Isolation of the major wheat domestication gene Tenacious glume1 reveals its multiple phenotypic effects and sheds light on evolution of wheat

Mutations at the Tenacious glume1 (Tg1) loci on chromosome 2A, 2B, and 2D were pivotal for evolution of free-threshing wheat. Here, we identified and validated a Tg1 candidate gene. The wheat 2A- and 2B-loci each contained a single copy of the gene but the 2D-locus was multigenic with at least one of the genes having a frameshift mutation. We found no fixed mutation in CDSs of the 2A- and 2B-genes and suggest that cis-regulatory mutations have led to evolution of free-threshing tetraploid wheat. Tg1 is equivalent to barley ELI-A gene controlling the development of leaf ligule and to the bread wheat reduced-height locus Rht8. In addition, mutations of Tg1 affected spike length, density, shape, and fertility, leaf rigidity, and lodging. Fluorescence in situ hybridization revealed association of Tg1 expression with vascular bundles and tissue boundaries. Durum wheat near isogenic lines harboring non-free-threshing and free-threshing 2B-alleles differed in the abundance of glume sclerenchyma. Our search for differentially expressed genes in the comparison of CRISPR/Cas9 free-threshing mutants vs the non-free-threshing parental line yielded genes for biogenesis of cell wall and cell wall functions. Past selection was centered on the 2A- and 2B-loci in durum wheat, but selection was primarily centered on the 2D-locus in bread wheat. This is consistent with the tetraploid parent of hexaploid wheat being free-threshing. Our haplotype analyses pinpointed the origin of hexaploid wheat in Iran, showed that European and Asian spelt originated separately and confirmed that European spelt and most Asian spelt were derived from free-threshing hexaploid wheat.