Genome-wide association study of copy number variation in flax through the lens of genome integrity

Classical methods for identification of genetic variants associated with certain macroscopic phenotypic traits are, as a rule, limited to analyses of single nucleotide polymorphisms. Copy number variations, and more broadly structural variants may provide a plethora of useful information due to the magnitude of the changes they induce. However, their use in genome-wide association studies is seriously limited mostly due to the uncertainties in their discovery (i.e., failure to resolve an event with nucleotide resolution) by computational algorithms from genomic data. Nevertheless, in certain cases, such analyses are possible and may still yield valuable results. Our recent work has revealed genetic variants (single nucleotide polymorphisms) possibly related to phenotypic traits determining fibre quality. Here, we decided to extend the analyses to structural variants, namely copy number variations. Importantly, we use a novel high-coverage dataset allowing for accurate prediction of copy number variations. Overall, we compiled a list of 41 candidate genes associated with five quantitative phenotypic traits. Furthermore, the genome stability metric developed earlier facilitated stratification of copy number variant loci with regard to their stability. On the whole, our analyses suggest that the genomic regions less resilient to external and internal stresses are more susceptible to changes associated with the studied phenotypic traits.

Linum usitasissimum L, copy number variation, genome integrity, Linum usitasissimum L, flax-fiber, Genome-Wide Association Study