Transcriptome Evolution Of The BBAA Component Of Bread Wheat During The Allohexaploid Trajectory

Speciation of common wheat was achived via allohexaploidization, which actsas main determinant for adaptation of bread wheat to surrounding environment. Atearly stage of the speciation, alternations in expression level of a large amount ofgenes in allohexaploid wheat indicated extensive interactions and discord amongunderlying subgenomes. An interesting question, during the evolution process anddomestication in past ten thousand years, whether expression level changes of thosegenes and interactions among subgenomes remain still as at the time that bread wheatspeciation, was raised and motivated us to pursue the answer. Fortunately, a ploidy-reversed wheat (Extracted-tetra), combined with various natural tetraploid wheat aswell as bread wheat, provides a unique opportunity to address the question. In thisstudy, techniques, such as microarray-based transcriptome profiling, quantitativeReal-Time PCR (qRT-PCR) and pyrosequecing, were employed to investigate thegenes that were reversible and irreversible underlying BB and/or AA subgenomes ofbread wheat in transcriptome.The integrity of subgenomes in bread wheat (BBAADD) makes extraction of itsBBAA component possible to restitute a novel ploidy-reversed wheat. Availability ofsuch ploidy-reversed wheat (Extracted-tetra) provides a unique opportunity to addresswhether and to what extent the BBAA component of bread wheat has been modifiedin karyotype and gene expression during the evolutionary trajectory as allohexaploidy,and their phenotypic effects. We report here that Extracted-tetra was severelydeteriorated in multiple phenotypic traits, but maintained a stabilized karyotype.Microarray-based transcriptome profiling identified a large number of differentiallyexpressed genes between Extracted-tetra and natural tetraploid wheat (T. turgidum),and the Extracted-tetra down-regulated genes were enriched for distinct GOcategories. qRT-PCR analysis showed that gene expression differences betweenExtracted-tetra and a set of diverse durum wheat cultivars were distinct from thosediverged at the tetraploid level. Pyrosequencing on51genes from the B and Asubgenomes of both Extracted-tetra and natural tetraploid revealed both concordantand independent alterations to the B and A homeologous transcripts in Extracted-tetra.Great majority of the genes showed additive expression in a resynthesizedallohexaploid wheat (parented by Extracted-tetra), confirming their irreversibility.Analysis of a synthetic allohexaploid wheat (parented by T. turgidum) and diversebread wheat cultivars revealed evidence for rapid occurrence of expression changes tothe BBAA subgenomes subsequent to allohexaploidization, and their evolutionaryperseverance. Then we report that the Extracted-tetra vs. T. turgidum differentiallyexpressed genes have been more prone to immediate modification in expressionfollowing allohexaploidization than those that did not differentiate in expression between the two types of tetraploid wheat. Expression analysis of the BBAAsubgenomes for a great majority of the189gene×genotype comparisons shows thatthey are highly conserved in the course of natural and breeding selection in thesebread wheat cultivars, which implicates that at least certain portion of the irreversiblegene expression modifications to the BBAA component of bread wheat should haveoccurred early and are under selective constraint.In contrast to the large number of genes encoded by the BBAA subgenomes ofcommon whea, which showed irreversible changes in expression after removing or re-adding the DD subgenomes, those showing reversible changes in expression(evidenced by nonaddtive expression in the resynthesized allohexaploid wheat XX329)are small in number. This suggests that only limited interactions between subgenomesof bread wheat are preserved in the contemparary common wheat cultivars.Expression analysis in a series of materials including a common wheat (TAA10), anExtracted-tetra wheat, a resynthesized allohexaploid wheat (and its middle-parentvalue or MPV), identified185genes, the expression of which by BBAA wassuppressed to variable extents by the DD subgenome. Further, expression of28ofthese185genes was analyzed in a large set of common wheat cultivars of diverseorigins and in five newly sytnhesized hexaploid wheats. We found that (1) only asmall number of genes showed immediate expression supression in the syntheticwheats, but the altered expression patterns are largely conserved in many of thecommon wheat cultivars;(2) most of the genes did not show immediate suppression,however, suppressed expression for majorrity of these genes are seen in majority ofthe common wheat cultivars. Together, it appeared that intersubgenomic suppressionof gene expression is likely a general phenomenon in common wheat, which mayhave either occured immediately after allohexaploidization or evolved so duringevolution and domestication of common wheat. Irrespective o the timing of theirgenesis, the suppressive patterns are conserved in many of the common wheatcultivars.