Fine mapping of Rcr1 and analyses of its effect on transcriptome patterns during infection by Plasmodiophora brassicae

Abstract

BackgroundThe protist Plasmodiophora brassicae is a biotrophic soil-borne pathogen that causes clubroot on Brassica crops worldwide. Clubroot disease is a serious threat to the 8 M ha of canola (Brassica napus) grown annually in western Canada. While host resistance is the key to clubroot management, sources of resistance are limited.ResultsTo identify new sources of clubroot resistance (CR), we fine mapped a CR gene (Rcr1) from B. rapa ssp. chinensis to the region between 24.26 Mb and 24.50 Mb on the linkage group A03, with several closely linked markers identified. Transcriptome analysis was conducted using RNA sequencing on a segregating F1 population inoculated with P. brassicae, with 2,212 differentially expressed genes (DEGs) identified between plants carrying and not carrying Rcr1. Functional annotation of these DEGs showed that several defense-related biological processes, including signaling and metabolism of jasmonate and ethylene, defensive deposition of callose and biosynthesis of indole-containing compounds, were up-regulated significantly in plants carrying Rcr1 while genes involved in salicylic acid metabolic and signaling pathways were generally not elevated. Several DEGs involved in metabolism potentially related to clubroot symptom development, including auxin biosynthesis and cell growth/development, showed significantly lower expression in plants carrying Rcr1.ConclusionThe CR gene Rcr1 and closely linked markers will be highly useful for breeding new resistant canola cultivars. The identification of DEGs between inoculated plants carrying and not carrying Rcr1 is an important step towards understanding of specific metabolic/signaling pathways in clubroot resistance mediated by Rcr1. This information may help judicious use of CR genes with complementary resistance mechanisms for durable clubroot resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1166) contains supplementary material, which is available to authorized users.

Integrative analysis of genome‐wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

“…Compared with the maternal parent, up‐regulated Bra019369 in the Brassica hexaploid encodes a SAUR (small auxin‐up RNA) protein (Chu et al., ), and this protein is tightly tied to auxin biosynthesis and the signaling pathway (Wu, Ma, Chen, Wang, & Wang, ; Wu, Liu et al., ; Wu, Okada et al., ). Up‐regulated TCONS_00018406, as a Bra019369 regulator, possibly take part in auxin‐dependent metabolism, thereby regulating plant growth and development.…”

“…AT1G05530, its orthologous genes, involved in IAA metabolic pathway, plays a vital role in IAA homeostasis (Tanaka et al, 2014), and TCONS_00009958, targeting Bra031483, could be involved in the protein (Chu et al, 2014), and this protein is tightly tied to auxin biosynthesis and the signaling pathway (Wu, Ma, Chen, Wang, & Wang, 2012;Wu, Liu et al, 2012;Wu, Okada et al, 2012 LncRNAs can function as a member of the miRNA regulation network to realize the regulation of gene expression (Wu, Wang, Wang, & Wang, 2013). For example, the interaction between miR-NAs and lncRNAs is an important mechanism to maintain phosphate homeostasis.…”

Comparative Transcriptome Analysis between Broccoli (Brassica oleracea var. italica) and Wild Cabbage (Brassica macrocarpa Guss.) in Response to Plasmodiophora brassicae during Different Infection Stages

“…To date, studies of the molecular basis of clubroot resistance from Brassica crops mainly focused on qualitative resistance, especially in Chinese cabbage (Chen et al, 2016) and canola (Chu et al, 2014). However, illuminating molecular mechanism of quantitative resistance could lead to insight into the relationship between qualitative and quantitative resistance, thus to guild utilization of the two types to produce durably resistant cultivar (Jubault et al, 2013).…”

“…Thus, previous studies have focused on understanding the mechanisms underlying clubroot disease resistance in Brassica species, including Brassica rapa and Brassica napus . Chu et al (2014) identified differentially expressed genes (DEGs) involved in the signaling metabolism of jasmonate and ethylene, defensive deposition of callose and the biosynthesis of indole-containing compounds, which were all significantly up-regulated in clubroot-resistant plants compared with susceptible cultivars. More recently, Chen et al (2016) confirmed that genes associated with PAMPs, calcium ion influx, hormone signaling, PR, transcription factors, and cell-wall modification played important roles in host– P. brassicae interactions during the early stages of infection by P. brassicae , based on transcriptome analysis of B. rapa .…”

An update on the arsenal: mining resistance genes for disease management of Brassica crops in the genomic era

“…The former encodes a TIR-NB-LRR and was functionally confirmed. With the development of genomic and molecular genetics, several loci were further identified using newly developed marker techniques 147 . Yu et al 148 applied BSA-seq and identified a novel resistance gene, Rcr1, and two candidates encoding TIR-NB-LRRs.…”