Webinar: Challenges and opportunities in positional cloning and structural variation in polyploid crops

Presenter

Ellie Taagen, PhD candidate, Cornell University, USA

Outline

Genomic structural variations are common among polyploids, but SNP-based approaches to characterize genetic diversity are frequently insensitive to these variants.

In this webinar we will present the results of a study we conducted to characterize a large deletion on wheat chromosome arm 5AS that had previously been misidentified as quantitative trait loci (QTL) harboring a causal gene for increased grain weight. Leveraging a fine-mapping population, genomic data, phenotypic associations, early grain development transcriptome profiles, and predicted gene function, we determined the QTL was a result of strong linkage disequilibrium with chromosome arm 5AS presence or absence.

This study highlights that chromosome structural variation linkages can overpower the considerable resources required for positional cloning and we present recommendations for more successful approaches to identifying causal variants. We also present nine candidate genes on chromosome arm 5AS that may impact yield components, laying the foundation for identifying hidden variation of homoeolog dosage-dependent and functionally redundant genes on the group five chromosome short arms.

Taken together, the discovery demonstrates the phenotypic resiliency of polyploid genomic structural variation and highlights a considerable challenge to routine positional cloning in wheat. All analysis conducted is reproducible and publicly available as a learning resource on GitHub.

References

• Taagen, E., Tanaka, J., Gul, A., & Sorrells, M. E. (2021). Positional-based cloning ‘fail-safe’ approach is overpowered by wheat chromosome structural variation. Plant Genome. 2021; https://doi.org/10.1002/tpg2.20106
• GitHub repository learning resource: https://github.com/etaagen/Taagen_2021_TPG

Recording