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

Pégard, Marie; Segura, Vincent; Muñoz, Facundo; Bastien, Catherine; Jorge, Véronique; Sanchez, Léopoldo

doi:10.3389/fpls.2020.581954

Cited by 24 publications

(37 citation statements)

References 96 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Spearman's rank correlations may have amplified the benefits of genomic models in black poplar (Pégard et al, 2020) whereas in Norway spruce they were similar between pedigree-based and genomic-based models (Chen et al, 2019), coinciding with our results.…”

Section: Predictive Ability Predictive Accuracy and Spearman Rank Correlationssupporting

confidence: 89%

“…(Ukrainetz and Mansfield, 2020). Given that the correlation between an individual phenotype and its true breeding value cannot be larger than the square root of heritability, r 2 is recognized as an unbiased estimation of accuracy of selection from n-fold-cross validation (Legarra et al, 2008;Meuwissen et al, 2013), thus r 2 has begun to be more standard used in forest tree GS studies (Lenz et al, 2019(Lenz et al, , 2020Calleja-Rodríguez et al, 2020;Klápšte et al, 2020;Pégard et al, 2020;Zhou et al, 2020). Similar r 1 were observed, for all models and traits evaluated for Scots pine, which agrees with previous studies (Bouvet et al, 2016;de Almeida Filho et al, 2016;Chen et al, 2019), but differs from other eucalyptus reports in which the genomic models performed better (Tan et al, 2018), yet in the same study inconsistencies in the original pedigree were detected, and a pseudo-pedigree was used.…”

Section: Predictive Ability Predictive Accuracy and Spearman Rank Correlationsmentioning

confidence: 99%

“…Low estimates of nonadditive genetic variation may not necessarily mean this source of variation is not present since a suitable family structure and a proper mating design are also needed to obtain reliable estimates of nonadditive genetic effects (Munoz et al, 2014 ; Chen et al, 2020 ). Also, the lack of a good mating design would lead to a poor estimation power of variance components (Framton and Huber, 1995 ; Pégard et al, 2020 ) and attention should be paid when exploiting full-sib family structures. The role of dominance effects in many clonal and full-sib breeding programs is well studied, whereas less is known of epistatic variance.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

et al. 2021

View full text Add to dashboard Cite

Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive × additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.

show abstract

Section: Predictive Ability Predictive Accuracy and Spearman Rank Correlationssupporting

confidence: 89%

Section: Predictive Ability Predictive Accuracy and Spearman Rank Correlationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The population used in the study included 1009 individuals from the French breeding population of Populus nigra (Pégard et al, 2020). All of them were genotyped with a 12k Infinium array (Faivre-Rampant et al, 2016) resulting in 5253 usable SNP markers after quality and frequency filtering (minor allele frequency higher than 0.05).…”

Section: Genomic Datamentioning

confidence: 99%

“…The resulting genotypes were phased, imputed and a consensus recombination map derived (Pégard et al, 2019) by using FImpute software (Sargolzaei et al, 2014). The allelic effects were estimated from a genomic multitrait evaluation using breedR (Muñoz & Sanchez, 2020). In this study, we considered the trunk circumference as a focal trait.…”

Section: Genomic Datamentioning

confidence: 99%

How to achieve a higher selection plateau in forest tree breeding? Fostering Heterozygote x Homozygote relationships in Optimal Contribution Selection in the case study of Populus nigra

Tiret

Pégard

Leopoldo

2021

Preprint

Self Cite

View full text Add to dashboard Cite

In breeding programs, balancing short-term genetic gain and loss of diversity per generation is essential to sustain a long-term genetic response. Depending on the dynamic of the species, the acceptable trade-off will be different. One of the most common and successful tools to achieve this management is the Optimal Contribution Selection (OCS), which readily mathematically formulate the trade-off between genetic gain and coancestry. However, OCS only accounts for the next generation gain and diversity, which can lead to suboptimality given the uncertainties of random mating and segregation. In this paper, we have extended the OCS by conveniently integrating a way to promote certain parental pairs, so that this method can account for the next t+2 generation. In the study case of Populus nigra, fully phenotyped and SNP array genotyped, we have shown that (i) a non negligible part of the long-term success of a breeding strategy depends on the implemented mating strategy, and (ii) favoring a compensatory mating can accelerate the selection without compromising the future diversity.

show abstract

Applied Genomics in Poplar: Innovative Breeding

Klápště,

Silva-Duque,

Cortés

2024

Compendium of Plant Genomes

View full text Add to dashboard Cite

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

Cited by 24 publications

References 96 publications

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

How to achieve a higher selection plateau in forest tree breeding? Fostering Heterozygote x Homozygote relationships in Optimal Contribution Selection in the case study of Populus nigra

Applied Genomics in Poplar: Innovative Breeding

Contact Info

Product

Resources

About