Dataset Information

Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

ABSTRACT: A crucial step in plant breeding is the selection and combination of parents to form new crosses. Genome-based prediction guides the selection of high-performing parental lines in many crop breeding programs which ensures a high mean performance of progeny. To warrant maximum selection progress, a new cross should also provide a large progeny variance. The usefulness concept as measure of the gain that can be obtained from a specific cross accounts for variation in progeny variance. Here, it is shown that genetic gain can be considerably increased when crosses are selected based on their genomic usefulness criterion compared to selection based on mean genomic estimated breeding values. An efficient and improved method to predict the genetic variance of a cross based on Markov chain Monte Carlo samples of marker effects from a whole-genome regression model is suggested. In simulations representing selection procedures in crop breeding programs, the performance of this novel approach is compared with existing methods, like selection based on mean genomic estimated breeding values and optimal haploid values. In all cases, higher genetic gain was obtained compared with previously suggested methods. When 1% of progenies per cross were selected, the genetic gain based on the estimated usefulness criterion increased by 0.14 genetic standard deviation compared to a selection based on mean genomic estimated breeding values. Analytical derivations of the progeny genotypic variance-covariance matrix based on parental genotypes and genetic map information make simulations of progeny dispensable, and allow fast implementation in large-scale breeding programs.

SUBMITTER: Lehermeier C

PROVIDER: S-EPMC5714471 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

Lehermeier Christina C Teyssèdre Simon S Schön Chris-Carolin CC

Genetics 20171016 4

A crucial step in plant breeding is the selection and combination of parents to form new crosses. Genome-based prediction guides the selection of high-performing parental lines in many crop breeding programs which ensures a high mean performance of progeny. To warrant maximum selection progress, a new cross should also provide a large progeny variance. The usefulness concept as measure of the gain that can be obtained from a specific cross accounts for variation in progeny variance. Here, it is ...[more]

PMID: 29038144

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Project description:BackgroundGenomic selection can be applied to select purebreds for crossbred performance (CP). The average performance of crossbreds can be considered as the summation of two components, i.e. the breed average (BA) of the parental breeds and heterosis (H) present in crossbreds. Selection of pure breeds for CP based on genomic estimated breeding values for crossbred performance (GEBV-C) or for purebred performance (GEBV-P) may differ in their ability to exploit BA and H and can affect the merit of crossbreds in both the short and long term. Selection based on GEBV-C is beneficial for CP, because H in crossbreds is efficiently exploited, whereas selection on GEBV-P results in more genetic progress in pure breeds, which increases the BA component of CP. To investigate the outcome of selection on GEBV-C and GEBV-P in both the short and long term, a two-way crossbreeding program was simulated to test the following hypotheses: (1) does selection on GEBV-P result in higher long-term CP compared to selection on GEBV-C and (2) does selection on a combination of GEBV-P and GEBV-C lead to more long-term gain in CP than selection on either separately.MethodsWe investigated the performance of crossbreds in a two-way crossbreeding program across 40 generations and considered different criteria to select purebred parents that ranged from selection on purebred performance to selection for CP with different weights on genomic evaluations based on purebred and CP. These criteria were compared under three genetic models to investigate the effects of the amount of dominance variance, absence of over-dominance, and the structure of the reference population on CP, both in the short and long term.Results and conclusionsAlthough beneficial in the short to medium term, genomic selection in pure breeds on a criterion that specifically targets CP was inferior to selection for purebred performance in the long term. A selection criterion that maximizes a combination of short- and long-term responses in CP, should improve the components that define crossbred merit (i.e., BA and H) simultaneously.

Project description:AimTo determine whether topical lidocaine benefits esophagogastroduoduenoscopy (EGD) by decreasing propofol dose necessary for sedation or procedure-related complications.MethodsThe study was designed as a prospective, single centre, double blind, randomised clinical trial and was conducted in 2012 between January and May (NCT01489891). Consecutive patients undergoing EGD were randomly assigned to receive supplemental topical lidocaine (L; 50 mg in an excipient solution which was applied as a spray to the oropharynx) or placebo (P; taste excipients solution without active substance, similarly delivered) prior to the standard propofol sedation procedure. The propofol was administered as a bolus intravenous (iv) dose, with patients in the L and P groups receiving initial doses based on the patient's American Society of Anaesthesiologists (ASA) classification (ASA I-II: 0.50-0.60 mg/kg; ASA III-IV: 0.25-0.35 mg/kg), followed by 10-20 mg iv dose every 30-60 s at the anaesthetist's discretion. Vital signs, anthropometric measurements, amount of propofol administered, sedation level reached, examination time, and the subjective assessments of the endoscopist's and anaesthetist's satisfaction (based upon a four point Likert scale) were recorded. All statistical tests were performed by the Stata statistical software suite (Release 11, 2009; StataCorp, LP, College Station, TX, United States).ResultsNo significant differences were found between the groups treated with lidocaine or placebo in terms of total propofol dose (310.7 ± 139.2 mg/kg per minute vs 280.1 ± 87.7 mg/kg per minute, P = 0.15) or intraprocedural propofol dose (135.3 ± 151.7 mg/kg per minute vs 122.7 ± 96.5 mg/kg per minute, P = 0.58). Only when the L and P groups were analysed with the particular subgroups of female, < 65-year-old, and lower anaesthetic risk level (ASA I-II) was a statistically significant difference found (L: 336.5 ± 141.2 mg/kg per minute vs P: 284.6 ± 91.2 mg/kg per minute, P = 0.03) for greater total propofol requirements). The total incidence of complications was also similar between the two groups, with the L group showing a complication rate of 32.2% (95%CI: 21.6-45.0) and the P group showing a complication rate of 26.7% (95%CI: 17.0-39.0). In addition, the use of lidocaine had no effect on the anaesthetist's or endoscopist's satisfaction with the procedure. Thus, the endoscopist's satisfaction Likert assessments were equally distributed among the L and P groups: unsatisfactory, [L: 6.8% (95%CI: 2.2-15.5) vs P: 0% (95%CI: 0-4.8); neutral, L: 10.1% (95%CI: 4.2-19.9) vs P: 15% (95%CI: 7.6-25.7)]; satisfactory, [L: 25.4% (95%CI: 10-29.6) vs P: 18.3% (95%CI: 15.5-37.6); and very satisfactory, L: 57.6% (95%CI: 54-77.7) vs P: 66.6% (95%CI: 44.8-69.7)]. Likewise, the anaesthetist's satisfaction Likert assessments regarding the ease of maintaining a patient at an optimum sedation level without agitation or modification of the projected sedation protocol were not affected by the application of lidocaine, as evidenced by the lack of significant differences between the scores for the placebo group: unsatisfactory, L: 5.8% (95%CI: 1.3-13.2) vs P: 0% (95%CI: 0-4.8); neutral, L: 16.9% (95%CI: 8.9-28.4) vs P: 16.7% (95%CI: 8.8-27.7); satisfactory, L: 15.2% (95%CI: 7.7-26.1) vs P: 20.3% (95%CI: 11.3-31.6); and very satisfactory, L: 62.7% (95%CI: 49.9-74.3) vs P: 63.3% (95%CI: 50.6-74.7).ConclusionTopical pharyngeal anaesthesia is safe in EGD but does not reduce the necessary dose of propofol or improve the anaesthetist's or endoscopist's satisfaction with the procedure.

Project description:Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set (TS) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of [Formula: see text] and hence genetic gain, but additional recombinations could not increase genetic gain.

Dataset Information

Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

Publications

Genetic Gain Increases by Applying the Usefulness Criterion with Improved Variance Prediction in Selection of Crosses.

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