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. 2019 Apr;17(4):789-800.
doi: 10.1111/pbi.13015. Epub 2018 May 31.

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome

Philipp E Bayer  1 , Agnieszka A Golicz  2 , Soodeh Tirnaz  1 , Chon-Kit Kenneth Chan  1   3 , David Edwards  1 , Jacqueline Batley  1
Affiliations

Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome

Philipp E Bayer et al. Plant Biotechnol J. 2019 Apr.

Abstract

Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.

Keywords: Brassica oleracea; PAV; Brassicaceae; RGAs; pangenomics; resistance genes.

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Conflict of interest statement

The authors have no conflicts of interest to declare.

Figures

Figure 1
Figure 1
Density of genes compared with the density of NBS, RLK, RLP as well as variable genes.
Figure 2
Figure 2
Expected (Evperm) and observed (Evobs) overlaps between NBS genes and PAV genes showing that the number of overlaps is higher than expected.
Figure 3
Figure 3
High impact, moderate impact and low impact SNPs per base pair compared with RGA class and presence/absence status.
Figure 4
Figure 4
Waterfall plot of the Sclerotinia resistance‐linked QTL qLR10‐3 (SWUC177 ‐ BoGMS1032). Gene order is determined by position in the reference assembly.
See this image and copyright information in PMC

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