Neofunctionalization Of Homoeologs Explains Multiple Mechanisms Of Chromosome Pairing Control Associated With the Ph1 Gene Of polyploid Wheat

Identified in 1958, the Ph1 gene was the first chromosome pairing regulator and homology search gene identified in eukaryotes. The Ph1 gene regulates chromosome pairing in polyploid wheat by differentiating homologs from homoeologs/orthologs. Multiple studies have shown that the Ph1 gene effect is mainly manifested by the 5B copy of the gene although the 5D copy was also shown to have a weak effect. This was evident from the higher order pairing observed in the absence of 5B that was not prevalent in the absence of 5D. Moreover, increased dosage of 5A or 5D does not compensate for the loss of 5B. Several conflicting hypotheses have been proposed for the Ph1 gene function. We have identified a gene (C-Ph1) silencing of which resulted in a phenotype similar to that of the Ph1 gene mutations. The gene has three structural copies which have both structure as well as expression pattern differences suggesting multiple functions explaining the observations and hypotheses for the Ph1 gene action. The 5B copy of the gene has a novel 60bp insertion resulting in two alternate splice variants that are very different from the 5D or the 5A copies. The 5A copy has a large 366bp deletion relative to 5D copy possibly rendering the corresponding protein ineffective. The expression of the 5B copy increased 39-fold between late prophaseI and metaphaseI coinciding with the expected stage for the Ph1 gene function. Differential expression pattern of the 5B copy along with the disruption of chromosome alignment on the metaphaseI plate in C-Ph1 silenced plants support one of the suggested Ph1 gene function via centromere-microtubule interaction. The gene also has orthologs in other diploid species including maize, rice, barley, and Brachypodium that resemble more with the 5D copy suggesting it to be the conserved and ancestral version of the gene. Novel function of the 5B in regulating homoeologous chromosome pairing evolved via polyploid-specific insertions, alternate splicing, and/or highly specific expression during MI stage. The neo-functionalized version of the gene as seen in the 5B copy, probably is present only in the polyploid species.