| Most of the higher plants, including some of the most important crop plants, are polyploids or ancient polyploids. The Ph1 (Pairing homoeologous 1) gene regulating chromosome pairing in wheat by differentiating homologous from homoeologous/non-homologous pairing was discovered in 1958 but was so far not cloned. 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 and 5A copies. In 2008, we had shown that the Ph1 gene localizes to a ∼2.5 Mb chromosomal region that is conserved in rice as a 450kb region containing 91 genes. These were analyzed for their putative function on the basis of detailed domain/motif analyses. Virus induced gene silencing of the selected candidates identified a gene (C-Ph1) , transient as well as stable silencing of which resulted in a phenotype characteristic of the Ph1 gene mutations. The gene has three structural copies which have both different structure as well as expression pattern 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 has a large 300bp deletion relative to 5D copy possibly rendering the corresponding protein ineffective. Specifically, the expression of the 5B copy increased 32-fold between prophase-I and metaphase-I coinciding with the expected stage for the Ph1 gene function. Furthermore, the C-Ph1 copy proteins are DNA-binding each with a different nucleic acid binding site again suggesting different functional properties. The gene also has orthologs in other diploid species including maize, rice, barley, and Brachypodium that are similar to the 5D copy suggesting it to be the conserved and ancestral version of the gene. Novel function of the 5B copy in regulating homoeologous chromosome pairing evolved due to polyploid-specific insertions, alternate splicing, and/or highly specific expression during metaphase-I stage. |
