Identification of subtelomeric sequences involved in specific homologous chromosome pairing in bread wheat

Abstract

Proper homologue recognition is required in order to ensure ordered pa1nng and legitimate recombination during meiosis. In a polyploid such as bread wheat, (hexaploid, 2n = 6x = 42), which has three related genomes (A, B and 0), the presence of homoeologous (related) chromosomes complicates the picture, since homologues also need to be distinguished from homoeologues (related) before the chromosomes can pair in an ordered way. The mechanism by which homologues identify one another is the most poorly understood aspect of meiosis. lt is accepted that the distal region of the chromosomes including the subtelomeric region, is critica! to the process of homologue recognition and pairing in many organisms, but the specific role of subtelomeres is still unclear. The Wheat Genome lnitiative has followed a flow cytometry strategy to separate 1 O chromosomes one by one or in groups, the construction of a tiling BAC physical map, and subsequent sequencing of each chromosome using a BAC-by-BAC strategy. The limitations of a shotgun correct assembly and annotations of wheat genome hinder sequencing and assembly of large and repetitive genomes. Currently only a pseudochromosome for wheat chromosome 38 is available. Therefore, the ldentification and molecular characterization of subtelomeric sequences in wheat chromosome arms is a challenge. The strategy we used consisted in consider a specific subtelomeric B-wheat probe contained in BAC clone 205008, which is located in the terminal bin 4BL-1 O (0,95-1 ,0) (Salina et al., 2009). In order to get a Chromosome 4BL contig including a subtelomeric region we used the application Blastn.sh in a MobaXterm Personal Edition v7.6 terminal screen connected to Picasso supercomputer (Plataforma Bioinformática Andaluza, Universidad de Málaga), which provides a basic set of Linux commands. A 5356 nt contig from chromosome 4BL was extracted from 4BL genomic chromosome arm using the BAC clone 205008 subtelomeric fragment. This strategy allowed us to isolate hypothetical subtelomeric contigs from the A, B and O wheat genomes. Currently we are validating by FISH the location of such subtelomeric probes in order to perform their molecular characterization.