Implications of structural genomic variants on agronomical traits in elite winter oilseed rape (Brassica napus L.)

Abstract

Brassica napus L. (oilseed rape) is an allotetraploid crop originated from a spontaneous hybridization event between its two diploid ancestors Brassica rapa L. (turnip) and Brassica oleracea L. (cabbage). It is assumed that this interspecific hybridization took place no more than 7,000 years ago, when turnip rape and cabbage were first cultivated in close proximity to each other. The A and C subgenomes of this relatively recent polyploid crop share highly similar homoeologous chromosomes with conserved gene order. Thus, there is a high probability of homoeologous exchanges during meiosis. Hence, highly frequent structural genome variations (SV), including deletions, insertions, inversion and translocation are expected and have already been demonstrated in several studies. In recent years, long-read sequencing technologies have added a powerful new dimension to eukaryote genomics. Long read sequencing technologies combine great read lengths with acceptable single base accuracies and allow the detection of small- to mid-scale SV that could not be revealed by Illumina short-read sequencing datasets. Applying long-read sequencing to investigate an interconnected multiparental population of European elite winter oilseed rape revealed that ~ 5% of the annotated genes harbored a potentially functional SV event. This relatively high number of intragenic SV justified a more detailed investigation regarding the association of SV with agricultural traits. In the present thesis, genome-wide association studies were performed to investigate flowering time modulation and quantitative blackleg resistance within a multiparental population derived from seven European elite winter oilseed rape cultivars. Several novel QTL were identified and previously known QTL regions were confirmed. Most interestingly, this work focused on SV within these QTL regions to evaluate the implications of SV on the investigated traits. The two major findings were a novel, previously undetected deletion within FLOWERING LOCUS T, a key gene of the flowering time pathway and a large, novel insertion within Rlm9, a well-investigated blackleg resistance gene. These SV were associated to quantitative phenotypic variation for flowering time and blackleg resistance, respectively. Furthermore, the results provided new insight into the suitability of long-read sequencing data for detection of single nucleotide variants and underlined the relevance of reference genome quality for SV analyses. In summary, increasing accuracies and decreasing prices of constantly evolving long-read sequencing technologies make long-read sequencing the method of choice for detection of genomic variation. The unexpectedly high prevalence and functional relevance of SV and their association with important agronomical traits allow the recommendation for intensification of their use in commercial breeding programs and further emphasize their potential value for the development of modern, high yielding and stress tolerant cultivar.