently detected and mapped a major gene for Fusarium wilt resistance in a common bean mapping population, we will now attempt to verify the gene's effect in other populations and accessions. We will also develop breeder-friendly molecular markers to track the gene more conveniently in marker-assisted selection. In Brassica, we will continue to evaluate canola QTL mapping populations phenotypically and genetically. The initial focus will be on agronomic suitability for Colorado conditions, especially under low soil moisture, but later may also involve analysis of oil content and oil profiles for biodiesel production and other uses.

Progress 07/01/12 to 06/30/17

Outputs
Target Audience:Colorado wheat growers, extension personnel, and members of the agricultural scientific community, especially wheat breeders and geneticists and germplasm bank curators. Changes/Problems:As mentioned previously, two research studies conducted under this project were not specifically mentioned in the 2012 project description. They are (1) an evaluation of the effects of microbial inoculation on performance of wheat under wet and dry field conditions; and (2) an evaluation of the effects on rye seeds of 25 years of cryopreservation. Both studies fall into the category defined by Objective 5, 'To pursue additional opportunities that may arise for applying genetic analyses to problems facing Colorado agriculture and natural ecosystems.' What opportunities for training and professional development has the project provided?Five PhD students and three MS students completed theirdegree programs during the project. An additional three MS students either finished their programs after the current reporting period or are still working on their degrees. An average of two undergraduate students per summer were employed each summer to assist with field work, and two or three undergrad students were employed part-time during the academic year. How have the results been disseminated to communities of interest?Results have been disseminated through publication in peer-reviewed journals, presentations at professional meetings, and presentations at grower meetings and field days. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Summarized accomplishments for each objective are presented below. (1) To locate and characterize quantitative trait loci (QTL) for important quantitative traits in winter wheat, focusing specifically on drought tolerance, yield potential, and end-use quality, and including other traits as opportunities arise. Five PhD students completed their dissertations during the life of this project, all related to some aspect of QTL discovery or drought tolerance investigation in wheat. Each student has been the lead author on at least one published journal article concerning their research. Their studies have detected or validated QTL either in biparental QTL populations or genome-wide association studies. Two QTL in particular, on chromosomes 6B and 7A, are the focus of ongoing work, with the eventual goal of cloning the responsible genes underlying the QTL. Other research has characterized root system traits related to drought tolerance and identified specific synthetic hexaploid wheat lines possessing potentially valuable root phenotypes. (2) To locate and characterize QTL for important quantitative traits in dry beans, concentrating specifically on disease resistance, and including other traits as opportunities arise. Research continued on detecting and characterizing QTL for Fusarium wilt resistance in the LEF-2RB/Sierra recombinant inbred line (RIL) population of dry bean. Additional phenotypic data were obtained from greenhouse inoculations, new high quality DNA samples were extracted from the RILs, and DNA was sent to a USDA-ARS lab in Beltsville, MD for SNP analysis. SNP data was obtained, screened for quality, and is now ready for analysis. (3) To collaborate with CSU's applied breeding programs for wheat and dry beans to incorporate marker-assisted selection into their breeding strategies. Information has been provided to CSU's wheat breeding program on allelic composition of 299 Great Plains cultivars and breeding lines at eight important loci controlling plant height and phenology: Rht-B1, Rht-D1, Ppd-A1, Ppd-B1, Ppd-D1, Vrn-A1, Vrn-B1, and Vrn-D1. Most of the variation in heading date was explained by the photoperiod sensitivity loci Ppd-D1, Ppd-B1, and their interaction. We also detected distinct geographical trends in allelic composition at Ppd and Rht alleles. In other research, genome-wide association analyses detected stable QTL for yield-related traits on chromosomes 3B, 6B, and 7A. Crosses have been made to incorporate the 6B and 7A QTL into lines of the CSU wheat breeding program. (4) To conduct genetic and phenotypic analyses in Brassica species relevant to biofuel production in Colorado. Three M.S. students completed and defended their thesis research on canola (Brassica napus) or camelina (Camelina sativa) during the reporting period. All three projects had the goal of QTL discovery under well-watered and water-limited conditions. QTL were detected in all environments and for most evaluated traits, but were not stably expressed in all environments. (5) To pursue additional opportunities that may arise for applying genetic analyses to problems facing Colorado agriculture and natural ecosystems. An additional opportunity that arose was a collaborative project with the USDA-ARS National Laboratory for Genetic Resources Preservation to evaluate the long-term effects of cryopreservation on seeds of rye, Secale cereale. Forty rye accessions (20 spring habit and 20 winter habit) that had been stored for 25 years under both conventional storage and cryogenic conditions were evaluated for phenotypic and epigenetic effects. Phenotypes evaluated were morphological traits under field conditions and percent germination under standard laboratory conditions. Epigenetic effects were assessed by evaluating DNA methylation changes detected by methylation-sensitive amplified fragment length polymorphism. Our study indicated that cryopreservation slowed seed deterioration, as shown by higher germination rates compared to conventional storage, had only minimal effects on other phenotypic traits, and had no significant effects on DNA methylation status.

Publications

  • Type: Theses/Dissertations Status: Published Year Published: 2017 Citation: Lu, J. 2017. Phenotypic changes and DNA methylation status in cryopreserved seeds of rye (Secale cereale L.). M.S. thesis, Colorado State University, Fort Collins.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dao, H.Q., P.F. Byrne, S.D. Reid, and S.D. Haley. 2017. Validation of quantitative trait loci for grain quality-related traits in a winter wheat mapping population. Euphytica 213:5. doi 10.1007/s10681-016-1793-0


Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Colorado wheat growers, extension personnel, and members of the agricultural scientific community, especially wheat breeders and geneticists and germplasm bank curators. Changes/Problems:This study was not specifically mentioned in the 2012 project description. However, it falls into the category defined by Objective 5, 'To pursue additional opportunities that may arise for applying genetic analyses to problems facing Colorado agriculture and natural ecosystems.' What opportunities for training and professional development has the project provided?One M.S. graduate student received training in designing and carrying out a field experiment, evaluating phenological and morphological traits in the field and seedling root traits in the lab, conducting DNA molecular marker analysis, and performing statistical analysis. Two undergraduate students assisted in the field evaluations and were trained in field trial design and trait measurement. How have the results been disseminated to communities of interest?Results of this experiment have been discussed with personnel of USDA's National Laboratory for Genetic Resources Preservation, who will be most able to act upon the findings. In addition, an abstract describing the study was submitted for the annual meeting of the Crop Science Society of America and a poster of the study was presented at that meeting in November, 2016. What do you plan to do during the next reporting period to accomplish the goals?We will continue data analysis and will draft a manuscript for publication. The M.S. student is expected to complete and defend her thesis in February, 2017.

Impacts
What was accomplished under these goals? This report focuses on one aspect of the project, namely a collaboration with the USDA-ARS National Laboratory for Genetic Resources Preservation (NLGRP) to assess the effects of cryopreservation of small grain seeds on phenotypic and genetic stability. The NLGRP currently uses two methods to conserve seeds: storage in a -18 C vault (conventional storage) and placing seeds in liquid nitrogen vapor phase at -173 C (cryopreservation). Cryopreservation is considered advantageous because seeds can retain viability for a much longer period of time compared to conventional storage. However, a major concern has been the physical and biochemical stability of cryopreserved plant material. To our knowledge, there had not been a study prior to this one that compared phenotypes and genotypes of seeds subjected to long-term storage by the two methods. The field component of this study included 40 accessions of rye (20 winter habit and 20 spring habit) that had been stored for 25 years under the two storage conditions. The accessions were evaluated for quantitative traits (plant height, heading and anthesis dates, spike length, and spike weight) and qualitative traits (straw, awn, and glume color, awn type, and glume pubescence). In a laboratory experiment, seed germination of the same accessions was evaluated, as well as seedling root length and diameter. To determine genetic stability, the DNA methylation status of two rye accessions was evaluated by a methylation-sensitive amplified fragment length polymorphism (metAFLP) method. Our results for the field evaluation showed a slight decrease in spike length for the cryopreserved samples, but no significant difference due to storage method for spike weight or any other trait. Germination tests revealed an increase in normal germination and a decrease in abnormal germination for cryopreserved seeds compared to conventionally stored seeds. For the metAFLP evaluation, our analysis did not detect any statistical differences in DNA methylation status between cryopreservation and conventional storage methods. Therefore, based on results of this study, cryopreservation appears to improve germination rates slightly, but does not appear to introduce any other substantive phenotypic or genotypic changes relative to conventional storage.

Publications

  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Grogan, S.M. 2015. Dissecting drought tolerance in winter wheat using phenotypic and genetic analyses of agronomic and spectral traits. Ph.D. dissertation. Colorado State University, Fort Collins.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Dao, H.Q. 2015. Bi-parental mapping and genome-wide association studies for grain quality traits in winter wheat under contrasting soil moisture conditions. Ph.D. dissertation. Colorado State University, Fort Collins.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Grogan, S.M. Anderson, J., Baenziger, P.S., Frels, K., Guttieri, M.J., Haley, S.D., Kim, K.-S., Liu, S., McMaster, G.S., Newell, M., Vara Prasad, P.V., Reid, S.D., Shroyer, K.J., Zhang, G., Akhunov, E., and Byrne, P.F. 2016. Phenotypic plasticity of winter wheat heading date and grain yield across the U.S. Great Plains. Crop Science 56:2223-2236.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Grogan, S.M., Brown-Guedira, G., Haley, S.D., McMaster, G.S., Reid, S.D., Smith, J., and Byrne, P.F. 2016. Allelic variation in developmental genes and effects on winter wheat heading date in the U.S. Great Plains. PLoS ONE 11(4): e0152852.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Becker, S.R., Byrne, P.F., Reid, S.D., Bauerle, W.L., McKay, J.K., and Haley, S.D. 2016. Root traits contributing to drought tolerance of synthetic hexaploid wheat in a greenhouse study. Euphytica 207:213-224.
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Tan, C.-T., Assanga, S., Zhang, G., Rudd, J.C., Haley, S.D., Xue, Q., Ibrahim, A., Bai, G., Zhang, X., Byrne, P., Fuentealba, M.P., and Liu, S. 2017. Development and validation of KASP markers for wheat streak mosaic virus resistance gene Wsm2. Crop Science 57:110.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Kim, K.S., Anderson, J.D., Newell, M.A., Grogan, S.M., Byrne, P.F., Baenziger, P.S., and Butler, T.J. 2016. Genetic diversity of Great Plains hard winter wheat germplasm for forage. Crop Science 56:22972305.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Dao, H.Q., Harrington, J., Reid, S., Manmathan, H., and Byrne, P. 2016. Genome-Wide Association Study in Bread Wheat Identifies Loci for Grain Protein Concentration and Test Weight. Poster P0834 presented at the Plant and Animal Genome Conference, Jan. 9-13, 2016, San Diego. https://pag.confex.com/pag/xxiv/meetingapp.cgi/Paper/21324
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Mutlucan, M., Tosun, M., Ilker, E., Tonk, F.A., Istipliler, D., Byrne, P., Haley, S., and Moragues, M. 2016. Genetic Analysis of Plant Height, Coleoptile Length and their Relationships with Rht12 and Rht13 Genes in Wheat. Poster P0854 presented at the Plant and Animal Genome Conference, Jan. 9-13, 2016, San Diego. https://pag.confex.com/pag/xxiv/meetingapp.cgi/Paper/19318
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Lu, J., Greene, S., Reid, S., and Byrne, P. 2016. Phenotypic changes and DNA methylation status of cryopreserved rye seeds. Poster presentation at Crop Science Society of America annual meeting, Phoenix, Nov. 6-9, 2016. https://scisoc.confex.com/scisoc/2016am/webprogram/Paper102663.html
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Moore, A., Becker, S., Reid, S., Haley, S., and Byrne, P. 2016. Exploiting the Genetic Diversity of Aegilops tauschii to Improve the Yield and Adaptation of Winter Wheat. Poster presentation at Crop Science Society of America annual meeting, Phoenix, Nov. 6-9, 2016. https://scisoc.confex.com/scisoc/2016am/webprogram/Paper102491.html
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Dao, H.Q., Byrne, P.F., Reid, S.D., and Haley, S.D. 2017. Validation of quantitative trait loci for grain quality-related traits in a winter wheat mapping population. Euphytica (In press)


Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Colorado wheat growers, extension personnel, and members of the agricltural scientific community, especially wheat breeders and geneticists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Three Ph.D. graduate students and a research associate contributed to this research by collecting data from field and lab experiments and conducting the genome-wide association analysis. They learned to use new software tools in the R programming language, and gained experience in interpreting and presenting the results. How have the results been disseminated to communities of interest?Three Ph.D. students presented their results at their dissertation defense seminars. Two manuscripts based on this research were submitted to peer-reviewed journals and have been tentatively accepted pending revisions. An oral presentation was given at the annual meeting of the Triticeae Coordinated Agricultural Project, Jan. 11, 2015 in San Diego. A poster on part of this work was accepted for presentation at the Plant and Animal Genome meeting, Jan. 9-13, 2016 in San Diego. Dr. Byrne presented partial results at an invited seminar at the University of Saskatchewan, Saskatoon, Mar. 24, 2015. What do you plan to do during the next reporting period to accomplish the goals?We will continue data analysis and drafting of at least two manuscripts for publication. We will attempt to validate the most significant and consistent marker-trait associations by analyzing markers in the same genomic regions in different sets of germplasm.

Impacts
What was accomplished under these goals? This report will focus on one aspect of the project, namely research into the association of molecular markers with agronomic and grain quality traits in a winter wheat genome-wide association analysis (GWAS). This work was undertaken as part of the national Triticeae Coordinated Agricultural Project. The population used for the analysis consisted of 299 wheat cultivars and breeding lines from public and private breeding programs in seven Great Plains states. Field trials were grown in four Colorado environments: well-watered and water-stressed environments in Greeley (USDA-LIRF) and Fort Collins (ARDEC). Evaluated traits included days to heading and maturity, plant height, grain yield and yield components, test weight, and grain protein and ash concentrations. Single-nucleotide polymorphism (SNP) marker data were obtained with the Illumina 90K iSelect chip and were provided by collaborators in other states. After filtering, the number of SNP markers used in the analysis was 16,052 distributed across the wheat genome. GWAS was conducted with the GAPIT software package in the R programming language. GWAS identified several dozen loci associated with various traits at or approaching statistical significance. However, we found relatively few associations having large effects or that were stable across environments, years, or moisture treatments. Among the consistent loci detected were those for test weight on chromosome 3B, grain protein concentration on 2D, spikelets per spike on 7A, and proportion fertile spikelets on 2D and 5A. GWAS is a powerful tool for detecting marker-trait associations, but the number of significant loci detected depends on the statistical criteria used and the analysis options selected.

Publications

  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Awad, W. 2015. Genome-wide association study and drought tolerance evaluation of a winter wheat association mapping panel. Ph.D. dissertation, Colorado State University, Fort Collins.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: El-Feki, W.M., Byrne, P.F., Reid, S.D., and Haley, S.D. 2015. Registration of CO940610/Platte wheat doubled haploid mapping population. Journal of Plant Registrations 9:419423.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Awad, W., Byrne, P., Reid, S., and Haley, S. Diversity of Root Traits in Great Plains Winter Wheat Under Drought Stress. Poster P0630 at the Plant and Animal Genome meeting, Jan. 10-14, 2015, San Diego.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Grogan, S., Haley, S., McMaster, G., Reid, S., and Byrne, P. Phenotypic Plasticity of Growing Degree-Days to Heading and Grain Yield in a Multi-Environment Trial of Winter Wheat. Poster presentation at Crop Science Society of America annual meeting, Minneapolis, Nov. 15-18, 2015.


Progress 10/01/13 to 09/30/14

Outputs
Target Audience: Colorado wheat growers, extension personnel, and members of the agricltural scientific community were reached through field day and professional meeting presentations, articles in a CSU Extension publications, articles in professional journals, and graduate student theses. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? A post-doctoral associate and a graduate student gained significant experience in conducting these studies. They helped to formulate the objectives, develop the methodologies, analyze the data, and interpret the results. They also were largely responsible for implementing the study, recording the data, and collecting the plant samples. As a result of this experience, both will be better able to conduct similar studies as independent researchers. How have the results been disseminated to communities of interest? Dr. Stromberger spoke about this project to the Rocky Mountain Agribusiness Association Meeting in Denver (January 15). An oral presentation was made at the annual Field Day of the USDA-ARS Central Great Plains Research Station, Akron, CO: P. Byrne and M. Stromberger, Breeding for Drought Tolerance in Winter Wheat through Above and Belowground Interactions (June 11). Information on this project was included in invited presentations made at the CSU Interdisciplinary Water Seminar (March 31) and the National Association of Plant Breeders annual meeting (Aug. 7). An article about this project was published in the 2014 Colorado State University Crops Testing Winter Wheat Report ‘Making Better Decisions’. The greenhouse experiments were featured in tours given to participants in the Biofuels Research Tour (April 17) and to students in the course Plant Breeding for Drought Tolerance (June 4). What do you plan to do during the next reporting period to accomplish the goals? We will try to determine whether the microbial associations that were helpful in the greenhouse studies are also present and beneficial in field environments. We will collect rhizosphere soil samples from a variety of cultivars under irrigated and rainfed conditions and evaluate the proportion of ACC+ bacteria. These data will be compared to yield performance and physiological indicators of water status of the plants to determine whether the bacteria in fact confer a drought tolerance benefit.

Impacts
What was accomplished under these goals? This report will focus on one aspect of the project, namely research into the association of specific soil microbial communities with drought tolerance in wheat. An important group of soil bacteria involved in plant abiotic stress tolerance is the ACC deaminase positive (ACC+) bacteria. Our previous research had demonstrated that winter wheat cultivars differed in their root exudate chemical profiles and ability to establish large populations of ACC+ bacteria in the rhizosphere. This year we expanded the study to include seven cultivars and conducted more detailed evaluation of plant growth and physiological status. Plants were grown in a greenhouse in PVC tubes (1 m tall × 10 cm diameter) filled with a fritted clay growing medium, under well-watered and moisture stress conditions, either inoculated with ACC+ bacteria or non-inoculated. Plants were evaluated for leaf relative water content, biomass, and root traits. After four weeks in the drought stress treatment, leaves of inoculated plants had greater relative water content than leaves of the control treatment, indicating that they were better able to acquire or conserve water compared to non-inoculated plants. In the next study, we evaluated growth and seed yield of a cultivar with a weak response to ACC+ bacteria together in the same tube with a cultivar with a strong positive response. We found that under drought stress and bacterial inoculation, the weak-responding cultivar produced more biomass and yielded more grain when grown with a strong responder. This result supports our hypothesis that root exudates of certain cultivars can improve the performance of other cultivars by enhancing the numbers or activity of ACC+ bacteria in the rhizosphere. Preliminary metabolomics analysis has shown that root exudates of wheat cultivars differ and that oxalic acid may be an important chemical factor that distinguishes exudates of strong responders from weak responders.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Edae, E.A., P.F. Byrne, S.D. Haley, M.S. Lopes, and M.P. Reynolds. 2014. Genome wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theoretical and Applied Genetics 127:791807.
  • Type: Other Status: Published Year Published: 2014 Citation: Byrne, P., Pendell, D., and Graff, G. 2014. Labeling of Genetically Engineered Foods. CSU Extension Fact Sheet no. 9.371. Available at http://www.ext.colostate.edu/pubs/foodnut/09371.html
  • Type: Journal Articles Status: Submitted Year Published: 2015 Citation: El-Feki, W., Byrne, P.F., Reid, S.D., and Haley, S.D. Registration of CO940610/Platte Wheat Doubled Haploid Mapping Population. Submitted to Journal of Plant Registrations.
  • Type: Journal Articles Status: Submitted Year Published: 2015 Citation: Becker, S.R., Byrne, P.F., Reid, S.D., Bauerle, W.L., McKay, J.K., and Haley, S.D. Root traits contributing to drought tolerance of synthetic hexaploid wheat. Submitted to Journal of Experimental Botany.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zuber, T., D. Holm, P. Byrne, L. Ducreux, M. Taylor, M. Kaiser and C. Stushnoff. 2014. Optimization of in vitro inhibition of HT-29 colon cancer cell cultures by Solanum tuberosum L. extracts. Food and Function. DOI: 10.1039/c4fo00649f
  • Type: Theses/Dissertations Status: Published Year Published: 2014 Citation: Becker, S.R. 2014.Exploiting drought tolerance traits and genetic diversity of synthetic hexaploid wheat in winter wheat breeding. PhD dissertation. Colorado State University, Fort Collins.
  • Type: Other Status: Published Year Published: 2014 Citation: Genetically Modified (GM) Crops: Techniques and Applications, CSU Extension Fact Sheet no. 0.710, August, 2014. http://www.ext.colostate.edu/pubs/crops/00710.html


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

Outputs
Target Audience: The primary target audience is the scientific community interested in wheat breeding and genetics. This group was reached through presentations at scientific conferences, publications in peer-reviewed journals, and in graduate student theses and dissertations. A secondary audience is grower groups, who were reached through presentations at field days and annual meetings. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Under the project described above, graduate student Erena Edae developed skills and expertisein wheat phenotypic evaluation, genetic analysis, and scientific communication. This project was the basis for Mr. Edae's Ph.D. dissertation, which he successfully defended in Summer, 2013. Based on the experience gained through this project, he obtained a post-doctoral position with USDA-ARS in Manhattan, KS. How have the results been disseminated to communities of interest? Results were disseminated through peer-reviewed publications (one already published in The Plant Genome, and another accepted for publication in Theoretical and Applied Genetics); and through presentations at professional meetings (Crop Science Society of America and Plant and Animal Genome). What do you plan to do during the next reporting period to accomplish the goals? The specific project described above has been completed. We will continue with our efforts in other wheat populations to identify and characterize QTL responsible for yield and drought tolerance traits.

Impacts
What was accomplished under these goals? This reportwill focus on one specific project undertaken as part of these goals, namelygenome-wide association mapping for yield, yield components,and drought tolerance-related traitsin spring wheat. The population of 294 wheat cultivars and lines was obtained from the International Maize and Wheat Improvement Center (CIMMYT), with the understanding that Colorado State University would evaluate the material under irrigated and limited moisture conditions in Colorado and Ethiopia. Data were collected on a large number of traits at Greeley, CO and Melkassa, Ethiopia.DNA molecular marker data were obtained from CIMMYT for over 1,800 Diversity Array Technology (DArT) markers. The trait and marker data were combined and association mapping undertaken toidentify markers that were significantly associated with the traits of interest.A stable QTL was detected for grain yield on the short arm of chromosome 2D both under irrigated and rainfed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on the short arm of chromosome 1B co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on the long arm of chromosome 1A and 5A. Clusters of QTL for flag leaf characters (area, length and width) were detected on the long arms of chromosomes 3B and 5B.After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield component,s and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs. In a related study, we characterized five drought tolerance candidate genes of wheat for DNA sequence diversity and analyzed sequence differences for associations with phenotypic traits. The gemes were dehydration responsive binding 1A (DREB1A), enhanced response to abscisic acid (ERA1-B and ERA1-D), and fructan 1-exohydrolase (1-FEH-A and 1-FEH-B). The germplasm used was a spring wheat association mapping panel (n=126) grown in Greeley, Colorado and Melkassa, Ethiopia. Our results indicated that DREB1Awas associated with normalized difference vegetation index, heading date, biomass and spikelet number. Both ERA1-A and ERA1-B were associated with harvest index, flag leaf width and leaf senescence. 1-FEH-A was associated with grain yield, and 1-FEH-B was associated with thousand kernel weight and test weight.

Publications

  • Type: Journal Articles Status: Published Year Published: 2013 Citation: El-Feki, W.M., Byrne, P.F., Reid, S.D., Lapitan, N.L.V., and Haley, S.D. 2013. Quantitative trait locus mapping for end-use quality traits in hard winter wheat under contrasting soil moisture levels. Crop Science 53:1953-1967.
  • Type: Theses/Dissertations Status: Published Year Published: 2013 Citation: Edae, E. 2013. Association mapping for yield, yield components, and drought tolerance traits in spring wheat grown under rainfed and irrigated condition. Ph.D. dissertation. Colorado State University, Fort Collins, CO.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Edae, E.A., P.F. Byrne, H. Manmathan, S.D. Haley, M. Moragues, M.S. Lopes, and M.P. Reynolds. 2013. Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat. The Plant Genome vol. 6, issue 2, doi:10.3835/plantgenome2013.04.0010.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Comas, L., Becker, S., Cruz, M.V., Byrne, P.F., and Dierig, D.A. 2013. Root traits contributing to plant productivity under drought. Frontiers in Plant Science doi: 10.3389/fpls.2013.00442.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Enjalbert, J.-N., Zheng, S., Johnson, J.J., Mullen, J.L., Byrne, P.F., and McKay, J.K. 2013. Brassicaceae germplasm diversity for agronomic and seed quality traits under drought stress. Industrial Crops and Products 47:176-185.


Progress 07/01/12 to 12/31/12

Outputs
OUTPUTS: This report covers just six months of this new project. It will focus on a study to detect markers linked to drought tolerance traits in an association mapping panel of spring wheat lines from the International Maize and Wheat Improvement Center. The 284 lines had been evaluated for phenotypic traits in wet and dry environments in Greeley, CO and Melkasa, Ethiopia. They had also been genotyped for a genome-wide set of DArT markers. For a subset of 126 lines, DNA sequences were obtained for five drought tolerance candidate genes (DREB1A, ERA1-B, ERA1-D, 1-FEH-A, and 1-FEH-B). The sequences were assembled and aligned for identification of single nucleotide polymorphisms (SNPs) within each gene. Differences were observed among the candidate genes for nucleotide diversity and patterns of linkage disequilibrium. Orthologous genes (i.e., the two ERA1 genes and the two 1-FEH genes) also demonstrated differences for some sequence variability parameters. SNPs within all genes were significantly associated with yield, yield component, morphological, and phenological traits in at least some environments. In general, more SNP-trait associations were detected for the ERA1 and 1-FEH genes than the DREB1A gene. PARTICIPANTS: Research Associate Scott Reid provided technical assistance for the field and lab portions of the project. Graduate students Erena Edae, Steve Becker, Wahid Mahmoud, Sarah Grogan, Craig Beil, and Melaku Mekonnen conducted dissertation or thesis research. Undergraduate students Angie Moore and Brian Campbell received training in trait evaluations and DNA analysis. TARGET AUDIENCES: The primary target audience consists of plant breeders and geneticists interested in the genetics of drought tolerance traits. This audience was reached through the poster presented at the Crop Science Society of America annual meeting. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Most of the significant trait associations were detected in non-moisture stressed environments, whereas we had hoped to find associations with traits under drought stress. This difference is likely due to the more uniform growing conditions of favorable environments, leading to more accurate estimates of phenotypic trait values. The reported results are encouraging, but need to be further validated in different genetic backgrounds. If confirmed, the results can be applied in functional marker-assisted breeding and to search for novel alleles at the evaluated candidate genes.

Publications

  • Edae, E., Byrne, P., Haley, S., Moragues, M., Reid, S., Lopes, M., and Reynolds, M. 2012. Association mapping for drought tolerance traits in spring wheat grown under rainfed and irrigated conditions. Crop Science Society of America Annual Meeting, Oct. 21-24, 2012, Cincinnati, OH. Abstract 73126.