Genome wide association mapping for identification of QTL(S) underlying resistance to Alternaria blight (Alternaria brassicae (Berk) Sacc.) in Indian mustard (Brassica juncea L. Czern. & Coss.)”

Abstract Disease screening against Alternaria blight under field condition showed that, none was free from disease only 13 genotypes were found MR and 152 genotypes were found MS, 252 S and 3HS. The high estimate of phenotypic and genotypic coefficient of variation was recorded for YPP and SB., high estimate of broad sense heritability was recorded all characters except YPP. The genetics advance in per cent of mean was found high for PB, high heritability along with high genetic advance was observed for HPF. At phenotypic and genotypic level both YPP shoes highly significant and positive correlation. At phenotypic and genotypic level path coefficient reveled that in HPF, PL. The genotypes were grouped into eight different non overlapping cluster (five 115, three 100, six 84, one 78, seven 37 and three, two and four 1, eight 36 genotypes). The maximum and minimum inter cluster distance was between six, eight and one, three. One highest cluster mean for PH, MAT, and HPF and two (MAT, PH, HPF). Three (MAT, PH, HPF) four (MAT, PH, HPF) five (PH, MAT, HPF) six (MAT, PH, HPF) seven (MAT, HPF. PH), eight had no values due to reason no geminated or un survived plant and GWAS analysis of identified six significant association for Alternaria blight resistance on chromosome (A07, A09, A03, B07, B04, B03) respectively, This study showed that the diversity panel of Indian mustard identified QTLs for controlling of disease resistance against Alternaria blight in Indian mustard.

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Genetic variability, character association and path analysis in Brassica rapa L. Genotypes

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v40i2.24570 ◽

2015 ◽

Vol 40 (2) ◽

pp. 305-323

Author(s):

S Naznin ◽

MA Kawochar ◽

S Sultana ◽

MSR Bhuiyan

Keyword(s):

Path Analysis ◽

Brassica Rapa ◽

Seed Yield ◽

Selection Criteria ◽

Significant Positive Correlation ◽

Path Coefficient ◽

Early Maturity ◽

Character Association ◽

High Heritability ◽

Genotypic Coefficient Of Variation

Thirty three genotypes of Brassica rapa L. were evaluated in order to find out their inter-genotypic variability; character association and path coefficient of seed yield/plant and its component characters. BARI sarisha-6 x TORI-7 S-45 showed best result in terms of early maturity (75 days) and higher seed yield/plant (5.28g) than check varieties. The character, plant height, was highly influenced by the environment whereas, all other characters influenced the least. Number of secondary branches/plant showed the highest phenotypic and genotypic coefficient of variation. Moreover, number of siliquae/plant, number of secondary branches/plant and number of primary branches/plant showed high heritability (93.16%, 75.69% and 68.03%, respectively) couple with high genetic advance in percent of mean (37.74%, 73.55% and 26.82%, successively). The seed yield/plant showed significant positive correlation with number of siliquae/plant (rg = 0.7011**, rp = 0.5684**), number of primary branches/plant (rg = 0.5611**, rp = 0.4016*) and number of secondary branches/plant (rg = 0.5160**, rp = 0.4098*) revealing that selection based on these traits would be judicious. Path analysis showed that the number of siliquae/plant (0.4679), number of primary branches/plant (0.2823) and number of secondary branches/plant (0.0092) were the most important contributors to seed yield/plant. The results indicated that number of siliquae/plant, number of primary branches/plant and number of secondary branches/plant can be used as selection criteria to increase seed yield/plant in rapeseed.Bangladesh J. Agril. Res. 40(2): 305-323 June 2015

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Genome wide association studies for yield and its component traits under terminal heat stress in Indian mustard (Brassica juncea L.)

Euphytica ◽

10.1007/s10681-019-2489-z ◽

2019 ◽

Vol 215 (11) ◽

Cited By ~ 1

Author(s):

Surinder K. Sandhu ◽

Lalit Pal ◽

Jasneet Kaur ◽

Dharminder Bhatia

Keyword(s):

Heat Stress ◽

Brassica Juncea ◽

Association Studies ◽

Indian Mustard ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Terminal Heat Stress ◽

Component Traits

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Including phenotypic causal networks in genome-wide association studies using mixed effects structural equation models

10.1101/251421 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mehdi Momen ◽

Ahmad Ayatollahi Mehrgardi ◽

Mahmoud Amiri Roudbar ◽

Andreas Kranis ◽

Renan Mercuri Pinto ◽

...

Keyword(s):

Structural Equation ◽

Structural Equation Models ◽

Association Studies ◽

Genome Wide Association ◽

Path Coefficient ◽

Genome Wide Association Studies ◽

Causal Relationships ◽

Multiple Phenotypes ◽

Genome Wide ◽

Highest Posterior Density

AbstractBackgroundPhenotypic networks describing putative causal relationships among multiple phenotypes can be used to infer single-nucleotide polymorphism (SNP) effects in genome-wide association studies (GWAS). In GWAS with multiple phenotypes, reconstructing underlying causal structures among traits and SNPs using a single statistical framework is essential for understanding the entirety of genotype-phenotype maps. A structural equation model (SEM) can be used for such purposes.MethodsWe applied SEM to GWAS (SEM-GWAS) in chickens, taking into account putative causal relationships among body weight (BW), breast meat (BM), hen-house production (HHP), and SNPs. We assessed the performance of SEM-GWAS by comparing the model results with those obtained from traditional multi-trait association analyses (MTM-GWAS).ResultsThree different putative causal path diagrams were inferred from highest posterior density (HPD) intervals of 0.75, 0.85, and 0.95 using the inductive causation algorithm. A positive path coefficient was estimated for BM→BW, and negative values were obtained for BM→HHP and BW→HHP in all implemented scenarios. Further, the application of SEM-GWAS enabled the decomposition of SNP effects into direct, indirect, and total effects, identifying whether a SNP effect is acting directly or indirectly on a given trait. In contrast, MTM-GWAS only captured overall genetic effects on traits, which is equivalent to combining the direct and indirect SNP effects from SEMGWAS.ConclusionsAlthough MTM-GWAS and SEM-GWAS use the same probabilistic models, we provide evidence that SEM-GWAS captures complex relationships and delivers a more comprehensive understanding of SNP effects compared to MTM-GWAS. Our results showed that SEM-GWAS provides important insight regarding the mechanism by which identified SNPs control traits by partitioning them into direct, indirect, and total SNP effects.

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Abstract 13: A Locus on Chromosome 6p21 is Associated with Large Artery Atherosclerotic Ischemic Stroke

Stroke ◽

10.1161/str.43.suppl_1.a13 ◽

2012 ◽

Vol 43 (suppl_1) ◽

Author(s):

Elizabeth G Holliday ◽

Jane M Maguire ◽

Tiffany-Jane Evans ◽

Jonathan Golledge ◽

Erik Biros ◽

...

Keyword(s):

Ischemic Stroke ◽

Genetic Risk ◽

Small Vessel Disease ◽

Genome Wide Association ◽

P Value ◽

Large Artery ◽

Association Analyses ◽

Stroke Subtypes ◽

Genome Wide ◽

High Heritability

Introduction Genetic influences upon ischemic stroke risk are supported by the trait’s familial aggregation, higher concordance among monozygotic than dizygotic twins, and the high heritability of intermediate phenotypes such as carotid intima-media thickness. In spite of this evidence, genome-wide association studies (GWAS) have detected few replicable genetic risk factors for ischemic stroke, potentially due to aetiological heterogeneity of this trait. Hypothesis We first assessed the hypothesis that common ischemic stroke subtypes differ in their heritability, defined as the proportion of observed phenotypic variation attributable to genetic variation. The second hypothesis was that GWAS may detect stronger and more replicable genetic associations for distinct stroke subtypes with high heritability, rather than the broad ischemic stroke diagnosis. Methods An Australian, European-ancestry sample of 1230 ischemic stroke cases and 1280 population controls was genotyped for a genome wide association study using the Illumina 610-Quad array. Ischemic stroke subtypes were assigned using TOAST criteria. The proportion of case-control variation attributable to genome wide genetic variation was estimated using a published approach based on linear mixed models. Genome wide association analyses incorporating approximately 2.5 million genotyped and imputed SNPs were subsequently performed using a one-degree of freedom trend test assuming an additive effect of allele dosage. Results Significant evidence for a genetic contribution to ischemic stroke risk was detected ( h 2 =0.39, SE=0.15, p-value = 0.0009), but this was higher and more significant for the large artery atherosclerosis (LAA) subtype ( h 2 =0.66, SE=0.21, p-value = 0.0001). The genetic contributions to small vessel disease and cardioembolic stroke were less significant than for overall ischemic stroke. Genome wide association analyses including 421 LAA cases and 1244 controls detected a novel LAA susceptibility locus on chromosome 6p21.1 (two SNPs with P <5×10 -8 ). The 6p21.1 locus showed markedly diminished association with the broader ischemic stroke phenotype. Conclusions In conclusion, this study detected higher heritability of large artery atherosclerotic stroke than cardioembolic stroke, small vessel disease or broad ischemic stroke. It suggests a genetic risk locus for large artery atherosclerosis on chromosome 6p21.1 and supports the analysis of aetiological subtypes to better identify genetic risk alleles for ischemic stroke.

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In vitro and in vivo effect of eco-friendly chemicals on alternaria blight disease (Alternaria brassicae) and yield attributes in Indian mustard (Brassica juncea)

Journal of Applied and Natural Science ◽

10.31018/jans.v7i1.561 ◽

2015 ◽

Vol 7 (1) ◽

pp. 43-51

Author(s):

Amarendra Kumar ◽

Santosh Kumar ◽

Rakesh Kumar ◽

Gireesh Chand ◽

S. J. Kolte

Keyword(s):

Brassica Juncea ◽

Indian Mustard ◽

Disease Index ◽

Maximum Effect ◽

Alternaria Brassicae ◽

Yield Attributes ◽

Alternaria Blight ◽

Blight Disease

The present investigation was done to evaluate the effect of different concentrations of five eco-friendly chemicals in vitro and in vivo, on the management of alternaria blight and yield attributes in Indian mustard (Brassica juncea cv. Varuna). Out of five eco-friendly chemicals, K2SO4 1000 ppm (64.28%) followed by ZnSO4 1000 ppm (63.88%) showed maximum inhibition of mycelial growth in comparison to check. 0.5% concentration of KCl (57.06%) followed by CaSO4 (59.50%) and K2SO4 (62.20%) showed significantly maximum effect on spore germination in comparison to check (74.60%). Spore intensity significantly increased by all the treatments except CaSO4 at 0.5% (40.18%) followed by K2SO4 at 0.5% (29.86%) and ZnSO4 0.75% (5.11% reduction) in comparison to check. The significantly minimum disease index on leaf over check was found by foliar spray of CaSO4 at 0.5%(23.58%) followed by CaSO4 at 1.5% (24.00%) and Na2B4O7.10H2O at 1.5% (24.08%). Na2B4O7.10H2O at 0.75% showed significantly lowest disease index (23.91%) on pod followed by K2SO4 at 1.5% (25.75%) and KCl at 1.5% (26.00%) in comparison to check. CaSO4 at 1.0% showed maximum number of primary branches (7.00), number of secondary branches (13.00) and total yield/ha (1917.30 kg/ha) in comparison to check. The results obtained from the present study suggested that K2SO4 showed maximum in vitro effect on Alternaria brassicae and CaSO4 and Na2B4O7.10H2O are providing maximum reduction of disease and increase in seed yield/ha that leads to efficient alternaria blight disease management strategies in field condition. These eco-friendly chemicals can protect the crops from alternaria blight diseases and increase the production and productivity of the Indian mustard crop.

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