Exploring the structural variant landscape in the highly dynamic genome of a recent allopolyploid crop species
Final Report Abstract
Long-read sequencing provides unique insight into how genome-wide structural variants (SV) impact crop evolution. By resequencing a species-wide panel of ecogeographically diverse accessions of the recent allopolyploid crop species Brassica napus (oilseed rape, canola, kale, swede/rutagaba), we confirmed that extensive exchanges among homoeologous chromosomes were important drivers in the formation and ecogeographical adaptation of distinct crop forms during B. napus evolution. A comprehensive B. napus pangenome SV Atlas was constructed describing species-wide distribution and frequencies for gene insertions, deletions, presence-absence variations (PAV) and inversions. We confirmed that many SV events contributing to diversification of B. napus crop morphotypes are not in linkage disequilibrium to SNP variants, supporting their more recent role in ecogeographical diversification following the formation of B. napus via allopolyploidisation. Gene presence-absence caused by homoeologous exchanges contributed particularly to differentiation between swede/ rutabaga and oilseed forms, and between winter and spring oilseed ecotypes. Analyses of impacted genes revealed changes of copy number in genes responsible for cell wall development, lignin biosynthesis and flowering regulation. A total of 94 high-quality reference-guided genome assemblies were generated for representative accessions from the publicly available BnASSYST B. napus Diversity Set, which we generated in a previous DFG-funded project as a global resource for B. napus breeding and genetics, covering the four major crop ecotypes of B. napus. The deposition of these assemblies in the public domain provides a comprehensive species-wide genome resource for future B. napus genome research and molecular breeding. Finally, using the generated datasets, we explored the utility of pangenome graphs for expression QTL analysis and elucidated the extent to which eQTL are impacted by SV in gene regulatory regions. Combined with the graph-based genotyping of SVs, we identified a large number of gene-proximal structural variants linked to gene expression regulation.
Publications
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Structural Variants Atlas: Exploring the deletion landscape in the highly dynamic genome of a recent allopolyploid crop species. German Plant Breeding Conference GPZ 2022, Düsseldorf, Germany
Afsharyan N.P., Golicz A.A. & Snowdon R.J.
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Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes. The Plant Genome, 16(2).
Yildiz, Gözde; Zanini, Silvia F.; Afsharyan, Nazanin P.; Obermeier, Christian; Snowdon, Rod J. & Golicz, Agnieszka A.
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Constructing a Brassica napus Structural Variation Pangenome Atlas. 16th International Rapeseed Congress, Sydney, Australia
Afsharyan N.P., Golicz A.A. & Snowdon R.J.
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Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus. openRxiv.
Afsharyan, Nazanin P.; Golicz, Agnieszka A. & Snowdon, Rod J.
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Species-wide genome structural variation in Brassica napus. Plant and Animal Genome XXXI Conference, San Diego, USA
Afsharyan N.P., Golicz A.A. & Snowdon R.J.
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Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus. Theoretical and Applied Genetics, 138(4).
Yildiz, Gözde; Zanini, Silvia F.; Weber, Sven; Kopalli, Venkataramana; Kox, Tobias; Abbadi, Amine; Snowdon, Rod J. & Golicz, Agnieszka A.
