Common wheat (Triticum aestivum L.) is an allohexaploid and consists of three similar genomes A, B and D. Wheat has a large genome size (16 million kb/haploid genome) but nearly 85% of the genome is repetitive DNA. The wheat genome thus can be divided into gene-rich and gene-poor regions. The gene-rich region present around fraction length 0.5 of the long arm of the group 5 chromosomes contains, along with many other important genes, the major chromosome pairing regulator gene, Ph1. The Ph1 regulates bivalent behavior of allohexaploid wheat by allowing only homologous chromosomes to pair with each other during meiosis. To physically characterize this gene-rich region with a special focus on Ph1, wheat ESTs and other group 5 DNA markers were mapped on aneuploids and Ph1 mutants to generate a high-density physical map for the region. The markers mapped to the '5L0.5 region' were compared across the Triticeae to identify agronomically important genes. Ph1 has been localized to the 'Ph1 gene region' encompassed by the breakpoints of the terminal deletion line 5BL-1 on the proximal side and distal breakpoint of the Ph1 gene mutant line ph1c on the distal side. Seven markers mapped in the 'Ph1 gene region' identified orthologous sequences on an approximately 450 KB region on rice (Oryza sativa) chromosome 9, revealing high synteny. Colinearity between the two species was further confirmed by the same marker order for the 'Ph1 gene region'. Twenty-six genes were selected for their putative Ph1 like function based on the presence of functional motifs and domains in 91 genes, present in the 450 kb region of rice including the genes involved in chromatin reorganization and microtubule attachment as key candidates for Ph1. The probes mapped to the 'Ph1 gene region' were used to identify positive BAC clones in barley (Hordeum vulgare) and tetraploid wheat (Triticum turgidum var durum), using Barley BAC library (Hordeum vulgare cv. Morex) and tetraploid wheat (Triticum turgidum var durum cv Langdon) BAC library. These probes identified 301 and 46 clones in the tetraploid wheat and barley BAC libraries, respectively
