Dataset Information

Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar.

ABSTRACT: Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining selection from phenotypic evaluation without affecting precision. In this study, we tried to compare GS to pedigree-based traditional evaluation, and evaluated under which conditions genomic evaluation outperforms classical pedigree evaluation. Several conditions were evaluated as the constitution of the training population by cross-validation, the implementation of multi-trait, single trait, additive and non-additive models with different estimation methods (G-BLUP or weighted G-BLUP). Finally, the impact of the marker densification was tested through four marker density sets. The population under study corresponds to a pedigree of 24 parents and 1,011 offspring, structured into 35 full-sib families. Four evaluation batches were planted in the same location and seven traits were evaluated on 1 and 2 years old trees. The quality of prediction was reported by the accuracy, the Spearman rank correlation and prediction bias and tested with a cross-validation and an independent individual test set. Our results show that genomic evaluation performance could be comparable to the already well-optimized pedigree-based evaluation under certain conditions. Genomic evaluation appeared to be advantageous when using an independent test set and a set of less precise phenotypes. Genome-based methods showed advantages over pedigree counterparts when ranking candidates at the within-family levels, for most of the families. Our study also showed that looking at ranking criteria as Spearman rank correlation can reveal benefits to genomic selection hidden by biased predictions.

SUBMITTER: Pegard M

PROVIDER: S-EPMC7655903 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar.

Pégard Marie M Segura Vincent V Muñoz Facundo F Bastien Catherine C Jorge Véronique V Sanchez Leopoldo L

Frontiers in plant science 20201028

Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining sel ...[more]

PMID: 33193528

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Project description:Infant sociability is generally conceived in terms of dyadic capacities and behaviors. Recently, quantitative evidence has been published to support arguments that infants achieve a criterion for groupness: the capacity to interact simultaneously with two others. Such studies equate this capacity with alternating dyadic acts to the two other members of an interacting trio. Here we propose a stricter threefold criterion for infant groupness, of which the crux is whether the social behavior of an infant at time B is shown to be influenced by what two or more group-members were previously doing at time A. We test the viability of this conceptualization: (a) through its justification of the novel laboratory procedure of studying infant sociability in infant-peer quartets (rather than trios); and, (b) in an analysis of a pilot study of gaze-behavior recorded in 5-min interactions among two quartets of infants aged 6-9 months. We call this a 'proof of concept' because our aim is to show that infants are capable of groupness, when groupness is conceptualized in a supra-dyadic way-not that all infants will manifest it, nor that all conditions will produce it, nor that it is commonplace in infants' everyday lives. We found that both quartets did achieve the minimum criterion of groupness that we propose: mutual gaze predicting coordinated gaze (where two babies, A and B, are looking at each other, and B is then looked at by C, and sometimes D) more strongly than the reverse. There was a significant absence of 'parallel mutual gaze,' where the four babies pair off. We conclude that, under specific conditions, preverbal infants can manifest supra-dyadic groupness. Infants' capacities to exhibit groupness by 9 months of age, and the paucity of parallel mutual gaze in our data, run counter to the assumption that infant sociability, when in groups, is always generated by a dyadic program. Our conceptualization and demonstration of groupness in 8-month-olds thus opens a host of empirical, theoretical, and practical questions about the sociability and care of young babies.

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Dataset Information

Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar.

Publications

Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar.

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