Homoeologous Pairing and Molecular Genotyping Reveal New Evolutionary Evidence of Wheat B Genome

Hexaploid wheat (Triticum aestivum L., 2n=6x = 42, AABBDD) originated from interspecific hybridization of three diploid ancestors followed by spontaneous chromosome doubling. Genomes A and D are derived from T. urartu (2n=2x=14, AA) and Aegilops tauschii (2n=2x=14, DD), respectively. The origin of B genome, however, remains controversial although Ae. speltoides (2n=2x=14, SS) has been considered the ancestor of B genome. Here we used a complete set of wheat B genome-Ae. speltoides disomic substitution lines, which dissected S genome into individual chromosomes in the wheat background by homoeologous S/B chromosome substitution, to investigate homoeologous pairing between individual B-genome and S-genome chromosomes in the presence and absence of Ph1 gene. We observed a significant higher pairing frequency between 1B and 1S (50.00%) than any other B-S homoeologous pairs (0.00-3.47%) in the presence of Ph1. No pairing was observed between 6B and 6S in 103 meiotic cells at metaphase I. In the absence of Ph1 (i.e. ph1bph1b genotype), pairing frequencies of the homoeologous pairs 1B-1S (60.00%), 2B-2S (67.21%), 4B-4S (52.21%), and 5B-5S (42.16%) were substantially higher than 3B-3S (21.30%), 6B-6S (16.67%), and 7B-7S (25.00%). Thus, meiotic pairing of the individual B-S homoeologous pairs was differentially enhanced by ph1b. All seven B-S homoeologous chromosome pairs were genotyped by the wheat 90K SNP array. Comparative analysis of the SNP data identified highly homologous regions in chromosomes 1B and 1S. All these results suggest varied levels of homology in different B-S homoeologous chromosome pairs with highest in 1B-1S.