Evaluation of Brassica oleracea accessions for resistance to Plasmodiophora brassicae and identification of genomic regions associated with resistance

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 91-101 ◽  
Author(s):  
Mehdi Farid ◽  
Rong-Cai Yang ◽  
Berisso Kebede ◽  
Habibur Rahman
Keyword(s):  
Brassica Oleracea ◽  
Crop Production ◽  
Plasmodiophora Brassicae ◽  
Snp Markers ◽  
Phenotypic Variance ◽  
Clubroot Disease ◽  
Brassica Crop ◽  
A Genome ◽  
C Genome ◽  
Genomic Regions

Clubroot disease caused by Plasmodiophora brassicae is a challenge to Brassica crop production. Breakdown of resistance controlled by major genes of the Brassica A genome has been reported. Therefore, identification of resistance in the Brassica C genome is needed to broaden the genetic base of resistance in Brassica napus canola. In this study, we evaluated 135 Brassica oleracea accessions, belonging to eight variants of this species to identify resistant accessions as well as to identify the genomic regions associated with resistance to two recently evolved P. brassicae pathotypes, F3-14 (3A) and F-359-13 (5X L-G2). Resistance to these pathotypes was observed more frequently in var. acephala (kale) followed by var. capitata (cabbage); few accessions also carried resistance to both pathotypes. Association mapping using single nucleotide polymorphism (SNP) markers developed through genotyping by sequencing technique identified 10 quantitative trait loci (QTL) from six C-genome chromosomes to be associated with resistance to these pathotypes; among these, two QTL associated with resistance to 3A and one QTL associated with resistance to 5X L-G2 carried ≥3 SNP markers. The 10 QTL identified in this study individually accounted for 8%–18% of the total phenotypic variance. Thus, the results from this study can be used in molecular breeding of Brassica crops for resistance to this disease.

scholarly journals Genome-Wide Identification and Expression Profiling of Sugar Transporter Protein (STP) Family Genes in Cabbage (Brassica oleracea var. capitata L.) Reveals their Involvement in Clubroot Disease Responses

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 71 ◽  
Author(s):  
Wei Zhang ◽  
Shenyun Wang ◽  
Fangwei Yu ◽  
Jun Tang ◽  
Li Yu ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Plasmodiophora Brassicae ◽  
Expression Profiles ◽  
Synonymous Substitution ◽  
Plant Responses ◽  
Sugar Transporter ◽  
Systematic Analysis ◽  
Clubroot Disease ◽  
Transporter Protein ◽  
Localization Analysis

Sugar transporter protein (STP) genes are involved in multiple biological processes, such as plant responses to various stresses. However, systematic analysis and functional information of STP family genes in Brassica oleracea are very limited. A comprehensive analysis was carried out to identify BoSTP genes and dissect their phylogenetic relationships and to investigate the expression profiles in different organs and in response to the clubroot disease. A total of 22 BoSTP genes were identified in the B. oleracea genome and they were further classified into four clades based on the phylogenetic analysis. All the BoSTP proteins harbored the conserved sugar transporter (Sugar_tr, PF00083) domain, and the majority of them contained 12 transmembrane helices (TMHs). Rates of synonymous substitution in B. oleracea relative to Arabidopsis thaliana indicated that STP genes of B. oleracea diverged from those of A. thaliana approximately 16.3 million years ago. Expression profiles of the BoSTP genes in different organs derived from RNA-Seq data indicated that a large number of the BoSTP genes were expressed in specific organs. Additionally, the expression of BoSTP4b and BoSTP12 genes were induced in roots of the clubroot-susceptible cabbage (CS-JF1) at 28 days after inoculation with Plasmodiophora brassicae, compared with mock-inoculated plants. We speculated that the two BoSTPs might be involved in monosaccharide unloading and carbon partitioning associated with P. brassicae colonization in CS-JF1. Subcellular localization analysis indicated that the two BoSTP proteins were localized in the cell membrane. This study provides insights into the evolution and potential functions of BoSTPs.

scholarly journals Managing clubroot disease (caused byPlasmodiophora brassicaeWor.) by exploiting the interactions between calcium cyanamide fertilizer and soil microorganisms

2016 ◽  
Vol 155 (4) ◽  
pp. 527-543 ◽  
Author(s):  
G. R. DIXON
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Plasmodiophora Brassicae ◽  
Soil Health ◽  
Biological Properties ◽  
Soil Conditions ◽  
Alkaline Soil ◽  
Clubroot Disease ◽  
Soil Nitrification ◽  
Calcium Cyanamide

SUMMARYCalcium cyanamide is a nitrogenous fertilizer used predominantly for over a century in field and glasshouse vegetable and salad production. The current review draws together, for the first time, knowledge concerning the biological properties of the compound that benefit crop production by encouraging sustainable soil health and quality. This is achieved through the increase of microorganisms antagonistic to plant pathogens. The review also reports on the natural occurence and degradation of cyanamide. The literature survey provides a perspective of research from the early 1900s to current studies. This identifies that nitrogen is released steadily into the rhizosphere from this fertilizer. Calcium is also readily available for plant roots and promotes the alkaline soil conditions beneficial to benign microorganisms. Consequently, soil suppressiveness towards organisms such asPlasmodiophora brassicae, the cause of clubroot disease in brassicas, develops. The effects of calcium and accompanying changes in soil pH values are discussed in relation to the life-cycle stages ofP. brassicaeand the development of clubroot disease. Formulations of calcium cyanamide contain the dimeric form, dicyandiamide. This compound slows soil nitrification and subsequent nitrate leaching into ground waters, reducing potential pollution. Calcium cyanamide is normally used for growing specialized fresh produce and is not available in quantities comparable with ammoniacal fertilizers. It is contended, however, that it has properties deserving wider assessment because of their implications for sustainable cropping.

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Rossi ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals MULTI-TRAIT MODELS FOR GENOMIC REGIONS ASSOCIATED WITH MAL DE RÍO CUARTO AND BACTERIAL DISEASE IN MAIZE

2021 ◽  
Vol 32 (Issue 1) ◽  
pp. 25-33
Author(s):  
M. Ruiz ◽  
E.A. Ross ◽  
N.C. Bonamico ◽  
M.G. Balzarini
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
Maize Germplasm ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Maize (Zea Mays L.) production has been greatly benefited from the improvement of inbred lines in regard to the resistance to diseases. However, the absence of resistant genotypes to bacteriosis is remarkable. The aim of the study was to identify genomic regions for resistance to Mal de Río Cuarto (MRC) and to bacterial disease (BD) in a diverse maize germplasm evaluated in the Argentinian region where MRC virus is endemic. A maize diverse population was assessed for both diseases during the 2019-2020 crop season. Incidence and severity of MRC and BD were estimated for each line and a genome wide association study (GWAS) was conducted with 78,376 SNP markers. A multi-trait mixed linear model was used for simultaneous evaluation of resistance to MRC and BD in the scored lines. The germplasm showed high genetic variability for both MRC and BD resistance. No significant genetic correlation was observed between the response to both diseases. Promising genomic regions for resistance to MRC and BD were identified and will be confirmed in further trials. Key words: maize disease; genome wide association study; SNP; multi-trait model

scholarly journals A Genome-Wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defense Genes

2020 ◽  
Vol 61 (7) ◽  
pp. 1285-1296
Author(s):  
Lorraine Mhoswa ◽  
Marja M O’Neill ◽  
Makobatjatji M Mphahlele ◽  
Caryn N Oates ◽  
Kitt G Payn ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Eucalyptus Grandis ◽  
Nucleotide Binding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Leptocybe Invasa ◽  
Genomic Regions

Abstract The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a genome-wide association study (GWAS) to identify single-nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip, and we identified 15,445 informative SNP markers in the test population. Multi-locus mixed-model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0) not infested, (1) infested showing evidence of oviposition but no gall development, (2) infested with galls on leaves, midribs or petioles and (3) stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment, we identified several putative candidate genes in associated genomic loci including Nucleotide-binding ARC- domain (NB-ARC) and toll-interleukin-1-receptor-Nucleotide binding signal- Leucine rich repeat (TIR-NBS-LRR) genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.

scholarly journals Genome-wide identification and expression analysis of the cytokinin gene family in Brassica oleracea L. reveals its role in clubroot resistance

2019 ◽  
Author(s):  
Mingzhao Zhu ◽  
Yu Ning ◽  
Longxiang Yan ◽  
Wenxue Cao ◽  
Congcong Kong ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Plant Immunity ◽  
Homologous Gene ◽  
Element Analysis ◽  
Clubroot Disease ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Abstract Background: cytokinins have important functions in regulating plant growth and response to abiotic stress. cytokinin family genes have been described in several plant species, but a comprehensive analysis of the cytokinin family genes in Brassica oleracea has not been reported to date, especially their roles in dealing with the invasion of P. brassicae. Results: Cytokinins are a class of phytohormones that promote cell division and differentiation and are thought to affect plant immunity to multiple pathogens. To reveal the mechanisms of the Brassica oleracea cytokinin family genes in response to clubroot disease, a total of 36 cytokinin genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into three groups. They were distributed unevenly across nine chromosomes in B. oleracea, and 15 of them did not contain introns. The results of colinear analysis showed that each cytokinin gene in the B. oleracea genome had at least one homologous gene in the Arabidopsis genome. A cis-element analysis indicated that these genes possessed several stress response cis-elements. The heatmap of the cytokinin gene family showed that these genes were expressed in various tissues and organs. Five and eight genes were up- and downregulated, respectively, in the susceptible material after inoculation. In addition, two and one genes were up- and downregulated, respectively, in resistant material. This may indicate that these cytokinin genes play important roles in the host plant response to clubroot disease. In addition, the results provide insights for better understanding the role of cytokinin in the B. oleracea–P. brassicae interaction. Conclusions: Our results are helpful to elucidate the role of cytokinin family genes in cabbage response to infection by P. brassicae, and lay a foundation for further study on the function of these genes. Keywords: Brassica oleracea, genome-wide, cytokinin family genes, clubroot

scholarly journals Variability in resistance to clubroot in European cauliflower cultivars

2012 ◽  
Vol 48 (No. 4) ◽  
pp. 156-161 ◽  
Author(s):  
P. Kopecký ◽  
I. Doležalová ◽  
M. Duchoslav ◽  
K. Dušek
Keyword(s):  
Plant Growth ◽  
Brassica Oleracea ◽  
Genetic Heterogeneity ◽  
Plasmodiophora Brassicae ◽  
Disease Index ◽  
Growth Chamber ◽  
Clubroot Disease ◽  
Controlled Conditions ◽  
Infested Field ◽  
Plant Growth Chamber

Fifty genotypes of cauliflovwer (Brassica oleracea var. botrytis) were evaluated for resistance to clubroot disease (Plasmodiophora brassicae Wor.) under controlled conditions in a plant growth chamber. The cultivars with the highest resistance were Brilant, Agora, and Bora, while the most susceptible were the cultivars White Top, White Fox, and Octavian. The variation in disease index is probably due to different pathogenicity rates of clubroot pathotypes and genetic heterogeneity of European cauliflower cultivars. The obtained results will be tested in an infested and non-infested field.  

A genetic map for Brassica oleracea based on RFLP markers detected with expressed DNA sequences and mapping of resistance genes to race 2 of Plasmodiophora brassicae (Woronin)

Genome ◽  
1992 ◽  
Vol 35 (3) ◽  
pp. 409-420 ◽  
Author(s):  
Benoit S. Landry ◽  
Nathalie Hubert ◽  
René Crete ◽  
Morgan S. Chang ◽  
Steven E. Lincoln ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Genetic Map ◽  
Dna Sequences ◽  
Leaf Morphology ◽  
Plasmodiophora Brassicae ◽  
Rflp Markers ◽  
Cdna Clones ◽  
Linkage Groups ◽  
Clubroot Disease ◽  
Race 2

F2 segregation analyses of DNA restriction fragment length polymorphisms (RFLPs) detected between a cabbage line (No. 86-16-5) resistant to race 2 of Plasmodiophora brassicae (Woronin), the fungus responsible for clubroot disease, and a rapid cycling line (CrGC No. 85) was used to construct a detailed genetic map of Brassica oleracea. RFLP markers were random and seedling-specific cDNA clones. The 201 loci so far mapped in B. oleracea covered 1112 cM. They are assembled into nine major linkage groups and four small linkage groups. Twelve loci were found unlinked to any other markers. Twenty-one loci were detected with the 18 seedling-specific cDNAs. Two dominant QTLs for resistance to race 2 of the clubroot disease causal agent were also identified. Leaf morphology and biennial flowering appeared to segregate as single Mendelian traits, but only leaf morphology could be linked to other markers. This RFLP study in B. oleracea is providing additional information on genome organization and complements current RFLP mapping effort in B. napus.Key words: genetic mapping, Brassica oleracea, Plasmodiophora brassicae, breeding, clubroot resistance, DNA markers, RFLP.

scholarly journals Identification of lncRNAs Responsive to Infection by Plasmodiophora brassicae in Clubroot-Susceptible and -Resistant Brassica napus Lines Carrying Resistance Introgressed from Rutabaga

2019 ◽  
Vol 32 (10) ◽  
pp. 1360-1377 ◽  
Author(s):  
Aarohi Summanwar ◽  
Urmila Basu ◽  
Habibur Rahman ◽  
Nat Kav
Keyword(s):  
Brassica Napus ◽  
Target Genes ◽  
Plasmodiophora Brassicae ◽  
Genome Chromosome ◽  
Clubroot Disease ◽  
Brassica Crops ◽  
A Genome ◽  
Microbe Interactions ◽  
Trait Locus ◽  
Plant Pathogen Interactions

Clubroot disease, caused by Plasmodiophora brassicae Woronin, is a major threat to the production of Brassica’ crops. Resistance to different P. brassicae pathotypes has been reported in the A genome, chromosome A08; however, the molecular mechanism of this resistance, especially the involvement of long noncoding RNAs (lncRNAs), is not understood. We have used a strand-specific lncRNA-Seq approach to catalog lncRNAs from the roots of clubroot-susceptible and -resistant Brassica napus lines. In total, 530 differentially expressed (DE) lncRNAs were identified, including 88% of long intergenic RNAs and 11% natural antisense transcripts. Sixteen lncRNAs were identified as target mimics of the microRNAs (miRNAs) and eight were identified as the precursors of miRNAs. KEGG pathway analysis of the DE lncRNAs showed that the cis-regulated target genes mostly belong to the phenylpropanoid biosynthetic pathway (15%) and plant–pathogen interactions (15%) while the transregulated target genes mostly belong to carbon (18%) and amino acid biosynthesis pathway (19%). In all, 24 DE lncRNAs were identified from chromosome A08, which is known to harbor a quantitative trait locus conferring resistance to different P. brassicae pathotypes; however, eight of these lncRNAs showed expression only in the resistant plants. These results could form the basis for future studies aimed at delineating the roles of lncRNAs in plant–microbe interactions.

scholarly journals KERAGAMAN MIKOFLORA TANAH SUPRESIF DALAM MENGENDALIKAN PENYAKIT AKAR GADA PADA TANAMAN KUBIS (BRASSICA OLERACEA L.)

2017 ◽  
Vol 11 (1) ◽  
pp. 70
Author(s):  
Ni Nengah Darmiati ◽  
I Made Sudarma
Keyword(s):  
Brassica Oleracea ◽  
Plasmodiophora Brassicae ◽  
Effective Control ◽  
Vegetable Crops ◽  
Clubroot Disease ◽  
Suppressive Soil ◽  
Potential Control ◽  
Plant Habitat ◽  
Brassica Oleracea L ◽  
Conducive Soil

DIVERSITY OF SUPRESSIVE LAND MICROFLORA IN CONTROL OF PALLDER DISEASE IN CUBES PLANT (BRASSICA OLERACEA L.)Cabbage (Brassica oleracea L.) was a vegetable crops cultivated in the highlands to meet the needs of the community vegetable. The main obstacle was the cultivation of cabbage root disease outbreak mace (clubroot), which until now have not found an effective control techniques. Clubroot disease caused by organisms that resemble fungi: Plasmodiophora brassicae Wor. which was the soil inhibitant and soil borne pathogen. Therefore, there must be a way to control environmentally friendly by using suppressive soil, find microbes antagonists related to the cabbage plant habitat in the soil. The results showed that the index of diversity both on suppressive and conducive soil of 1.2304 and 1.2811 respectively, and the index of dominance on the suppressive and conducive soil were 0.6677 and 0.6838.  Prevalence micoflora of the suppressive soil amounted to 44.22 % and 43.06 % conducive soil all dominated by Fusarium spp. Microbial antagonist as a potential control of P. brassicae was Trichoderma sp. Based on the analysis in the suppressive soil as much as 171 x 103 cfu /g soil, higher than on the conducive soil to 90 x 103 cfu /g soil.

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