2013 Annual Report
1a.Objectives (from AD-416):
1) Apply molecular biology and genomics to understand the structure, function and expression of wheat seed protein genes;.
2)Contribute to the understanding of the organization of the wheat genome, with a focus on the group 1 chromosomes; and.
3)Develop and utilize Brachypodium as a model system for Triticeae research for grain quality and other traits.
1b.Approach (from AD-416):
1) Use combinations of molecular alterations, heterologous expression, and plant transformations in the application of molecular biology and genetic engineering to wheat high-molecular-weight (HMW) glutenin class seed storage protein genes and other seed protein classes to understand more of the molecular bases of wheat quality and utilization. .
2)Contribute to the understanding of the organization of the wheat genome through in-depth studies of wheat seed protein genetic loci and participation in national and international wheat genome characterization projects. .
3)Employ DNA microarrays to profile gene expression during wheat seed development and changes in storage protein gene activity and wheat quality..
4)Contribute to the development of Brachypodium as a model for small grains research, to include use in studying wheat seed protein gene controls. BSL-1 (4/08). Previously was 5325-21430-011-00D (10/03). Replacing 5325-21000-011-00D (04/08).
This is the final report for this project which was terminated on 5/12/2013 and replaced by 5325-21000-019-00D, "Enhancement of Wheat through Genomics and Molecular Approaches". Important discoveries were achieved under this project, including the following: The draft of the genome for bread wheat was completed and published as an original research article in Nature; An integrated genetic and physical map for wheat (D genome) was developed; genomic markers (RJMs and SNPs) were developed to accelerate wheat germplasm improvement by marker assisted selection; A new class of gliadin genes and proteins were characterized; bread wheat lines deficient in specific seed storage proteins were generated as an initial step to develop healthier wheat varieties; Genes critical for the development of cold tolerance in wheat were identified. Significant results were also accomplished in our collaborative effort to develop and utilize Brachypodium as a model system for Triticeae research for grain quality and other traits: The draft of the Brachypodium genome was completed and was also published in Nature; Results from the deep sequencing of genes expressed in Brachypodium were released to the public; T-DNA tagged lines of Brachypodium were generated and distributed to the public; and the major seed storage protein in Brachypodium was identified.
A new class of wheat gliadin proteins identified. Analysis of the sequenced genome and expressed genes of bread wheat and its relatives made it possible for ARS scientists to identify a new class of wheat seed gliadin genes and proteins. The major seed storage proteins including gliadin are the major determinant of the quality of wheat dough processing, thus, the complete identification of the components that form the gluten polymer is important. The wheat gluten-proteins are also associated with gluten-related disorders including celiac-disease. The identification of new gluten proteins reported here is a step in developing a successful strategy to eliminate or reduce causative factors for gluten-sensitivity.
A new wheat germplasm released. ‘Dy10-DLC’ wheat, an elite line deficient in one of the high molecular weight subunit proteins will be useful in understanding the roles of different prolamin proteins in dough processing. Dy10-DLC, together with other glutenin deficient lines, will be useful in the development of low-gluten wheat that is safer for consumers with gluten-related sensitivity. The shorter mixing time exhibited by D10-DLC, could provide a genetic source to manipulate to shorten dough development. A shorter dough development time could potentially save significant energy cost in commercial bread production.
Bread wheat genome sequenced. Using the latest technologies in DNA sequencing ARS scientists together with their international collaborators completed the whole-genome shotgun sequencing of common bread wheat. Analysis of the sequence and structure of the large and complex wheat genome revealed the identity of more than 94,000 encoded genes. This new genetic resource will facilitate the development of tools and strategies to improve wheat germplasm. This is a major step in meeting the challenges of maintaining/improving wheat yield and quality in a changing environmental condition.
Chingcuanco, D.L. 2013. Registration of ‘Dy10-DLC’ wheat. Journal of Plant Registrations. doi: 10.3198/jpr2012.08.0019crg.
Munkvold, J.D., Chingcuanco, D.L., Sorrells, M. 2013. Systems genetics of environmental response in the mature wheat embryo. Genetics. doi:10.1534/genetics.113.150052.
Anderson, O.D., Dong, L., Huo, N., Gu, Y.Q. 2012. A new class of wheat gliadin genes and proteins. PLoS One. 7:e52139.
Anderson, O.D., Huo, N., Gu, Y.Q. 2013. The gene space in wheat: the complete y-gliadin gene family from the wheat cultivar Chinese Spring. Functional and Integrative Genomics. 10.1007/s10142-013-0321-8.
Nyaku, S.T., Kantety, R.V., Gu, Y.Q., Venkateswara, S.R., Sharma, G.V., Lawrence, K. 2013. Sequencing and characterization of full-length sequence of 18S rRNA gene from the reniform nematode. PLoS One. 8:e60891.
You, F., Huo, N., Gu, Y.Q., Lazo, G.R., Dvorak, J., Anderson, O.D. 2009. ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery. BMC Bioinformatics. 10:331.
Alnemer, L.M., Seetan, R., Bassi, F.M., Chitaranjan, C., Helsene, A., Loree, P., Goshn, S.B., Gu, Y.Q., Luo, M.C., Iqbal, M., Lazo, G.R., Kianian, S.F., Denton, A.M. 2013. Wheat Zapper: a flexible online tool for colinearity studies in plants. Functional and Integrative Genomics. 13:11-17.
Michalak De Jimenez, M.K., Bassi, F.M., Ghavami, F.G., Simons, K., Dizon, R., Setan, R.I., Alnemer, L.M., Denstin, A.M., Dogramaci, M., Simkova, H., Dolezel, J., Seth, K., Luo, M., Dvorak, J., Gu, Y.Q., Kianian, S.F. 2013. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat. Functional and Integrative Genomics. 13:19-32.
Luo, M., Gu, Y.Q., You, F., Deal, K.R., Ma, Y., Hu, N., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C.M., Zhang, Y., Mcguire, P.E., Pastrnak, S., Stein, J.C., Ware, D.H., Mccombie, W.R., Juanuan, S.F., Martis, M.M., Mayer, K.F., Sehgal, S., Gill, B.S., Bevan, M.W., Dolezel, J., Lazo, G.R., Anderson, O.D., Dvorak, J. 2013. A 4-gigbase physical map unlocks the structure and evolution of the complex genome of Aegilop tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences. 110:7940-7945.
Anderson, O.D. 2013. The B-hordein prolamin family of barley. Genome. 56:179-185.