Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Using Seven De Novo Genome Assemblies.

Genomic characterization of has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of . All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a -mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among genotypes. We leveraged linkage maps constructed from F progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for to accelerate future research efforts.