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Title: Dynamic evolution of alpha-gliadin prolamin gene family in homeologous genomes of hexaploid wheat

item HUO, NAXIN - University Of California, Davis
item ZHU, TINGTING - University Of California, Davis
item Altenbach, Susan
item DONG, LINGLI - Chinese Academy Of Sciences
item WANG, WI - University Of California, Davis
item Mohr, Toni
item LIU, ZHIYONG - Chinese Academy Of Sciences
item DVORAK, JAN - University Of California, Davis
item WANG, DAOWEN - Chinese Academy Of Sciences
item LUO, MING-CHENG - University Of California, Davis
item Gu, Yong

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/13/2018
Publication Date: 3/26/2018
Citation: Huo, N., Zhu, T., Altenbach, S.B., Dong, L., Wang, W., Mohr, T.J., Liu, Z., Dvorak, J., Wang, D., Luo, M., Gu, Y.Q. 2018. Dynamic evolution of alpha-gliadin prolamin gene family in homeologous genomes of hexaploid wheat. Scientific Reports. 8:5181.

Interpretive Summary: The end-use quality of wheat flour is primarily determined by wheat seed storage proteins called prolamins. However, wheat prolamins are also the major triggers of food allergies and intolerances such as celiac disease. Among the wheat prolamins, alpha-gliadins are important because they are abundant in wheat flour and contain the most significant triggers of the immune response in celiac patients. To better understand the properties of the genes encoding wheat prolamins, we determined high-quality DNA sequences of the chromosome regions that span the three alpha-gliadin gene loci in the bread wheat cultivar "Chinese Spring". Among a total of 47 alpha-gliadin genes we identified, 25 encode full-length alpha-gliadin proteins and 22 were inactive due to mutations. The sequences of the full complement of alpha-gliadin genes not only allows us to understand their evolutionary relationships, but also provides a better picture of the distribution and levels of protein regions that trigger wheat allergies. For instance, we found that a single insertion/deletion event in the evolution of alpha-gliadin genes in one of the three subgenomes of bread wheat resulted in generation of the one of the most toxic amino acid sequences for celiac patients. The knowledge gained from this study will provide insights into the roles of the alpha-gliadins in flour functionality and human health as well as facilitate the development of novel strategies for breeding elite wheat varieties with improved end-use traits and reduced immunogenic potential.

Technical Abstract: Bread wheat is an allohexaploid species containing the three closely related A, B, and D subgenomes. Homeologous Gli-2 loci located on chromosomes 6A, 6B and 6D encode complex groups of alpha-gliadin seed storage proteins that contribute to the functional properties of wheat flour, but also trigger the serious food intolerance celiac disease (CD). A better understanding of the genomic organization of the alpha-gliadins will provide knowledge to produce wheat with better end-use properties and reduced immunogenic potential for human consumption. The Gli-2 loci contain several tandemly duplicated genes and highly repetitive DNA, making sequence assembly of these genomic regions challenging. To gain insight into the origin and evolution of alpha-gliadin genes, we constructed high-quality genomic sequences spanning the three homeologous loci by aligning hexaploid wheat PacBio-based genome sequence contigs with restriction enzyme-based BioNano genome maps. Following validation of sequence assembly, a total of 47 alpha-gliadin genes were identified, 26 of which encoded full-length proteins; the remainder were pseudogenes. Alpha-gliadin genes are the youngest and largest group of wheat prolamin genes and originated from duplication and translocation of other gliadin genes from a different location. Analyses of the genomic organization and phylogenetic tree reconstruction indicate that significant expansion of alpha-gliadin genes occurred rapidly and independently in the last 2.4 to 2.5 million years after the divergence of the A, B and D subgenomes. Transcriptome analysis showed an equally dramatic divergence in expression of alpha-gliadin genes. The greater than 50-fold expression differences among full-length intact genes could not be attributed to sequence variations in the promoter regions. The study also provided insights into the evolution of CD epitopes and identified a single indel event in the hexaploid wheat D subgenome that likely resulted in the generation of the highly toxic 33-amino acid CD epitope. This research will help to define targets for improvements in the functional and immunogenic properties of wheat flours.