Structural Variation of a Wheat Chromosome Arm Revealed By Optical Mapping

Optical mapping in nanochannel arrays (BioNano mapping) provides an affordable approach to validate and improve DNA sequence assemblies and to study structural variation among individuals, cultivars or species. Coupling the optical mapping with flow sorting of individual chromosomes of bread wheat enables zooming in on particular regions of the complex (17 Gb) and hexaploid genome, making the studies more cost-efficient and reliable. In this work we purified 7DS chromosome arm (381 Mb) from ditelosomic lines of two accessions - cv. Chinese Spring (CS) and CI2401 - in which 7DS arm is maintained as a pair of stable telocentric chromosomes. Using Irys platform, we generated 68 (180x) and 78 Gb (206x) size-filtered data for CS and CI2401, respectively. The data were assembled into 371 (CS) and 468 (CI2401) genome maps with N50 of 1.3 Mb for both accessions. Comparison of the two maps showed a high degree of similarity between them. 83% of the CI2401 optical map length could be aligned to the CS map under high stringency. Alignment of the optical maps to a reference genome, generated from ‘Chinese Spring’ by IWGSC, revealed a significant variability in (sub)telomeric and (peri)centromeric regions. The two accessions differ in susceptibility to Diuraphis noxia and we previously located a gene underlying resistance to this pest to a 350-kb region on the 7DS. Comparison of optical maps spanning the region disclosed a 8-kb insertion in the proximity of a candidate gene in the susceptible ‘Chinese Spring’. The variable regions will be scrutinized on the sequence level.