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

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.

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

“…In a previous study, Bayer et al . () reported that in B. oleracea, core genes had more low‐ and moderate‐impact SNPs than variable genes, while core genes and variable genes showed almost identical numbers of high‐impact SNPs. Our result is different from that previously reported in soya bean, where the variable genes in the soya bean pangenome have a higher proportion of SNPs (Li et al ., ).…”

“…The pangenome size was 1044 Mbp and contained 1749 predicted R-genes. Gene PAV discovery was performed using the SGSGe-neLoss package (Golicz et al, 2015) as described in Hurgobin et al (2018) and Bayer et al (2018).…”

“…Moreover, a total of 1989 RGA candidates were identified in the B. oleracea pangenome by Bayer et al . ().…”

“…For example, Alamery et al (2017) found 641, 443 and 249 NBS-LRR genes in B. napus, B. oleracea and B. rapa, respectively, while Yu et al (2014) identified 157, 206 and 167 NBS-LRR genes in B. oleracea, B. rapa and A. thaliana, respectively, which may be due to using different approaches. Moreover, a total of 1989 RGA candidates were identified in the B. oleracea pangenome by Bayer et al (2018).…”

Doubled haploid based parental lines are most suitable in predicting heterosis using microsatellites and in development of highly heterotic F1hybrids inBrassica oleracea

“…In the plant kingdom, the family Brassicaceae holds a great agronomic, scientific and economically important position and comprises more than 372 genera and 4060 species [2]. Of the diverse species, Brassica oleracea (CC, 2n = 18) constitutes well defined group of economically and nutritionally important morphotypes, referred to as cole vegetables (kale, kohlrabi, cabbage, cauliflower, broccoli, brussels sprout) [52].…”