Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat

Wheat Gli-2 loci encode complex groups of alpha-gliadin prolamins that are important for breadmaking, but also major triggers of celiac disease (CD). Elucidation of alpha-gliadin evolution provides knowledge to produce wheat with better end-use properties and reduced immunogenic potential. The Gli-2 loci contain a large number of tandemly duplicated genes and highly repetitive DNA, making sequence assembly of their genomic regions challenging. Here, we constructed high-quality sequences spanning the three wheat homeologous alpha-gliadin loci by aligning PacBio-based sequence contigs with BioNano genome maps. A total of 47 alpha-gliadin genes were identified with only 26 encoding intact full-length protein products. Analyses of alpha-gliadin loci and phylogenetic tree reconstruction indicate significant duplications of alpha-gliadin genes in the last similar to 2.5 million years after the divergence of the A, B and D genomes, supporting its rapid lineage-independent expansion in different Triticeae genomes. We showed that dramatic divergence in expression of alpha-gliadin 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 genome that likely resulted in the generation of the highly toxic 33-mer CD epitope.