scholarly journals Analysis of genotype by environment interactions in a maize mapping population

2021 ◽  
Author(s):  
Asher I Hudson ◽  
Sarah G Odell ◽  
Pierre Dubreuil ◽  
Marie-Helene Tixier ◽  
Sebastien Praud ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Crop Breeding ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Covariances

Genotype by environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype by environment interaction in a maize multi-parent advanced generation intercross population grown across five environments. We found that genotype by environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. In order to understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype by environment variance. We also performed a genome-wide association study to identify markers associated with genotype by environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype by environment interactions in this population.

scholarly journals Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit

2017 ◽  
Author(s):  
Lianne Merchuk-Ovnat ◽  
Roi Silberman ◽  
Efrat Laiba ◽  
Andreas Maurer ◽  
Klaus Pillen ◽  
...  
Keyword(s):  
Flowering Time ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Grain Filling ◽  
Genotype By Environment Interactions ◽  
Shoot Morphology ◽  
Genotype By Environment ◽  
A Genome ◽  
Wild Allele ◽  
Novel Alleles

AbstractIncreasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA), plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits. One QxE locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA, however this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 showed the wild allele confers an advantage over the cultivated in PGY, GN and harvest index as well as modified shoot morphology, longer grain filling period and reduced senescence (only under drought), therefore suggesting adaptation mechanism against water deficit other than escape. This study highlights the value of evaluating wild relatives in search of novel alleles and clues to resilience mechanism underlying crop adaptation to abiotic stress.HighlightA flowering-time independent reproductive advantage of wild over cultivated allele under drought identified in a barley GWAS for genotype-by-environment interactions, with modified shoot morphology, reduced senescence and longer grain filling

The genetic variation in the timing of heteroblastic transition in Eucalyptus globulus is stable across environments

2011 ◽  
Vol 59 (2) ◽  
pp. 170 ◽  
Author(s):  
M. G. Hamilton ◽  
P. A. Tilyard ◽  
D. R. Williams ◽  
R. E. Vaillancourt ◽  
T. J. Wardlaw ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Phase Change ◽  
Eucalyptus Globulus ◽  
Developmental Change ◽  
Genetic Correlations ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Narrow Sense Heritability ◽  
Genotype By Environment ◽  
Analyse Data

Eucalyptus globulus is one of the best known examples of a heteroblastic plant. It exhibits a dramatic phase change from distinctive juvenile to adult leaves, but the timing of this transition varies markedly. We examined the genetic variation in the timing of heteroblastic transition using five large open-pollinated progeny trials established in north-western Tasmania. We used univariate and multi-variate mixed models to analyse data on the presence/absence of adult or intermediate foliage at age 2 years from a total of 14 860 trees across five trials, as well as height to heteroblastic phase change from one trial. Up to 566 families and 15 geographic subraces of E. globulus were represented in the trials. The timing of the heteroblastic transition was genetically variable and under strong genetic control at the subrace and within-subrace level, with single-trial narrow-sense heritability estimates for the binary trait averaging 0.50 (range 0.44–0.65). The degree of quantitative trait differentiation in the timing of heteroblastic transition among subraces, as measured by QST, exceeded the published level of neutral molecular marker (FST) differentiation in all cases, arguing that diversifying selection has contributed to shaping broad-scale patterns of genetic differentiation. Most inter-trial genetic correlations were close to one at the subrace and additive genetic levels, indicating that the genetic variation in this important developmental change is expressed in a stable manner and that genotype-by-environment interaction is minimal across the environments studied.

scholarly journals Predicting Moisture Content During Maize Nixtamalization Using Machine Learning with NIR Spectroscopy

2021 ◽  
Author(s):  
Michael Burns ◽  
Jonathan Renk ◽  
David Eickholt ◽  
Amanda Gilbert ◽  
Travis Hattery ◽  
...  
Keyword(s):  
Machine Learning ◽  
Moisture Content ◽  
High Throughput ◽  
Genome Wide Association Study ◽  
Rank Correlation ◽  
Quantitative Measure ◽  
Support Vector ◽  
Environment Interaction ◽  
Genome Wide ◽  
A Genome

Lack of high throughput phenotyping systems for determining moisture content during the maize nixtamalization cooking process has led to difficulty in breeding for this trait. This study provides a high throughput, quantitative measure of kernel moisture content during nixtamalization based on NIR scanning of uncooked maize kernels. Machine learning was utilized to develop models based on the combination of NIR spectra and moisture content determined from a scaled-down benchtop cook method. A linear support vector machine (SVM) model with a Spearman's rank correlation coefficient of 0.852 between wet lab and predicted values was developed from 100 diverse temperate genotypes grown in replicate across two environments. This model was applied to NIR data from 501 diverse temperate genotypes grown in replicate in five environments. Analysis of variance revealed environment explained the highest percent of the variation (51.5%), followed by genotype (15.6%) and genotype-by-environment interaction (11.2%). A genome-wide association study identified 26 significant loci across five environments that explained between 5.04% and 16.01% (average = 10.41%). However, genome-wide markers explained 10.54% to 45.99% (average = 31.68%) of the variation, indicating the genetic architecture of this trait is likely complex and controlled by many loci of small effect. This study provides a high-throughput method to evaluate moisture content during nixtamalization that is feasible at the scale of a breeding program and provides important information about the factors contributing to variation of this trait for breeders and food companies to make future strategies to improve this important processing trait.

scholarly journals Genetics of addictive behavior: the example of nicotine dependence

2017 ◽  
Vol 19 (3) ◽  
pp. 237-245 ◽  
Keyword(s):  
Lung Cancer ◽  
Nicotine Dependence ◽  
Genome Wide Association Study ◽  
Environment Interaction ◽  
Addictive Disorders ◽  
Gene Environment ◽  
Genome Wide ◽  
A Genome ◽  
Significant Heritability ◽  
Parent Monitoring

The majority of addictive disorders have a significant heritability—roughly around 50%. Surprisingly, the most convincing association (a nicotinic acetylcholine receptor CHRNA5-A3-B4 gene cluster in nicotine dependence), with a unique attributable risk of 14%, was detected through a genome-wide association study (GWAS) on lung cancer, although lung cancer has a low heritability. We propose some explanations of this finding, potentially helping to understand how a GWAS strategy can be successful. Many endophenotypes were also assessed as potentially modulating the effect of nicotine, indirectly facilitating the development of nicotine dependence. Challenging the involved phenotype led to the demonstration that other potentially overlapping disorders, such as schizophrenia and Parkinson disease, could also be involved, and further modulated by parent monitoring or the existence of a smoking partner. Such a complex mechanism of action is compatible with a gene-environment interaction, most clearly explained by epigenetic factors, especially as such factors were shown to be, at least partly, genetically driven.

Sensitivity of genotypes to feeding systems for production, weight and feed intake in dairy cattle

2000 ◽  
Vol 2000 ◽  
pp. 112-112 ◽  
Author(s):  
J.E. Pryce ◽  
R.F. Veerkamp
Keyword(s):  
Dry Matter ◽  
Genetic Parameter ◽  
Genetic Correlations ◽  
Genotype By Environment Interaction ◽  
Parameter Estimates ◽  
Environment Interaction ◽  
Combine Data ◽  
Genotype By Environment ◽  
University Of Edinburgh ◽  
Feeding Systems

Getting reliable genetic parameter estimates for dry matter intake is difficult because recording it is expensive, hence it is tempting to combine data from research herds. However, there are large differences in feeding and management systems, which causes differences in means across herds. Furthermore, variances or heritabilities may differ and genetic correlations may be less than one between herds. This is one of the reasons why it is important to investigate effects of genotype by environment interaction (GxE). Another reason is that it is important to understand how high genetic merit cows perform in different feeding systems. The objective of this study was to estimate the effect of GxE for three feeding systems at two research herds belonging to ID-Lelystad (ID) and to SAC/University of Edinburgh (Langhill).

scholarly journals Genome-Wide Contribution of Genotype by Environment Interaction to Variation of Diabetes-Related Traits

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e77442 ◽  
Author(s):  
Ju-Sheng Zheng ◽  
Donna K. Arnett ◽  
Yu-Chi Lee ◽  
Jian Shen ◽  
Laurence D. Parnell ◽  
...  
Keyword(s):  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
Genome Wide

scholarly journals A molecular investigation of genotype by environment interactions.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 19-33 ◽  
Author(s):  
A M Dean
Keyword(s):  
Genotype By Environment Interaction ◽  
Metabolic Control Analysis ◽  
Environment Interaction ◽  
Control Analysis ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Natural Isolates ◽  
Selection Intensities ◽  
Beta Galactosidase ◽  
Control Coefficients

Abstract The fitnesses conferred by seven lactose operons, which had been transduced into a common genetic background from natural isolates of Escherichia coli, were determined during competition for growth rate-limiting quantities of galactosyl-glycerol, a naturally occurring galactoside. The fitnesses of these same operons have been previously determined on lactose and three artificial galactosides, lactulose, methyl-galactoside and galactosyl-arabinose. Analysis suggests that although marked genotype by environment interactions occur, changes in the fitness rankings are rare. The relative activities of the beta-galactosidases and the permeases were determined on galactosyl-glycerol, lactose, lactulose and methyl-galactoside. Both enzymes display considerable kinetic variation. The beta-galactosidase alleles provide no evidence for genotype by environment interactions at the level of enzyme activity. The permease alleles display genotype by environment interactions with a few causing changes in activity rankings. The contributions to fitness made by the permeases and the beta-galactosidases were partitioned using metabolic control analysis. Most of the genotype by environment interaction at the level of fitness is generated by changes in the distribution of control among steps in the pathway, particularly at the permease where large control coefficients ensure that its kinetic variation has marked fitness effects. Indeed, changes in activity rankings at the permease account for the few changes in fitness rankings. In contrast, the control coefficients of the beta-galactosidase are sufficiently small that its kinetic variation is in, or close to, the neutral limit. The selection coefficients are larger on the artificial galactosides because the control coefficients of the permease and beta-galactosidase are larger. The flux summation theorem requires that control coefficients associated with other steps in the pathway must be reduced, implying that the selection at these steps will be less intense on the artificial galactosides. This suggests that selection intensities need not be greater in novel environments.

scholarly journals Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain

2021 ◽  
pp. annrheumdis-2020-219624
Author(s):  
Md Shafiqur Rahman ◽  
Bendik S Winsvold ◽  
Sergio O Chavez Chavez ◽  
Sigrid Børte ◽  
Yakov A Tsepilov ◽  
...  
Keyword(s):  
Association Study ◽  
Musculoskeletal Pain ◽  
Tissue Specificity ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
The Body ◽  
Genome Wide Association ◽  
Suggestive Association ◽  
Genome Wide ◽  
A Genome

Background and objectivesChronic widespread musculoskeletal pain (CWP) is a symptom of fibromyalgia and a complex trait with poorly understood pathogenesis. CWP is heritable (48%–54%), but its genetic architecture is unknown and candidate gene studies have produced inconsistent results. We conducted a genome-wide association study to get insight into the genetic background of CWP.MethodsNorthern Europeans from UK Biobank comprising 6914 cases reporting pain all over the body lasting >3 months and 242 929 controls were studied. Replication of three independent genome-wide significant single nucleotide polymorphisms was attempted in six independent European cohorts (n=43 080; cases=14 177). Genetic correlations with risk factors, tissue specificity and colocalisation were examined.ResultsThree genome-wide significant loci were identified (rs1491985, rs10490825, rs165599) residing within the genes Ring Finger Protein 123 (RNF123), ATPase secretory pathway Ca2+transporting 1 (ATP2C1) and catechol-O-methyltransferase (COMT). The RNF123 locus was replicated (meta-analysis p=0.0002), the ATP2C1 locus showed suggestive association (p=0.0227) and the COMT locus was not replicated. Partial genetic correlation between CWP and depressive symptoms, body mass index, age of first birth and years of schooling were identified. Tissue specificity and colocalisation analysis highlight the relevance of skeletal muscle in CWP.ConclusionsWe report a novel association of RNF123 locus and a suggestive association of ATP2C1 locus with CWP. Both loci are consistent with a role of calcium regulation in CWP. The association with COMT, one of the most studied genes in chronic pain field, was not confirmed in the replication analysis.

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