Understanding the Genetics of Clubroot Resistance for Effectively Controlling this Disease in Brassica Species

Clubroot disease is one of the most serious diseases of Brassica species, which is caused by soil-borne pathogen Plasmodiophora brassicae Woronin. Clubroot disease has a long history on vegetable crops belonging to the Brassica species; most recently, this disease is also invading rapeseed/canola crop around the globe. The clubroot disease causes significant yield and quality losses in highly infected fields. Clubroot pathogens invade into the host plant roots and infect root tissues with the formation of abnormal clubs, named as galls, which results in incompetent plant roots to intake water and nutrients and eventually dead plants. As it is a soil-borne disease and accomplishes its disease cycle in two different phases and both phases are highly efficient to damage root system as well as to release more inoculum, there are many challenges to control this disease through chemical and other cultural practices. In general, clubroot disease can be effectively managed by developing resistant cultivars. In this chapter, various resistance sources of clubroot disease in different Brassica species have been discussed with potential applications in canola/rapeseed breeding programs worldwide. Importance of gene mapping and molecular marker development efforts by different research studies for clubroot in B. rapa, B. oleracea, and B. napus has been stressed. Transcriptomic and metabolomic changes occurring during host–pathogen interactions are also covered in this chapter, which would enhance our understanding and utilization of clubroot resistance in Brassica species

Analyses of virulence of European isolates of clubroot (Plasmodiophora brassicae Wor.) and mapping of resistance genes in rapeseed (Brassica napus L.)

Clubroot caused by the obligate biotrophic protist Plasmodiophora brassicae is a serious soilborne disease of cruciferous crops including oilseed rape (Brassica napus L.). Physiological specialisation of pathogen populations causes differences in pathogenicity, rendering breeding for resistance difficult. Therefore, it is important to get more detailed information on the virulence of P. brassicae in Europe. Samples of infected plants were collected all over the main European oilseed rape growing regions and forty-eight isolates were characterised under greenhouse conditions by artificial inoculation on the European Clubroot Differential (ECD) series and the differential set of Somé et al. (1996) followed by optical rating of disease symptoms. In total, 33 different ECD triplet codes were detected of which classifications ‘16/14/31’, ‘16/31/31’ and ‘17/31/31’ were most common. Based on results obtained on the differentials of Somé et al. (1996) P1 is the prevalent pathotype on oilseed rape fields in the maritime region of Northern Europe whereas P3 was most frequently detected in the continental part of Europe. As breeding for resistance is the most powerful tool to control clubroot, broadening of the genetic basis of resistance in oilseed rape is needed. Therefore, clubroot resistances derived from two rutabaga (Brassica napus var. napobrassica) varieties, i.e., ‘Invitation’ and ‘Wilhelmsburger’, were genetically mapped in doubled haploid (DH) populations of crosses to the susceptible oilseed rape (Brassica napus L.) cultivar ‘Ladoga’. The DH populations were analysed for resistance against two P. brassicae isolates showing different virulence patterns in the greenhouse. The segregation ratios indicated the effectiveness of one, two and three resistance genes, respectively, conferring resistance in these DH populations depending on the P. brassicae isolate used. Studies on F1 plants give hint to dominant resistance genes in both donor lines located on chromosomes A03, A05 and A08.Clubroot caused by the obligate biotrophic protist Plasmodiophora brassicae is a serious soilborne disease of cruciferous crops including oilseed rape (Brassica napus L.). Physiological specialisation of pathogen populations causes differences in pathogenicity, rendering breeding for resistance difficult. Therefore, it is important to get more detailed information on the virulence of P. brassicae in Europe. Samples of infected plants were collected all over the main European oilseed rape growing regions and forty-eight isolates were characterised under greenhouse conditions by artificial inoculation on the European Clubroot Differential (ECD) series and the differential set of Somé et al. (1996) followed by optical rating of disease symptoms. In total, 33 different ECD triplet codes were detected of which classifications ‘16/14/31’, ‘16/31/31’ and ‘17/31/31’ were most common. Based on results obtained on the differentials of Somé et al. (1996) P1 is the prevalent pathotype on oilseed rape fields in the maritime region of Northern Europe whereas P3 was most frequently detected in the continental part of Europe. As breeding for resistance is the most powerful tool to control clubroot, broadening of the genetic basis of resistance in oilseed rape is needed. Therefore, clubroot resistances derived from two rutabaga (Brassica napus var. napobrassica) varieties, i.e., ‘Invitation’ and ‘Wilhelmsburger’, were genetically mapped in doubled haploid (DH) populations of crosses to the susceptible oilseed rape (Brassica napus L.) cultivar ‘Ladoga’. The DH populations were analysed for resistance against two P. brassicae isolates showing different virulence patterns in the greenhouse. The segregation ratios indicated the effectiveness of one, two and three resistance genes, respectively, conferring resistance in these DH populations depending on the P. brassicae isolate used. Studies on F1 plants give hint to dominant resistance genes in both donor lines located on chromosomes A03, A05 and A08

Identification and Genetic Mapping of Clubroot Resistance in Two Brassica nigra Lines

Clubroot, caused by the protist Plasmodiophora brassicae Woronin, is one of the most serious diseases to affect members of the plant family Brassicaceae. This biotrophic soil-borne pathogen is an emerging threat to canola and mustard production in western Canada. To manage the disease, it is important to identify and use new sources of clubroot resistance (CR). The purpose of this research is to map CR genes in the mustard species, Brassica nigra, and to analyze host differential gene expression during P. brassicae infection. Lines of Brassica nigra with a broad spectrum of resistance to clubroot were recently identified. Plant materials utilized in this study include resistant (R) lines BRA192/78 and PI 219576; and susceptible (S) line CR2748. The two resistant lines of B. nigra were crossed with CR2748 female susceptible line to produce the F1. F1 plants were self-pollinated to produce F2. F1 plants from CR2748 x PI 219576 and CR2748 x BRA192/78 were backcrossed with the CR2748 plants to produce BC1 populations. Genetic mapping of CR genes was carried out using bulked segregant RNA-Sequencing (RNA-Seq). Validation and genotyping of single nucleotide polymorphism (SNP) markers were carried out using the Kompetitive Allele Specific PCR (KASP) method. Complete resistance to clubroot was found in all F1 plants derived from crosses of CR2748 with PI 219576 or BRA192/78. Evaluation for resistance to clubroot showed ratios of 1R:1S in BC1 and 3R:1S in F2 for both R genotypes, indicating that CR is controlled by a single dominant gene in both PI 219576 and BRA192/78. Short reads from R and S bulked RNA-Seq samples in the BC1 population derived from PI 219576 and BRA192/78 were assembled into the B. rapa, B. oleracea and B. nigra reference genomes. Transcriptome analysis was conducted, with 11 differentially expressed genes (DEGs) identified in PI 219576 and 382 DEGs identified in BRA192/78 at 95% confidence. Several of the DEGs annotated were involved in CR, such as genes encoding Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat (TIR-NBS-LRR)-class disease resistance proteins and pathogenesis-related (PR) transcriptional factors. An ethylene-responsive gene was up-regulated, whereas auxin-responsive genes and a gene associated with cell growth/development were down-regulated in resistant plants. A CR gene designated Rcr6a in PI 219576 was mapped to the region between 14.36 Mb and 14.84 Mb on chromosome B3, in a region homologous to one on chromosome A08 of B. rapa. SNP markers closely linked to Rcr6a were developed. Plants in the BC1 population from BRA192/78 were also analyzed with the SNP markers linked to Rcr6a and results showed that resistance in BRA192/78 was linked on B3 chromosome, in the region between 12.76 Mb and 14.84 Mb, indicating that the CR gene namely Rcr6b in BRA192/78 was likely in the Rcr6a region. This is the first report on mapping of two single dominant CR alleles, Rcr6a and Rcr6b, in B. nigra. In addition, several SNP markers closely linked to the genes were developed and these markers will be useful in marker-assisted breeding for clubroot resistant canola cultivars. There has been limited research done on the B. nigra genome compared to the vegetable species, B. rapa and B. oleracea, and its potential for CR is poorly understood. However, some B. nigra accessions are highly resistant to clubroot, and CR genes in B. nigra may be transferred into canola (B. napus) as well as mustard species, B. juncea and B. carinata. The identification of DEGs is a significant step in better understanding CR mechanisms so CR genes with potentially different modes of action against clubroot can be utilized

Live Cell Imaging of Plasmodiophora brassicae Infection and Host Interactions

Plasmodiophora brassicae Woronin, is a soil-borne obligate biotrophic plant pathogen responsible for clubroot, one of the most devastating diseases of Brassicaceae. Previous studies into the lifecycle of P. brassicae have focused on fixed tissue samples for histological or transmission electron microscopic investigations due to the lack of a pathogen-specific stain for live cell/tissue study. Using the fluorophore Nile red to stain lipid droplets in all life stages of P. brassicae allows for live cell microscopic investigation of this pathogen. Nile red can be used to label P. brassicae ex planta in the soil during the resting spore and infective zoospore phases, and in planta during its obligate life cycle phases. This Nile red labelling technique combined with transgenic Arabidopsis thaliana plants expressing fluorescent protein-labelled organelle markers permits imaging of the zoospore penetration of the host cell wall, subsequent pathogen development within the intracellular environment, and further allows the investigation of pathogen-induced organelle recruitment and/or disruption during the P. brassicae-A. thaliana interaction. Specifically, the translocation of the nucleus to the penetration site and its subsequent envelopment by plasmodia, and the establishment of a cytoplasmic vacuole-derived encasement termed the parasitophorus vacuole. This staining technique has provided insight pertaining to the cellular interactions of P. brassicae and its hosts

Live Cell Imaging of Plasmodiophora brassicae Infection and Host Interactions

Plasmodiophora brassicae Woronin, is a soil-borne obligate biotrophic plant pathogen responsible for clubroot, one of the most devastating diseases of Brassicaceae. Previous studies into the lifecycle of P. brassicae have focused on fixed tissue samples for histological or transmission electron microscopic investigations due to the lack of a pathogen-specific stain for live cell/tissue study. Using the fluorophore Nile red to stain lipid droplets in all life stages of P. brassicae allows for live cell microscopic investigation of this pathogen. Nile red can be used to label P. brassicae ex planta in the soil during the resting spore and infective zoospore phases, and in planta during its obligate life cycle phases. This Nile red labelling technique combined with transgenic Arabidopsis thaliana plants expressing fluorescent protein-labelled organelle markers permits imaging of the zoospore penetration of the host cell wall, subsequent pathogen development within the intracellular environment, and further allows the investigation of pathogen-induced organelle recruitment and/or disruption during the P. brassicae-A. thaliana interaction. Specifically, the translocation of the nucleus to the penetration site and its subsequent envelopment by plasmodia, and the establishment of a cytoplasmic vacuole-derived encasement termed the parasitophorus vacuole. This staining technique has provided insight pertaining to the cellular interactions of P. brassicae and its hosts

Diseases of Edible Oilseed Crops

Diseases of Edible Oilseed Crops presents an unprecedentedly thorough collection of information on the diseases of cultivated annual oilseed crops, including peanut, rapeseed-mustard, sesame, soybean, sunflower, and safflower. Written by internationally recognized researchers, this book covers and integrates worldwide literature in the field up to 2014, setting it apart from other books that are only of regional importance. The book focuses on major diseases of economic importance to each crop. Each chapter is devoted to a type of crop and a profile of affecting diseases according to geographical occurrence, epidemiology, symptoms, causal pathogens, host-pathogen interactions, biotechnological aspects, and the latest approaches to understanding host-pathogen interactions. It also includes discussions on developments on controversial subjects in research in order to stimulate thinking and further conversation with an eye toward improvements and resolutions. Research on oilseed crop diseases has expanded tremendously in the past 30 years, primarily as an effort to reduce losses to various stresses, including crop diseases. In the war against hunger and malnutrition, it is necessary to enhance and update knowledge about crop diseases and managing them. By compiling decades of information from previously scattered research into a single globally minded volume, Diseases of Edible Oilseed Crops provides these much-needed updates and enhancements

Translational Genomics for Crop Breeding: Biotic Stress, Volume 1

Genomic Applications for Crop Breeding: Biotic Stress is the first of two volumes looking at the latest advances in genomic applications to crop breeding. This volume focuses on genomic-assisted advances for improving economically important crops against biotic stressors, such as viruses, fungi, nematodes, and bacteria. Looking at key advances in crops such as rice, barley, wheat, and potato amongst others, Genomic Applications for Crop Breeding: Biotic Stress will be an essential reference for crop scientists, geneticists, breeders, industry personnel and advanced students in the field

Understanding Trichoderma bio-inoculants in the root ecosystem of Pinus radiata

Oral presentation on understanding Trichoderma bio-inoculants in the root ecosystem of Pinus radiat

Recent Advances in Genetics and Breeding of Major Staple Food Crops

To meet the global food demand of an increasing population, food production has to be increased by 60% by 2050. The main production constraints, such as climate change, biotic stresses, abiotic stresses, soil nutrition deficiency problems, problematic soils, etc., have to be addressed on an urgent basis. More than 50% of human calories are from three major cereals: rice, wheat, and maize. The harnessing of genetic diversity by novel allele mining assisted by recent advances in biotechnological and bioinformatics tools will enhance the utilization of the hidden treasures in the gene bank. Technological advances in plant breeding will provide some solutions for the biofortification, stress resistance, yield potential, and quality improvement in staple crops. The elucidation of the genetic, physiological, and molecular basis of useful traits and the improvement of the improved donors containing multiple traits are key activities for variety development. High-throughput genotyping systems assisted by bioinformatics and data science provide efficient and easy tools for geneticists and breeders. Recently, new breeding techniques applied in some food crops have become game-changers in the global food crop market. With this background, we invited 18 eminent researchers working on food crops from across the world to contribute their high-quality original research manuscripts. The research studies covered modern food crop genetics and breeding