scholarly journals Modeling first order additive × additive epistasis improves accuracy of genomic prediction for sclerotinia stem rot resistance in canola

2021 ◽  
Author(s):  
Mark C Derbyshire ◽  
Yuphin Khentry ◽  
Anita Severn‐Ellis ◽  
Virginia Mwape ◽  
Nur Shuhadah Mohd Saad ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Stem Rot ◽  
Sclerotinia Stem Rot ◽  
First Order

scholarly journals Genome-Wide Association Mapping and Genomic Prediction for Adult Stage Sclerotinia Stem Rot Resistance in Brassica Napus (L) Under Field Environments

2021 ◽  
Author(s):  
Jayanta Roy ◽  
T M Shaikh ◽  
Luis E. del Río Mendoza ◽  
Shakil Hosain ◽  
Venkat Chapara ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Stem Rot ◽  
Lesion Length ◽  
Sclerotinia Stem Rot ◽  
Agar Plug ◽  
Genome Wide ◽  
Full Flowering ◽  
Gp Model

Abstract Sclerotinia stem rot (SSR) is a fungal disease of rapeseed/canola that causes significant seed yield losses and reduces its oil content and quality. In the present study, the reaction of 187 diverse canola genotypes to SSR was characterized at full flowering stage using the agar plug to stem inoculation method in four environments. Genome-wide association study (GWAS) using three different algorithms identified 133 significant SNPs corresponding with 123 loci for disease traits like stem lesion length (LL), lesion width (LW), and plant mortality at 14 (PM_14D) and 21 (PM_21D) days. The explained phenotypic variation of these SNPs ranged from 3.6–12.1%. Nineteen significant SNPs were detected in two or more environments, disease traits with at least two GWAS algorithms. The strong correlations observed between LL and other three disease traits evaluated, suggest they could be used as proxies for SSR resistance phenotyping. Sixty-nine candidate genes associated with disease resistance mechanisms were identified. Genomic prediction (GP) analysis with all the four traits employing genome-wide markers resulted in 0.43–0.63 prediction accuracy. However, the prediction efficiency was further improved 0.55–0.88 when we integrated the GWAS information in the GP model. From our study, the identified resistant genotypes and stable significant SNP markers will serve as a valuable resource for future SSR resistance breeding. Our study also suggests that genomic selection holds promise for accelerating canola breeding progress by enabling breeders to select SSR resistance genotypes at the early stage by reducing the need to phenotype large numbers of genotypes.

scholarly journals Genome-wide association mapping and genomic prediction for adult stage sclerotinia stem rot resistance in Brassica napus (L) under field environments

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jayanta Roy ◽  
T. M. Shaikh ◽  
Luis del Río Mendoza ◽  
Shakil Hosain ◽  
Venkat Chapara ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Predictive Ability ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Stem Rot ◽  
Lesion Length ◽  
Sclerotinia Stem Rot ◽  
Agar Plug ◽  
Genome Wide ◽  
Full Flowering

AbstractSclerotinia stem rot (SSR) is a fungal disease of rapeseed/canola that causes significant seed yield losses and reduces its oil content and quality. In the present study, the reaction of 187 diverse canola genotypes to SSR was characterized at full flowering stage using the agar plug to stem inoculation method in four environments. Genome-wide association study (GWAS) using three different algorithms identified 133 significant SNPs corresponding with 123 loci for disease traits like stem lesion length (LL), lesion width (LW), and plant mortality at 14 (PM_14D) and 21 (PM_21D) days. The explained phenotypic variation of these SNPs ranged from 3.6 to 12.1%. Nineteen significant SNPs were detected in two or more environments, disease traits with at least two GWAS algorithms. The strong correlations observed between LL and other three disease traits evaluated, suggest they could be used as proxies for SSR resistance phenotyping. Sixty-nine candidate genes associated with disease resistance mechanisms were identified. Genomic prediction (GP) analysis with all the four traits employing genome-wide markers resulted in 0.41–0.64 predictive ability depending on the model specifications. The highest predictive ability for PM_21D with three models was about 0.64. From our study, the identified resistant genotypes and stable significant SNP markers will serve as a valuable resource for future SSR resistance breeding. Our study also suggests that genomic selection holds promise for accelerating canola breeding progress by enabling breeders to select SSR resistance genotypes at the early stage by reducing the need to phenotype large numbers of genotypes.

scholarly journals Genetic Mapping and Genomic Prediction of Sclerotinia Stem Rot Resistance to Rapeseed/Canola (Brassica Napus L.) at Seedling Stage

2021 ◽  
Author(s):  
Jayanta Roy ◽  
Luis E. del Río Mendoza ◽  
Nonoy Bandillo ◽  
Phillip E. McClean ◽  
Mukhlesur Rahman
Keyword(s):  
Genomic Prediction ◽  
Predictive Ability ◽  
Resistance Breeding ◽  
Significant Snps ◽  
Stem Rot ◽  
Post Inoculation ◽  
Phenotypic Variance ◽  
Sclerotinia Stem Rot ◽  
Brassica Napus L ◽  
Genome Wide

Abstract The lack of complete host resistance and a complex resistance inheritance nature between rapeseed/canola and Sclerotinia sclerotiorum often limits the development of functional molecular markers that enable breeding for sclerotinia stem rot (SSR) resistance. However, genomics-assisted selection has the potential to accelerate the breeding for SSR resistance. Therefore, genome-wide association (GWA) mapping and genomic prediction (GP) was performed using a diverse panel of 337 rapeseed/canola genotypes. Three-weeks old seedlings were screened using the petiole inoculation technique (PIT). Days to wilt (DW) up to 2 weeks and lesion phenotypes (LP) at 3, 4, and 7 days post inoculation (dpi) were recorded. A strong correlation (r = -0.94) between DW and LP_4dpi implied that a single time point scoring at four days could be used as a proxy trait. GWA analyses using single-locus (SL) and multi-locus (ML) models identified a total of 35, and 219 significantly associated SNPs, respectively. Out of these, seventy-one SNPs were identified by a combination of the SL model and any of the ML models, at least two ML models, or two traits. These SNPs explained 1.4-13.3% of the phenotypic variance, and considered as significant, could be associated with SSR resistance. Eighty-one candidate genes with a function in disease resistance were associated with the significant SNPs. Six GP models resulted in moderate to high (0.45-0.68) predictive ability depending on SSR resistance traits. The resistant genotypes and significant SNPs will serve as valuable resources for future SSR resistance breeding. Our results also highlight the potential of genomic selection to improve rapeseed/canola breeding for SSR resistance.

MicroRNA319a regulates plant resistance to Sclerotinia stem rot

2021 ◽  
Author(s):  
Weiguo Dong ◽  
Wenqing Ren ◽  
Xuan Wang ◽  
He Yuke
Keyword(s):  
Plant Resistance ◽  
Host Susceptibility ◽  
Stem Rot ◽  
Sclerotinia Stem Rot ◽  
Sequencing Data ◽  
Mobility Shift ◽  
Expression Levels ◽  
Affected Plant ◽  
Mobility Shift Assay ◽  
Rot Disease

Abstract MicroRNA319a (miR319a) controls cell division arrest in plant leaves by inhibiting the expression of TCP (TEOSINTE BRANCHED 1/CYCLOIDEA/PCF) family genes. However, it is unclear whether miR319a influences infections by necrotrophic pathogens and host susceptibility. In this study, we revealed that miR319a affected plant resistance to stem rot disease of Sclerotinia sclerotiorum. In the plants of Brassica rapa infected with S. sclerotiorum, miR319a levels increased while expression levels of several BraTCP genes significantly decreased compared with those of the uninfected plants. The overexpression of BraMIR319a in B. rapa increased the susceptibility of the plants to S. sclerotiorum and aggravated stem rot disease, whereas the overexpression of BraTCP4-1 promoted the plant resistance. Our RNA-sequencing data revealed a potential relationship between miR319a and pathogen-related WRKY genes. Chromatin immunoprecipitation (ChIP) assay, electrophoretic mobility shift assay (EMSA) and reporter transaction assay showed that BraTCP4-1 was bound to the promoters of WRKY75, WRKY70, and WRKY33 genes and directly activated these pathogen-related genes. Moreover, the expression levels of WRKY75, WRKY70, and WRKY33 in the plants overexpressing BraMIR319a declined significantly whereas those of the plants overexpressing BraTCP4-1 increased significantly. These results suggest that miR319a and its targeted gene BraTCP4 regulate stem rot resistance through pathways of WRKY genes.

Prevalence of sclerotinia stem rot of canola in New South Wales

2003 ◽  
Vol 43 (2) ◽  
pp. 163 ◽  
Author(s):  
T. L. Hind ◽  
G. J. Ash ◽  
G. M. Murray
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
New South ◽  
New South Wales ◽  
Stem Rot ◽  
Sclerotinia Stem Rot ◽  
Mean Values ◽  
Stem Infection ◽  
South Wales

Surveys of petal infestation and stem infection conducted in 1998, 1999 and 2000 indicated that Sclerotinia sclerotiorum poses a threat to the Australian canola industry. Inoculum was present throughout all canola-growing regions of New South Wales and the stem disease was widespread throughout southern New South Wales. Percentage petal infestation increased over the 3 years surveyed with values ranging from 0 to 99.4%. The highest petal infestation values were observed in 2000 (maximum of 99.4%, mean of 82.2%), with lower mean values in 1998 (38.4%) and 1999 (49.6%). Stem infection ranged from 0 to 37.5% and most fields had less than 10% stem infection. Stem rot incidence before harvest did not relate to percentage petal infestation determined during flowering. This indicated that factors other than percentage petal infestation were important in influencing stem rot incidence. While there was no relationship between percentage petal infestation and stem rot incidence, stem infection never occurred without prior petal infestation.

Nitrogen management strategies on plant growth and severities of Sclerotinia stem rot of canola in eastern Canada

2021 ◽  
Author(s):  
Fen Gao ◽  
Yuanhong Chen ◽  
SeaRa Lim ◽  
Allen Xue ◽  
Bao-Luo Ma
Keyword(s):  
Plant Growth ◽  
Seed Yield ◽  
Management Strategies ◽  
Stem Rot ◽  
Sclerotinia Stem Rot ◽  
Split Application ◽  
Eastern Canada ◽  
N Application ◽  
Application Rates ◽  
N Management

Effective nitrogen (N) management strategies are important for ensuring a balance between optimizing plant growth and minimizing disease damage. A field experiment was conducted for three years to (i) assess the effects of N fertilizer application on the growth and seed yield of canola, and severities of Sclerotinia stem rot (SSR), and (ii) determine a reasonable N-rate for optimizing plant growth and minimizing the loss from SSR in eastern Canada. The experiment was designed with factorial combinations of eight N treatments and two canola hybrids. All N-treatments reduced canola emergence with increasing preplant N application rates above 100 kg ha–1, but had a positive impact on plant height, fresh weight, dry weight and seed yield. The development of SSR showed differential responses to N application rates. Of all the treatments, the split application (50 kg N ha–1 at preplant plus 100 kg N ha–1 side-dressed at the 6-leaf stage) increased canola growth, and often produced the highest or similar seed yields to those of equivalent N rate applied as preplant. At the 150 kg ha–1 N rate, no severe development of SSR was observed in either preplant-only or split application. Overall, this study demonstrates that the split-N management strategy (50+100 kg ha–1) maintained a balance between enhancing plant growth and mitigating the negative impacts of SSR on canola.

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