scholarly journals Genetic Analysis of Yield and Quality Traits in Switchgrass Based on Population Crosses

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2220
Author(s):  
Serge Edmé ◽  
Rob Mitchell
Keyword(s):  
Genetic Variation ◽  
Combining Ability ◽  
Dry Matter ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Ethanol Yield ◽  
Lignin Content ◽  
Block Design ◽  
Likelihood Method ◽  
Single Pair

Obtaining greater genetic gains, particularly for biomass yield, requires a good understanding of the gene action governing the inheritance of traits with economic importance in switchgrass (Panicum virgatum L.). Individual genotypes from three different accessions were crossed in single-pair matings with reciprocals to assess the relative importance of additive to nonadditive genetic variation and the potential of using inter-ecotypic crosses to improve dry matter yield (DMY), in vitro dry matter digestibility (IVDMD), lignin content (ADL and KL), and ethanol yield (ETOH). Crosses and four reference populations were planted in a randomized complete block design with eight replications of single family-rows plots, with five-plants each and 1 m spacings. A linear mixed model was applied as per the restricted maximum likelihood method, integrated with a pedigree tracing back to the original founders of these parental populations, and augmented with the designation of four genetic groups. Variation due to SCA (specific combining ability) was predominant for all traits, contributing from 20% to 57% of the total phenotypic variation and with Baker’s ratios (GCA/SCA) varying from 0.003 to 0.67. Heritability values calculated at the fullsib-family mean level were moderate to very high. Variation due to GCA (general combining ability) was detected with a lesser significance for DMY and ETOH. A reciprocal GCA effect was present in the form of maternal inheritance for DMY, suggesting the use of the highest biomass-yielding parent as female in inter-ecotypic breeding. Selecting and deploying fullsib families, deploying clonal hybrids, and adopting an introgression breeding approach are all possibilities available to switchgrass breeders to exploit the complementary genes from this germplasm and capitalize on the non-additive genetic variation present in these crosses.

scholarly journals PSVII-9 Effects of a multi-species direct-fed microbial on growth performance and carcass characteristics of grow-finish pigs

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 216-216
Author(s):  
Mariana Boscato Menegat ◽  
Joel M DeRouchey ◽  
Jason C Woodworth ◽  
Mike D Tokach ◽  
Steve S Dritz ◽  
...  
Keyword(s):  
Growth Performance ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Block Design ◽  
Control Diet ◽  
Random Effect ◽  
Carcass Characteristics ◽  
Experimental Unit ◽  
Feeding Duration ◽  
Corn Distillers

Abstract This study was conducted to determine the effects of a multi-species direct-fed microbial (DFM) product based on lactic acid bacteria and Bacillus subtilis on growth performance and carcass characteristics of grow-finish pigs. A total of 1,188 pigs (PIC 359 × 1050; initially 25.8 kg BW) were used in a 121-d growth trial with 27 pigs/pen and 22 pens/treatment. Pigs were allotted to treatments based on initial BW in a randomized complete block design. Treatments included a control diet and the control diet with added DFM (BiOWiSH Technologies Inc., Cincinnati, OH) included at 0.055% of the diet at the expense of corn. Diets were based on corn, distillers dried grains with solubles, and soybean meal and fed in four dietary phases. Data were analyzed using a linear mixed model (PROC GLIMMIX, SAS®) with treatment as fixed effect, block as random effect, and pen as experimental unit. Overall (d 0 to 121), pigs fed the control diet had greater ADG (P < 0.05) and final BW (P < 0.001) compared to pigs fed the DFM diet (Table 1). There was no evidence for differences (P > 0.05) in ADFI or G:F between treatments. The difference in final BW resulted in heavier (P < 0.05) HCW in control pigs compared to DFM pigs, but no evidence for differences (P > 0.05) was observed in carcass yield, backfat, loin depth, and percentage lean between treatments. In conclusion, the inclusion of this multi-species DFM in growing-finishing diets reduced ADG in this commercial study. This response could be related to inclusion rate, feeding duration, or other factors not identified in this study, warranting further research to characterize the effects on pig performance.

A threshold linear mixed model for identification of treatment-sensitive subsets in a clinical trial based on longitudinal outcomes and a continuous covariate

2020 ◽  
Vol 29 (10) ◽  
pp. 2919-2931
Author(s):  
Xinyi Ge ◽  
Yingwei Peng ◽  
Dongsheng Tu
Keyword(s):  
Clinical Trial ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Likelihood Function ◽  
Specific Treatment ◽  
Likelihood Method ◽  
Simulation Studies ◽  
Longitudinal Outcomes ◽  
Continuous Covariate

Identification of a subset of patients who may be sensitive to a specific treatment is an important problem in clinical trials. In this paper, we consider the case where the treatment effect is measured by longitudinal outcomes, such as quality of life scores assessed over the duration of a clinical trial, and the subset is determined by a continuous baseline covariate, such as age and expression level of a biomarker. A threshold linear mixed model is introduced, and a smoothing maximum likelihood method is proposed to obtain the estimation of the parameters in the model. Broyden-Fletcher-Goldfarb-Shanno algorithm is employed to maximize the proposed smoothing likelihood function. The proposed procedure is evaluated through simulation studies and application to the analysis of data from a randomized clinical trial on patients with advanced colorectal cancer.

scholarly journals A generalized linear mixed model for understanding determinant factors of student's interest in pursuing bachelor's degree at Universitas Syiah Kuala

2021 ◽  
Vol 21 (2) ◽  
pp. 72-80
Author(s):  
ASEP RUSYANA ◽  
KHAIRIL ANWAR NOTODIPUTRO ◽  
BAGUS SARTONO
Keyword(s):  
High Schools ◽  
Normal Distribution ◽  
Random Effects ◽  
Fixed Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Likelihood Method ◽  
Response Variable ◽  
Banda Aceh

Generalized Linear Mixed Model (GLMM) is a framework that has a response variable, fixed effects, and random effects. The response variable comes from an exponential family, whereas random effects have a normal distribution. Estimating parameters can be calculated using the maximum likelihood method using the Laplace approach or the Gauss-Hermite Quadrature (GHQ) approach. The purpose of this study was to identify factors that trigger student's interest to continue studying at Universitas Syiah Kuala (USK) using both techniques.  The GLMM is suitable for the data because the variable response has a Bernoulli distribution, and the random effects are assumed to be having a normal distribution. Also, the model helps identify the relationship between the dependent variable and the predictors. This study utilizes data from six high schools in Banda Aceh city drawn using a two-stage sampling technique. Stage 1, we randomly chose six out of sixteen public senior high schools in Banda Aceh. Stage 2, we selected students from each school from four different major classes. The GLMM model includes one binary response variable, five numerical fixed-effects, and two random effects. The response variable is the interest of high school students to continue study at USK (yes or no). The five fixed effects in the model including scores of collaboration (C), Action (A), Emotion (E), Purposes (P), and Hope (H).  Finally, the random effects are schools (S) and majors (M). In this study, both Laplace and GHQ techniques produce identical results. The predictors that can explain student interest are A, E, and H. These predictors have a positive effect. The random effects of schools and majors are not significantly different from zero. The model with three significant predictors is better than the complete predictor model.

scholarly journals Effect of Herbage Density, Height and Age on Nutrient and Invertebrate Generalist Predator Abundance in Permanent and Temporary Pastures

Land ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 164
Author(s):  
Rémi Toupet ◽  
Alastair T. Gibbons ◽  
Sara L. Goodacre ◽  
Matt J. Bell
Keyword(s):  
Perennial Ryegrass ◽  
Crude Protein ◽  
Dry Matter ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Grass Species ◽  
Nutrient Concentrations ◽  
Generalist Predator ◽  
Diverse Range ◽  
Predator Abundance

The aim of this research was to assess differences in the quantity and quality of herbage and invertebrate generalist predator abundance among permanent and temporary pastures. Two permanent pastures and four temporary ley pastures (either one year or two years since being sown) were monitored weekly for 10 weeks in the spring. Permanent pastures included a diverse range of native UK grass species, and temporary ley pastures were predominantly perennial ryegrass (Lolium perenne) with or without white clover (Trifolium repens). Weekly measurements of herbage height (in centimeters), herbage cover (fresh and dry matter in kg per hectare) and herbage density (fresh and dry matter in kg per hectare per centimeter) were obtained for each field, along with lycosid spider and carabid beetle abundance. Weekly pasture samples were used to obtain nutrient concentrations of dry matter, crude protein, neutral detergent fibre (NDF), acid detergent fibre (ADF), ash, oil, sugars, digestible organic matter in the dry matter (DOMD) and metabolisable energy (ME) in the herbage as a measure of forage quality for grazing or harvesting. A linear mixed model was used to assess the effect of sward age, herbage density and height on herbage production, nutrient concentrations and invertebrate abundance. Although this study showed that permanent pastures were associated with lower nutrient concentrations of crude protein, ash, oil and ME compared to younger and predominantly perennial ryegrass pastures, the older pastures were associated with higher carabid numbers. Furthermore, permanent pastures had a higher density of dry matter herbage compared to younger pastures, and more dense and taller swards were associated with higher lycosid numbers. The study suggests that within pastures of 3 to 20 cm height, increasing the height and density of swards increases both ME and oil concentrations in herbage, therefore enhancing forage nutrient quality. Older and more permanent pastures can be beneficial for plant and invertebrate generalist predator populations, and still provide a useful source of nutrients for forage production.

scholarly journals PSV-7 Effects of a Bacillus-based probiotic on sow and litter performance, fecal consistency, and fecal microflora

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 192-193
Author(s):  
Mariana Boscato Menegat ◽  
Kiah M Gourley ◽  
Michaela B Braun ◽  
Joel M DeRouchey ◽  
Jason C Woodworth ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Litter Size ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Block Design ◽  
Experimental Unit ◽  
Bacillus Sp ◽  
Fecal Microflora ◽  
Microbial Analysis ◽  
Cross Fostering

Abstract This study evaluated the effects of supplementation of sow diets with Bacillus subtilis C-3102 (Calsporin®, Calpis Co. Ltd., Tokyo, Japan) during gestation and lactation. A total of 29 sows (DNA 241) with confirmed pregnancy on d 30 of gestation were assigned to dietary treatments in a randomized complete block design based on BW and parity. Treatments were: control diet or probiotic diet with Calsporin® at 500,000 and 1,000,000 CFU/g of diet in gestation and lactation, respectively. Data were collected on d 30 and 112 of gestation and d 2 and 19 of lactation. Fecal consistency was assessed on a 1-to-5 scale for each litter. Fecal samples were collected from sows and piglets for microbial analysis by culture method and bacterial quantification of Bacillus subtilis C-3102, total Bacillus sp., Lactobacillus sp., Clostridium perfringens, Salmonella spp., Enterococcus sp., Enterobacteriaceae, total aerobes, and total anaerobes. Data were analyzed using a linear mixed model (PROC GLIMMIX, SAS®) with sow as experimental unit. Probiotic-fed sows had a marginally significant (P < 0.10) increase in lactation ADFI, but it did not result (P > 0.10) in improvement in sow or piglet weight at weaning. Probiotic-fed sows had a marginally significant (P < 0.10) larger litter size after cross-fostering, but it did not result (P > 0.10) in larger litter size at weaning. Fecal consistency of piglets was not influenced (P > 0.10) by sow diet. Microbial analysis revealed an increase (P < 0.01) in Bacillus subtilis C-3102 and, consequently, total Bacillus sp. in fecal microflora of probiotic-fed sows and piglets born and nursed by probiotic-fed sows. In conclusion, this study demonstrates that providing Calsporin® to sows during gestation and lactation improved lactation ADFI and cross-fostering litter size, although further larger-scale studies are required for elucidation. The probiotic diet did not influence fecal consistency, but altered the fecal microbial population in sows and nursing piglets by increasing total Bacillus sp.

scholarly journals Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design

2021 ◽  
Author(s):  
Yuhua Chen ◽  
Hainan Wu ◽  
Wenguo Yang ◽  
Wei Zhao ◽  
Chunfa Tong
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Block Design ◽  
Tree Height ◽  
Genome Wide Association ◽  
Hybrid Population ◽  
Time Points ◽  
Genome Wide ◽  
Randomized Complete Block Design ◽  
Traditional Breeding

Abstract With the advances in high-throughput sequencing technologies, it is not difficult to extract tens of thousands of single nucleotide polymorphisms (SNPs) across many individuals in a fast and cheap way, making it possible to perform genome-wide association studies (GWAS) of quantitative traits in outbred forest trees. It is very valuable to apply traditional breeding experiments in GWAS for identifying genome variants associated to ecologically and economically important traits in Populus. Here, we reported a GWAS of tree height measured at multiple time points from a randomized complete block design (RCBD), which was established with clones from an F1 hybrid population of Populus deltoides and Populus simonii. A total of 22,670 SNPs across 172 clones in the RCBD were obtained with restriction site-associated DNA sequencing (RADseq) technology. The multivariate mixed linear model was applied by incorporating the pedigree relationship matrix of individuals to test the association of each SNP to the tree heights over 8 time points. Consequently, 41 SNPs were identified significantly associated to the tree height under the p-value threshold determined by Bonferroni correction at the significant level of 0.01. These SNPs were distributed on all but 2 chromosomes (Chr02 and Chr18) and explained the phenotypic variance ranged from 0.26% to 2.64%, amounting to 63.68% in total. Comparison with previous mapping studies for poplar height as well as the candidate genes of these detected SNPs were also investigated. We therefore demonstrated that the application of multivariate linear mixed model to the longitudinal phenotypic data from the traditional breeding experimental design facilitated to identify far more genome-wide variants for tree height in poplar. The significant SNPs identified in this study would enhance understanding of molecular mechanism for growth traits and would accelerate marker-assisted breeding programs in Populus.

scholarly journals Stability of Rice Mutant Lines By Linear Mixed Model And Suggestion A New Index Based For Yield Performance And Stability

2021 ◽  
Author(s):  
Peyman Sharifi ◽  
Ali Akbar Ebadi ◽  
Mohammad Taher Hallajian
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Block Design ◽  
Weighted Average ◽  
Principal Component ◽  
Fars Province ◽  
Yield Performance ◽  
Rice Mutant ◽  
Superior Genotypes ◽  
Mutant Lines

Abstract Fourteen rice mutant lines with four cultivars were evaluated in a randomized complete block design with three replications in three locations in Iran (Rasht, ChaparSar and Fars province) during two growing seasons (2014-2016). In addition, a new index namely as equivalent index of stability and performance (EISP) is suggested for simultaneous evaluation of yield performance and stability. The heat map of yield performance and WAASB (weighted average of absolute scores based on BLUP (best linear unbiased prediction)) identified G3, G9, G6, G12 and G5 as highly productive and stable genotypes. Based on the analysis by multi-trait stability index (MTSI) G7, G5 and G1 were selected as superior genotypes. The top five superior genotypes based on harmonic mean and of the relative performance of genotypic values (HMRPGV) were G5, G12, G7, G2 and G1. For verification of EISP, its value was calculated for some of multi and univariate stability indices and identified genotypes G5 and G12 as the best ones. Principal component analysis indicated yield positively correlated with HMGV, RPGV, HMRPGV, EIS2P EIbP and EIPiP. In conclusion, G12, G5 and G9 had a significant advantage over all genotypes and could undergo selection or cultivar introduction processes.

205 Dietary Strategies to Limit Average Daily Gain of Late Finishing Pigs

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 64-64
Author(s):  
Devin Goehring ◽  
Katherine A McCormick ◽  
Julie Mahoney ◽  
Rodney Hinson
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Block Design ◽  
Average Daily Gain ◽  
Finishing Pigs ◽  
Compensatory Gain ◽  
And Gender ◽  
Dietary Treatments ◽  
Dietary Strategies ◽  
Daily Gain

Abstract A total of 2,164 pigs [DNA610 x DNA241; initially 100.7 ± 2.14 kg body weight (BW)] were used in a 54.1 ± 3.85-day study to determine dietary strategies to limit average daily gain (ADG) in late finishing pigs raised in a commercial environment. Mixed-sex pens (20.0 ± 0.85 pigs/pen) balanced by initial BW and gender ratio were randomly assigned to 1 of 4 dietary treatments fed ad libitum with 27 replications each: (1) Nutritionally replete corn soybean-meal control (CTRL), (2) Treatment 1 with 21% reduced lysine and other amino acids (AAR), (3) Corn/vitamin/mineral diet (CVM), and (4) Treatment 3 fed for 21 days then switched to CTRL. Data were analyzed as a randomized complete block design using a linear mixed model. Relative to CTRL, feeding AAR or CVM for 21 days reduced ADG (P &lt; 0.001), average daily feed intake (ADFI; P = 0.005), and gain-to-feed (G:F, P &lt; 0.001). Over 55-days, AAR and CVM diets reduced (P &lt; 0.001) cumulative ADG, ADFI, G:F, and final BW compared to CTRL. Transitioning to CTRL diet from CVM diet after 21-days increased ADG (P &lt; 0.001) and improved G:F (P &lt; 0.001) from day 21 to marketing compared to 55-day CTRL, AAR, and CVM; nevertheless, the compensatory CTRL period was insufficient for the 21-day CVM fed pigs to fully compensate resulting in reduced cumulative BW, ADG (P &lt; 0.001) and poorer G:F (P &lt; 0.001) than the 55-day CTRL. All holding strategies decreased (P &lt; 0.001) carcass yield, hot carcass weight (HCW), and loin depth compared to CTRL. Utilizing a CVM diet for 21 or 55 days increased (P &lt; 0.001) backfat compared to CTRL or AAR. In summary, utilizing lysine deficient or corn/vitamin/mineral diets can limit ADG along with poorer G:F. Transitioning to a non-holding diet after feeding a corn/vitamin/mineral diet for 21-days resulted in compensatory gain, but reductions in growth performance and carcass traits remained evident.

scholarly journals Quantitative genetic basis of floral design in a natural plant population

2020 ◽  
Author(s):  
Juannan Zhou ◽  
Charles B. Fenste ◽  
Richard J. Reynolds
Keyword(s):  
Genetic Variation ◽  
Genetic Parameters ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Genetic Correlations ◽  
Natural Populations ◽  
Plant Evolution ◽  
Floral Traits ◽  
Floral Trait ◽  
Evolutionary Trajectory

AbstractThe amount of genetic variation of floral traits and the degree to which they are genetically correlated are important parameters for the study of plant evolution. Estimates of these parameters can reveal the effect of historical selection relative to neutral processes such as mutation and drift, and allow us to predict the short-term evolutionary trajectory of a population under various selective regimes. Here, we assess the heritability and genetic correlation of the floral design of a native N. American tetraploid plant, Silene stellata (Caryophyllaceae), in a natural population. Specifically, we use a linear mixed model to estimate the genetic parameters based on a genealogy reconstructed from highly variable molecular markers. Overall, we found significant heritabilities in five out of nine studied traits. The level of heritability was intermediate (0.027 – 0.441). Interestingly, the floral trait showing the highest level of genetic variation was previously shown to be under strong sexually conflicting selection, which may serve as a mechanism for maintaining the observed genetic variation. Additionally, we also found prevalent positive genetic correlations between floral traits. Our results suggest that S. stellata is capable of responding to phenotypic selection on its floral design, while the abundant positive genetic correlations could also constrain the evolutionary trajectories to certain directions. Furthermore, this study demonstrates the utility and feasibility of marker-based approaches for estimating genetic parameters in natural populations.

scholarly journals A Small Area Estimation Method for Investigating the Relationship between Public Perception of Drug Problems with Neighborhood Prognostics: Trends in London between 2012 and 2019

2021 ◽  
Vol 18 (17) ◽  
pp. 9016
Author(s):  
Arun Sondhi ◽  
Alessandro Leidi ◽  
Emily Gilbert
Keyword(s):  
Public Perception ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Statistical Significance ◽  
Local Population ◽  
Random Effect ◽  
Gaussian Quadrature ◽  
Estimation Method ◽  
Likelihood Method ◽  
Drug Problems

The correlation of the public’s perception of drug problems with neighborhood characteristics has rarely been studied. The aim of this study was to investigate factors that correlate with public perceptions in London boroughs using the Mayor’s Office for Policing and Crime (MOPAC) Public Attitude Survey between 2012 and 2019. A subject-specific random effect deploying a Generalized Linear Mixed Model (GLMM) using an Adaptive Gaussian Quadrature method with 10 integration points was applied. To obtain time trends across inner and outer London areas, the GLMM was fitted using a Restricted Marginal Pseudo Likelihood method. The perception of drug problems increased with statistical significance in 17 out of 32 London boroughs between 2012 and 2019. These boroughs were geographically clustered across the north of London. Levels of deprivation, as measured by the English Index of Multiple Deprivation, as well as the percentage of local population who were non-UK-born and recorded vehicle crime rates were shown to be positively associated with the public’s perception of drug problems. Conversely, recorded burglary rate was negatively associated with the public’s perception of drug problems in their area. The public are influenced in their perception of drug problems by neighborhood factors including deprivation and visible manifestations of antisocial behavior.

Sign in / Sign up

Export Citation Format

Share Document