scholarly journals A low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat

2018 ◽  
Author(s):  
Nicholas Santantonio ◽  
Jean-Luc Jannink ◽  
Mark E. Sorrells
Keyword(s):  
Mixed Model ◽  
Agronomic Traits ◽  
Statistical Tests ◽  
Covariance Matrices ◽  
Low Resolution ◽  
Model Framework ◽  
Epistatic Interactions ◽  
Epistatic Effects ◽  
Chromosome Arm ◽  
Homeologous Chromosome

1AbstractEpistasis is an important contributor to genetic variance, even in inbred populations where it is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the search space for modest numbers of markers is large. Additionally, single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while drastically minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Two additive genetic covariance matrices are constructed from markers on two different chromosome arms. The Hadamard product of these additive covariance matrices is then used to produce the additive by additive epistasis covariance matrix between the two chromosome arms. The covariance matrices are subsequently used to estimate an epistatic interaction variance parameter in a mixed model framework, while correcting for background additive and epistatic effects. We find significant epistatic interactions for 2% of interactions tested for four agronomic traits in a population of winter wheat. Interactions across homeologous chromosome arms were identified, but were less abundant than other interaction chromosome arm pairs. Of these, homeologous chromosome arm pair 4BL and 4DL showed a strong relationship between the product of their additive effects and the interaction effect that may be indicative of functional redundancy. Several chromosome arms were involved in many interactions across the genome, suggesting that they may contain important large effect regulatory factors. The differential patterns of epistasis across different traits suggests that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of relatively lower precision.

Hierarchical Modelling of Facial Perceptions: A Secondary Analysis of Aggressiveness Ratings

2020 ◽  
Author(s):  
Mark Christopher Adkins ◽  
Nataly Beribisky ◽  
Stephan Bonfield ◽  
Linda Farmus
Keyword(s):  
Factor Analysis ◽  
Mixed Model ◽  
Structural Information ◽  
Secondary Analysis ◽  
Specific Factor ◽  
Primary Analysis ◽  
Model Framework ◽  
Psychological Science ◽  
Individual Traits ◽  
Confirmatory Factor

The Psychological Science Accelerator’s (PSA) primary project tested for latent structure using exploratory factor analysis and confirmatory factor analysis but we decided to diverge from this approach and model individual traits separately. Our interest mainly was in examining the interplay between “stimulus ethnicity” and “stimulus sex” to discover how differing levels of these criterion differ across region, country, lab etc. While the necessary and prerequisite hierarchical structural information about each trait could certainly be found within the primary project’s dataset, we did not assume that any specific factor structure from the PSA’s primary analysis would necessarily hold, therefore we based our decision to model the data from each trait separately using a mixed model framework.

Genetic Effects of 1BS Chromosome Arm on the Main Agronomic Traits in Chuanmai 42

2009 ◽  
Vol 35 (12) ◽  
pp. 2167-2173 ◽  
Author(s):  
Jun LI ◽  
Hui-Ting WEI ◽  
Su-Jie YANG ◽  
Chao-Su LI ◽  
Yong-Lu TANG ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Genetic Effects ◽  
Chromosome Arm

Epistatic Effects and QTL×Environment Interaction Effects of QTLs for Yield and Agronomic Traits in Soybean

2014 ◽  
Vol 40 (1) ◽  
pp. 37
Author(s):  
Hui-Zhen LIANG ◽  
Yong-Liang YU ◽  
Hong-Qi YANG ◽  
Hai-Yang ZHANG ◽  
Wei DONG ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interaction Effects ◽  
Environment Interaction ◽  
Epistatic Effects

scholarly journals Genetic Variability, Correlation among Agronomic Traits, and Genetic Progress in a Sugarcane Diversity Panel

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 533
Author(s):  
Fernanda Zatti Barreto ◽  
Thiago Willian Almeida Balsalobre ◽  
Roberto Giacomini Chapola ◽  
Antonio Augusto Franco Garcia ◽  
Anete Pereira Souza ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Mixed Model ◽  
Agronomic Traits ◽  
Average Increase ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Future Studies ◽  
Diversity Panel ◽  
Adjusted Means ◽  
Historical Series

Sugarcane breeding programs require 15 years of experimentation to create more productive cultivars, and estimates of genetic progress can indicate the efficiency of breeding programs. In this study, we used a diversity panel, the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) to estimate, through a mixed model, the adjusted means and genetic parameters of ten traits evaluated over three harvest years; (ii) to estimate genotypic correlation among those traits; and (iii) to estimate genetic progress over six decades of breeding. The heritabilities ranged from 0.43 to 0.88, and we detected 42 significant correlations, 9 negative and 33 positive. Over six decades, the sucrose-related traits BRIX, POL%C, and POL%J showed an average increase per decade of 0.27 °Brix (0.26% and 0.31%, respectively). Stalk number, height, and weight of the plot, and cane and sucrose yields revealed average increases per decade of 3.27 stalks, 0.06 m, 9.42 kg, 11.22 t/ha, and 2.08 t/ha, respectively. The genetic progress of the main agronomic traits is discussed through a historical series of sugarcane genotypes present in the BPSG. The findings of this study could contribute to the management of new breeding strategies and allow for future studies of associative mapping.

scholarly journals A linear mixed model framework for gene-based gene-environment interaction tests in twin studies

2018 ◽  
Vol 42 (7) ◽  
pp. 648-663 ◽  
Author(s):  
Brandon J. Coombes ◽  
Saonli Basu ◽  
Matt McGue
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Twin Studies ◽  
Environment Interaction ◽  
Model Framework ◽  
Gene Environment Interaction ◽  
Gene Environment

Grass-fed vs. grain-fed beef systems: performance, economic, and environmental trade-offs

2021 ◽  
Author(s):  
S C Klopatek ◽  
E Marvinney ◽  
T Duarte ◽  
A Kendall ◽  
X Yang ◽  
...  
Keyword(s):  
Environmental Impacts ◽  
Mixed Model ◽  
Cropping Systems ◽  
Carcass Quality ◽  
Marbling Score ◽  
Model Framework ◽  
Land Occupation ◽  
Final Body Weight ◽  
Systems Model ◽  
Trade Offs

Abstract Between increasing public concerns over climate change and heightened interest of niche market beef on social media, the demand for grass-fed beef has increased considerably. However, the demand increase for grass-fed beef has raised many producers' and consumers' concerns regarding product quality, economic viability, and environmental impacts that have thus far gone unanswered. Therefore, using a holistic approach, we investigated the performance, carcass quality, financial outcomes, and environmental impacts of four grass-fed and grain-fed beef systems currently being performed by ranchers in California. The treatments included: 1) steers stocked on pasture and feedyard finished for 128 days (CON); 2) steers grass-fed for 20 months (GF20); 3) steers grass-fed for 20 months with a 45-day grain finish (GR45); and 4) steers grass-fed for 25 months (GF25). The data were analyzed using a mixed model procedure in R with differences between treatments determined by Tukey HSD. Using carcass and performance data from these systems, a weaning-to-harvest life cycle assessment (LCA) was developed in the Scalable, Process-based, Agronomically Responsive Cropping Systems model framework, to determine global warming potential (GWP), consumable water use, energy, smog, and land occupation footprints. Final body weight varied significantly between treatments (P <0.001) with the CON cattle finishing at 632 kg, followed by GF25 at 570 kg, GR45 at 551 kg, and GF20 478 kg. Dressing percentage (DP) differed significantly between all treatments (P < 0.001). The DP was 61.8% for CON followed by GR45 at 57.5%, GF25 at 53.4%, and GF20 had the lowest DP of 50.3%. Marbling scores were significantly greater for CON compared to all other treatments (P < 0.001) with CON marbling score averaging 421 (low-choice ≥ 400). Breakeven costs with harvesting and marketing for the CON, GF20, GR45, and GF25 were $6.01, $8.98, $8.02, and $8.33 per kg hot carcass weight (HCW), respectively. The GWP for the CON, GF20, GR45, and GF25 were 4.79, 6.74, 6.65 and 8.31 CO2e/kg HCW, respectively. Water consumptive use for CON, GF20, GR45, and GF25 were 933, 465, 678 and 1250 L /kg HCW, respectively. Energy use for CON, GF20, GR45, and GF25 were 18.7, 7.65, 13.8 and 8.85 MJ /kg HCW, respectively. Our results indicated that grass-fed beef systems differ in both animal performance and carcass quality resulting in environmental and economic sustainability tradeoffs with no system having absolute superiority.

scholarly journals A Novel Approach to the Design and Analysis of Field Experiments to Study Variation in the Tolerance and Resistance of Cultivars to Root Lesion Nematodes (Pratylenchus spp.)

2020 ◽  
Vol 110 (10) ◽  
pp. 1623-1631
Author(s):  
Karyn L. Reeves ◽  
Clayton R. Forknall ◽  
Alison M. Kelly ◽  
Kirsty J. Owen ◽  
Joshua Fanning ◽  
...  
Keyword(s):  
Mixed Model ◽  
Field Experiments ◽  
Linear Mixed Model ◽  
Random Regression ◽  
Yield Response ◽  
Response Curves ◽  
Model Framework ◽  
Management Options ◽  
Nematode Reproduction ◽  
Yield Response Curves

The root lesion nematode (RLN) species Pratylenchus thornei and P. neglectus are widely distributed within cropping regions of Australia and have been shown to limit grain production. Field experiments conducted to compare the performance of cultivars in the presence of RLNs investigate management options for growers by identifying cultivars with resistance, by limiting nematode reproduction, and tolerance, by yielding well in the presence of nematodes. A novel experimental design approach for RLN experiments is proposed where the observed RLN density, measured prior to sowing, is used to condition the randomization of cultivars to field plots. This approach ensured that all cultivars were exposed to consistent ranges of RLN in order to derive valid assessments of relative cultivar tolerance and resistance. Using data from a field experiment designed using the conditioned randomization approach and conducted in Formartin, Australia, the analysis of tolerance and resistance was undertaken in a linear mixed model framework. Yield response curves were derived using a random regression approach and curves modeling change in RLN densities between sowing and harvest were derived using splines to account for nonlinearity. Groups of cultivars sharing similar resistance levels could be identified. A comparison of slopes of yield response curves of cultivars belonging to the same resistance class identified differing tolerance levels for cultivars with equivalent exposures to both presowing and postharvest RLN densities. As such, the proposed design and analysis approach allowed tolerance to be assessed independently of resistance.

scholarly journals Modeling Relations between Compacted and Uncompacted Crown Ratio for the Northern United States

2019 ◽  
Vol 65 (5) ◽  
pp. 593-601
Author(s):  
James A Westfall ◽  
Megan B E Westfall ◽  
KaDonna C Randolph
Keyword(s):  
United States ◽  
Random Effects ◽  
Goodness Of Fit ◽  
Tree Mortality ◽  
Mixed Model ◽  
The United States ◽  
Repeated Measurements ◽  
Growth Potential ◽  
Model Framework ◽  
Northern United States

Abstract Tree crown ratio is useful in various applications such as prediction of tree mortality probabilities, growth potential, and fire behavior. Crown ratio is commonly assessed in two ways: (1) compacted crown ratio (CCR—lower branches visually moved upwards to fill missing foliage gaps) and (2) uncompacted crown ratio (UNCR—no missing foliage adjustment). The national forest inventory of the United States measures CCR on all trees, whereas only a subset of trees also are assessed for UNCR. Models for 27 species groups are presented to predict UNCR for the northern United States. The model formulation is consistent with those developed for other US regions while also accounting for the presence of repeated measurements and heterogeneous variance in a mixed-model framework. Ignoring random-effects parameters, the fit index values ranged from 0.43 to 0.78, and root mean squared error spanned 0.08–0.15; considerable improvements in both goodness-of-fit statistics were realized via inclusion of the random effects. Comparison of UNCR predictions with models developed for the southern United States exhibited close agreement, whereas comparisons with models used in Forest Vegetation Simulator variants indicated poor association. The models provide additional analytical flexibility for using the breadth of northern region data in applications where UNCR is the appropriate crown characteristic.

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