Abstract
SummaryMethods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.
Highlights
Brassica napus, belonging to the Brassicaceae family, is one of the three allotetraploid species in the triangle of U (UN, 1935) (AACC, n = 19)
A total of 1749 resistance gene analogs (RGAs) were identified in the B. napus pangenome, comprising 503 NBS-encoding genes and TX, 148 receptor-like proteins (RLPs) and 1098 RLKs
A total of 644 RGAs were on the A genome (493 core and 151 variable genes), 700 were on the C genome (484 core and 216 variable genes), 368 RGAs were found in the pangenome additional contigs, and 37 RGAs were identified on the reference genome unplaced contigs (19 core and 18 variable; Table 1)
Summary
A single reference genome cannot cover the entire gene content of a species due to structural variations, such as gene presence/ absence variations (PAVs) or copy number variations (CNVs) (Gan et al, 2011; Golicz et al, 2016a; Hurgobin and Edwards, 2017). To address this issue, pangenomes have been constructed for a number of plant species, including maize, soya bean, rice, wheat and Brassica species (Golicz et al, 2016b; Hirsch et al, 2014; Hurgobin et al, 2018; Li et al, 2014; Lin et al, 2014; Montenegro et al, 2017; Yao et al, 2015)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
