Dataset Information

Phenotypic Selection in Ornamental Breeding: It's Better to Have the BLUPs Than to Have the BLUEs.

ABSTRACT: Plant breeders always face the challenge to select the best individuals. Selection methods are required that maximize selection gain based on available data. When several crosses have been made, the BLUP procedure achieves this by combining phenotypic data with information on pedigree relationships via an index, known as family-index selection. The index, estimated based on the intra-class correlation coefficient, exploits the relationship among individuals within a family relative to other families in the population. An intra-class correlation coefficient of one indicates that the individual performance can be fully explained based on the family background, whereas an intra-class correlation coefficient of zero indicates the performance of individuals is independent of the family background. In the case the intra-class correlation coefficient is one, family-index selection is considered. In the case the intra-class correlation coefficient is zero, individual selection is considered. The main difference between individual and family-index selection lies in the adjustment in estimating the individual's effect depending on the intra-class correlation coefficient afforded by the latter. Two examples serve to illustrate the application of the BLUP method. The efficiency of individual and family-index selection was evaluated in terms of the heritability obtained from linear mixed models implementing the selection methods by suitably defining the treatment factor as the sum of individual and family effect. Family-index selection was found to be at least as efficient as individual selection in Dianthus caryophyllus L., except for flower size in standard carnation and vase life in mini carnation for which traits family-index selection outperformed individual selection. Family-index selection was superior to individual selection in Pelargonium zonale in cases when the heritability was low. Hence, the pedigree-based BLUP procedure can enhance selection efficiency in production-related traits in P. zonale or shelf-life related in D. caryophyllus L.

SUBMITTER: Molenaar H

PROVIDER: S-EPMC6230591 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

Phenotypic Selection in Ornamental Breeding: It's Better to Have the BLUPs Than to Have the BLUEs.

Molenaar Heike H Boehm Robert R Piepho Hans-Peter HP

Frontiers in plant science 20181105

Plant breeders always face the challenge to select the best individuals. Selection methods are required that maximize selection gain based on available data. When several crosses have been made, the BLUP procedure achieves this by combining phenotypic data with information on pedigree relationships via an index, known as family-index selection. The index, estimated based on the intra-class correlation coefficient, exploits the relationship among individuals within a family relative to other fami ...[more]

PMID: 30455707

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Project description:Key messageA breeding strategy combining genomic with one-stage phenotypic selection maximizes annual selection gain for net merit. Choice of the selection index strongly affects the selection gain expected in individual traits. Selection indices using genomic information have been proposed in crop-specific scenarios. Routine use of genomic selection (GS) for simultaneous improvement of multiple traits requires information about the impact of the available economic and logistic resources and genetic properties (variances, trait correlations, and prediction accuracies) of the breeding population on the expected selection gain. We extended the R package "selectiongain" from single trait to index selection to optimize and compare breeding strategies for simultaneous improvement of two traits. We focused on the expected annual selection gain (ΔGa) for traits differing in their genetic correlation, economic weights, variance components, and prediction accuracies of GS. For all scenarios considered, breeding strategy GSrapid (one-stage GS followed by one-stage phenotypic selection) achieved higher ΔGa than classical two-stage phenotypic selection, regardless of the index chosen to combine the two traits and the prediction accuracy of GS. The Smith-Hazel or base index delivered higher ΔGa for net merit and individual traits compared to selection by independent culling levels, whereas the restricted index led to lower ΔGa in net merit and divergent results for selection gain of individual traits. The differences among the indices depended strongly on the correlation of traits, their variance components, and economic weights, underpinning the importance of choosing the selection indices according to the goal of the breeding program. We demonstrate our theoretical derivations and extensions of the R package "selectiongain" with an example from hybrid wheat by designing indices to simultaneously improve grain yield and grain protein content or sedimentation volume.

Project description:In migratory birds, early arrival on breeding sites is typically associated with greater breeding success, but the mechanisms driving these benefits are rarely known. One mechanism through which greater breeding success among early arrivers can potentially be achieved is the increased time available for replacement clutches following nest loss. However, the contribution of replacement clutches to breeding success will depend on seasonal variation in nest survival rates, and the consequences for juvenile recruitment of hatching at different times in the season. In particular, lower recruitment rates of late-hatched chicks could offset the benefits to early arrivers of being able to lay replacement clutches, which would reduce the likelihood of replacement clutch opportunities influencing selection on migratory timings. Using a simulation model of time-constrained capacity for replacement clutches, paramaterized with empirically-derived estimates from avian migratory systems, we show that greater reproductive success among early-arriving individuals can arise solely through the greater time capacity for replacement clutches among early arrivers, even when later renesting attempts contribute fewer recruits to the population. However, these relationships vary depending on the seasonal pattern of nest survival. The benefits of early arrival are greatest when nest survival rates are constant or decline seasonally, and early arrival is least beneficial when nest success rates increase over the breeding season, although replacement clutches can mitigate this effect. The time benefits of early arrival facilitating replacement clutches following nest loss may therefore be an important but overlooked source of selection on migratory timings. Empirical measures of seasonal variation in nest survival, renesting, and juvenile recruitment rates are therefore needed in order to identify the costs and benefits associated with individual migration phenology, the selection pressures influencing migratory timings, and the implications for ongoing shifts in migration and breeding phenology.

Project description:Key messageWe evaluated genomic selection across five breeding cycles of bread wheat breeding. Bias of within-cycle cross-validation and methods for improving the prediction accuracy were assessed. The prospect of genomic selection has been frequently shown by cross-validation studies using the same genetic material across multiple environments, but studies investigating genomic selection across multiple breeding cycles in applied bread wheat breeding are lacking. We estimated the prediction accuracy of grain yield, protein content and protein yield of 659 inbred lines across five independent breeding cycles and assessed the bias of within-cycle cross-validation. We investigated the influence of outliers on the prediction accuracy and predicted protein yield by its components traits. A high average heritability was estimated for protein content, followed by grain yield and protein yield. The bias of the prediction accuracy using populations from individual cycles using fivefold cross-validation was accordingly substantial for protein yield (17-712 %) and less pronounced for protein content (8-86 %). Cross-validation using the cycles as folds aimed to avoid this bias and reached a maximum prediction accuracy of [Formula: see text] = 0.51 for protein content, [Formula: see text] = 0.38 for grain yield and [Formula: see text] = 0.16 for protein yield. Dropping outlier cycles increased the prediction accuracy of grain yield to [Formula: see text] = 0.41 as estimated by cross-validation, while dropping outlier environments did not have a significant effect on the prediction accuracy. Independent validation suggests, on the other hand, that careful consideration is necessary before an outlier correction is undertaken, which removes lines from the training population. Predicting protein yield by multiplying genomic estimated breeding values of grain yield and protein content raised the prediction accuracy to [Formula: see text] = 0.19 for this derived trait.

Project description:Key messageSelection response in truncation selection across multiple sets of candidates hinges on their post-selection proportions, which can deviate grossly from their initial proportions. For BLUPs, using a uniform threshold for all candidates maximizes the selection response, irrespective of differences in population parameters. Plant breeding programs typically involve multiple families from either the same or different populations, varying in means, genetic variances and prediction accuracy of BLUPs or BLUEs for true genetic values (TGVs) of candidates. We extend the classical breeder's equation for truncation selection from single to multiple sets of genotypes, indicating that the expected overall selection response (ΔGTot) for TGVs depends on the selection response within individual sets and their post-selection proportions. For BLUEs, we show that maximizing ΔGTot requires thresholds optimally tailored for each set, contingent on their population parameters. For BLUPs, we prove that ΔGTot is maximized by applying a uniform threshold across all candidates from all sets. We provide explicit formulas for the origin of the selected candidates from different sets and show that their proportions before and after selection can differ substantially, especially for sets with inferior properties and low proportion. We discuss implications of these results for (a) optimum allocation of resources to training and prediction sets and (b) the need to counteract narrowing the genetic variation under genomic selection. For genomic selection of hybrids based on BLUPs of GCA of their parent lines, selecting distinct proportions in the two parent populations can be advantageous, if these differ substantially in the variance and/or prediction accuracy of GCA. Our study sheds light on the complex interplay of selection thresholds and population parameters for the selection response in plant breeding programs, offering insights into the effective resource management and prudent application of genomic selection for improved crop development.

Dataset Information

Phenotypic Selection in Ornamental Breeding: It's Better to Have the BLUPs Than to Have the BLUEs.

Publications

Phenotypic Selection in Ornamental Breeding: It's Better to Have the BLUPs Than to Have the BLUEs.

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