Significance Maintaining diploid-like pairing behavior is essential for a polyploid to establish as a new species. The Pairing homeologous 1 ( Ph1 ) gene, regulating such behavior in polyploid wheat, was identified in 1958, but its molecular function remained elusive. The present communication reports identification of the candidate Ph1 ( C-Ph1 ) gene that is expressed exclusively during meiotic metaphase I, whose silencing resulted in formation of multivalents like the Ph1 gene mutations. Although the C-Ph1 gene has three homoeologous copies, the 5B copy has diverged in sequence from the other two copies. Heterologous gene silencing of the Arabidopsis homologue of the C-Ph1 gene also confirmed its function. Molecular characterization of this gene will make it possible to develop precise alien introgression strategies.

Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76–87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.