Single‐Step Reaction Norm Models for Genomic Prediction in Multienvironment Recurrent Selection Trials

Crop Science ◽  
2018 ◽  
Vol 58 (2) ◽  
pp. 592-607 ◽  
Author(s):  
Odilon P. Morais Júnior ◽  
João Batista Duarte ◽  
Flávio Breseghello ◽  
Alexandre S. G. Coelho ◽  
Orlando P. Morais ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Recurrent Selection ◽  
Reaction Norm ◽  
Single Step ◽  
Single Step Reaction

scholarly journals Inter- and Intra-Generation Genomic Predictions for Douglas-fir Growth in Unobserved Environments

2019 ◽  
Author(s):  
Blaise Ratcliffe ◽  
Francis Thistlethwaite ◽  
Omnia Gamal El-Dien ◽  
Eduardo P. Cappa ◽  
Ilga Porth ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Environmental Heterogeneity ◽  
Prediction Models ◽  
Reaction Norm ◽  
Douglas Fir ◽  
Single Step ◽  
Exome Capture ◽  
Experimental Population ◽  
Training Population ◽  
The Impact

ABSTRACTConifers are prime candidates for genomic selection (GS) due to their long breeding cycles. Previous studies have shown much reduced prediction accuracies (PA) of breeding values in unobserved environments, which may impede its adoption. The impact of explicit environmental heterogeneity modeling including genotype-by-environment (G×E) interaction effects using environmental covariates (EC) in a reaction-norm genomic prediction model was tested using single-step GBLUP (ssGBLUP). A three-generation coastal Douglas-fir experimental population with 14 genetic trials (n = 13,615) permitted estimation of intra- and inter-generation PA in unobserved environments using 66,969 SNPs derived from exome capture. Intra- and inter-generation PAs ranged from 0.447-0.640 and 0.317-0.538, respectively. The inclusion of ECs in the prediction models explained up to 23% of the phenotypic variation for the fully specified model and resulted in the best model fit. Modeling G×E effects in the training population increased PA up to 6% and 13% over the base model for inter- and intra-generations, respectively. GS-PA can be substantially improved using ECs to explain environmental heterogeneity and G×E effects. The ssGBLUP methodology allows historical genetic trials containing non-genotyped samples to contribute in genomic prediction, and, thus, effectively boosting training population size which is a critical step. Further pheno- and enviro-typing developments may improve GS-PA.

Computational Study on the Kinetics and Mechanisms of Unimolecular Reactions of (Z)-(Z)-N-(λ5-phosphanylidene) Formohydrazonic Formic Anhydride: Intramolecular aza-Wittig Reaction in Competition with Mumm Rearrangement

2020 ◽  
Vol 17 (11) ◽  
pp. 884-889
Author(s):  
Somayeh Mirdoraghi ◽  
Hamed Douroudgari ◽  
Farideh Piri ◽  
Morteza Vahedpour
Keyword(s):  
Rate Constants ◽  
Density Functional ◽  
Wittig Reaction ◽  
Computational Study ◽  
Single Step ◽  
Low Energy ◽  
Coupled Cluster ◽  
Unimolecular Reaction ◽  
Single Step Reaction ◽  
Good Agreement

For (Z)-(Z)-N-(λ5-phosphanylidene) formohydrazonic formic anhydride, Aza-Wittig reaction and Mumm rearrangement are studied using both density functional and coupled cluster theories. For this purpose, two different products starting from one substrate are considered that are competing with each other. The obtained products, P1 and P2, are thermodynamically favorable. The product of the aza-Wittig reaction, P1, is more stable than the product of Mumm rearrangement (P2). For the mentioned products, just one reliable pathway is separately proposed based on unimolecular reaction. Therefore, the rate constants based on RRKM theory in 300-600 K temperature range are calculated. Results show that the P1 generation pathway is a suitable path due to low energy barriers than the path P2. The first path has three steps with three transition states, TS1, TS2, and TS3. The P2 production path is a single-step reaction. In CCSD level, the computed barrier energies are 14.55, 2.196, and 10.67 kcal/mol for Aza-Wittig reaction and 42.41 kcal/mol for Mumm rearrangement in comparison with the corresponding complexes or reactants. For final products, the results of the computational study are in a good agreement with experimental predictions.

scholarly journals Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rui Shi ◽  
Luiz Fernando Brito ◽  
Aoxing Liu ◽  
Hanpeng Luo ◽  
Ziwei Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Dairy Cattle ◽  
Candidate Genes ◽  
Heat Tolerance ◽  
Reaction Norm ◽  
Single Step ◽  
Conception Rate ◽  
Critical Periods ◽  
Genotype By Environment ◽  
Fertility Traits

Abstract Background The effect of heat stress on livestock production is a worldwide issue. Animal performance is influenced by exposure to harsh environmental conditions potentially causing genotype-by-environment interactions (G × E), especially in highproducing animals. In this context, the main objectives of this study were to (1) detect the time periods in which heifer fertility traits are more sensitive to the exposure to high environmental temperature and/or humidity, (2) investigate G × E due to heat stress in heifer fertility traits, and, (3) identify genomic regions associated with heifer fertility and heat tolerance in Holstein cattle. Results Phenotypic records for three heifer fertility traits (i.e., age at first calving, interval from first to last service, and conception rate at the first service) were collected, from 2005 to 2018, for 56,998 Holstein heifers raised in 15 herds in the Beijing area (China). By integrating environmental data, including hourly air temperature and relative humidity, the critical periods in which the heifers are more sensitive to heat stress were located in more than 30 days before the first service for age at first calving and interval from first to last service, or 10 days before and less than 60 days after the first service for conception rate. Using reaction norm models, significant G × E was detected for all three traits regarding both environmental gradients, proportion of days exceeding heat threshold, and minimum temperature-humidity index. Through single-step genome-wide association studies, PLAG1, AMHR2, SP1, KRT8, KRT18, MLH1, and EOMES were suggested as candidate genes for heifer fertility. The genes HCRTR1, AGRP, PC, and GUCY1B1 are strong candidates for association with heat tolerance. Conclusions The critical periods in which the reproductive performance of heifers is more sensitive to heat stress are trait-dependent. Thus, detailed analysis should be conducted to determine this particular period for other fertility traits. The considerable magnitude of G × E and sire re-ranking indicates the necessity to consider G × E in dairy cattle breeding schemes. This will enable selection of more heat-tolerant animals with high reproductive efficiency under harsh climatic conditions. Lastly, the candidate genes identified to be linked with response to heat stress provide a better understanding of the underlying biological mechanisms of heat tolerance in dairy cattle.

scholarly journals Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 266
Author(s):  
Hossein Mehrban ◽  
Masoumeh Naserkheil ◽  
Deuk Hwan Lee ◽  
Chungil Cho ◽  
Taejeong Choi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Beef Cattle ◽  
Genomic Prediction ◽  
Quantitative Trait ◽  
Carcass Traits ◽  
Best Linear Unbiased Prediction ◽  
Single Step ◽  
Linear Unbiased Prediction ◽  
Single Nucleotide ◽  
Best Linear Unbiased

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

scholarly journals Genomic prediction in a nuclear population of layers using single-step models

2018 ◽  
Vol 97 (2) ◽  
pp. 397-402 ◽  
Author(s):  
Yiyuan Yan ◽  
Guiqin Wu ◽  
Aiqiao Liu ◽  
Congjiao Sun ◽  
Wenpeng Han ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Single Step

scholarly journals The Accuracy and Bias of Single-Step Genomic Prediction for Populations Under Selection

2017 ◽  
Vol 7 (8) ◽  
pp. 2685-2694 ◽  
Author(s):  
Wan-Ling Hsu ◽  
Dorian J. Garrick ◽  
Rohan L. Fernando
Keyword(s):  
Genomic Prediction ◽  
Single Step

scholarly journals Kinetics of solvolysis in water of four secondary alkyl nitrates

1982 ◽  
Vol 60 (13) ◽  
pp. 1780-1785 ◽  
Author(s):  
Ross Elmore Robertson ◽  
Kalvelil Matthew Koshy ◽  
Adrianne Annessa ◽  
Jan N. Ong ◽  
John Marshall William Scott ◽  
...  
Keyword(s):  
Heat Capacity ◽  
Rate Constant ◽  
Analytical Methods ◽  
Kinetic Data ◽  
Activation Parameters ◽  
Single Step ◽  
Alkyl Nitrates ◽  
Two Stage ◽  
Kinetics Of ◽  
Single Step Reaction

Kinetic data are reported for the solvolysis in water of propane-2-nitrate, butane-2-nitrate, cyclopentyl nitrate, and cyclohexyl nitrate. In each case, the dependence of rate constant on temperature is analysed in terms of two mechanisms for the solvolytic reaction. First it is assumed that the rate constant describes a single step reaction, the analysis leading to estimates of the heat capacity of activation ΔCp≠. Three different analytical methods are discussed in this regard. Second it is assumed that the rate constant describes a two stage mechanism, the first stage being reversible. In this case the explanation of the ΔCp≠ term calculated according to the first mechanism is quite different. We comment on the alternative explanations of trends in activation parameters.

scholarly journals Crystal structure of 2-(4-chlorophenyl)-2-oxoethyl 3-bromobenzoate

2014 ◽  
Vol 70 (11) ◽  
pp. 301-304 ◽  
Author(s):  
Imtiaz Khan ◽  
Aliya Ibrar ◽  
Shahid Hameed ◽  
Jonathan M. White ◽  
Jim Simpson
Keyword(s):  
Crystal Structure ◽  
Single Step ◽  
Stacking Interactions ◽  
Axis Direction ◽  
Π Stacking ◽  
Methylene Group ◽  
Single Step Reaction ◽  
Aryl Ester ◽  
Aryl Ketone

2-(4-Chlorophenyl)-2-oxoethyl 3-bromobenzoate, C15H10BrClO3, was synthesized in a single-step reaction by condensation of 3-bromobenzoic acid with 2-bromo-1-(4-chlorophenyl)ethanone in dimethylformamide in the presence of triethylamine as a catalyst. The structure consists of an aryl ketone moiety linked to an aryl ester unit by a methylene group. Both units are reasonably planar (r.m.s. deviations of 0.119 and 0.010 Å for the aryl ketone and aryl ester units, respectively) and are almost orthogonal, with an angle of 88.60 (3)° between them. In the crystal, molecules form five separate sets of inversion dimers. Three of these are generated by two C—H...O interactions and a C—H...Br contact, and form chains alongcand along theabcell diagonal. In addition, two inversion-related π–π stacking interactions between like aryl rings again form chains of molecules but in this instance along thebcdiagonal. These contacts generate infinite layers of molecules parallel to (011) and stack the molecules along thea-axis direction.

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