Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat

Abstract

The Q gene encodes an AP2 -like transcription factor that played an important role in domestication of polyploid wheat. The chromosome 5A Q alleles ( 5AQ and 5Aq ) have been well studied, but much less is known about the q alleles on wheat homoeologous chromosomes 5B ( 5Bq ) and 5D ( 5Dq ). We investigated the organization, evolution, and function of the Q/q homoeoalleles in hexaploid wheat ( Triticum aestivum L.). Q/q gene sequences are highly conserved within and among the A, B, and D genomes of hexaploid wheat, the A and B genomes of tetraploid wheat, and the A, S, and D genomes of the diploid progenitors, but the intergenic regions of the Q/q locus are highly divergent among homoeologous genomes. Duplication of the q gene 5.8 Mya was likely followed by selective loss of one of the copies from the A genome progenitor and the other copy from the B, D, and S genomes. A recent V 329 -to-I mutation in the A lineage is correlated with the Q phenotype. The 5Bq homoeoalleles became a pseudogene after allotetraploidization. Expression analysis indicated that the homoeoalleles are coregulated in a complex manner. Combined phenotypic and expression analysis indicated that, whereas 5AQ plays a major role in conferring domestication-related traits, 5Dq contributes directly and 5Bq indirectly to suppression of the speltoid phenotype. The evolution of the Q/q loci in polyploid wheat resulted in the hyperfunctionalization of 5AQ , pseudogenization of 5Bq , and subfunctionalization of 5Dq , all contributing to the domestication traits.

Evidence from principal component analysis for improvement of grain shape- and spikelet morphology-related traits after hexaploid wheat speciation

“…Therefore, the tetraploid wheat genome mainly contributed to grain shape in synthetic hexaploid wheat. It has been considered that the A genome predominantly controls morphological traits including spike shape, grain shape, and thickness of empty glumes in allopolyploid wheat (Peng et al, 2003;Zhang et al, 2011). The predominant effects of the A genome on wheat morphology might result in limitation of the Dgenome contribution to wheat grain shape.…”

QTL analysis of genetic loci affecting domestication-related spike characters in common wheat

“…The Q gene in wheat was cloned as a homolog of Arabidopsis APETALA2 (Simons et al, 2006). Although the Q genes of CS and LDN have identical coding sequences (Simons et al, 2006;Abdollahi et al, 2012), we found an insertion/ deletion 1.5 kb upstream of the translation initiation site of the Q gene (Zhang et al, 2011; Supplementary Fig. S1).…”

“…JF701619) and LDN (acc. JF701620) (Zhang et al, 2011) were aligned using CLC sequence viewer version 6.6.2 (Supplementary Fig. S1).…”

Genomic innovation for crop improvement

“…This formed a stable hexaploid spelt (hulled) wheat, from which a freethreshing derivative was derived by selection. New characteristics such as elastic dough for bread-making were introduced from the A. tauschii genome, with gene dosage effects and pseudogenization contributing to some polyploid-specific traits 58,59 . Genetic diversity in bread wheat was constrained during the domestication of emmer wheat and by the small number of individual plants that contributed to the formation of the new hexaploid bread-wheat species 60 .…”