Genetic parameter estimates informed by a marker-based pedigree: a case study with Eucalyptus cladocalyx in southern Australia

Bush, David R.; Kain, Dominic; Kanowski, Peter; Matheson, A. C.

doi:10.1007/s11295-014-0798-x

Cited by 18 publications

(19 citation statements)

References 32 publications

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“…Notably, other studies have confirmed that some whole-regression methods could overestimate the heritability values [50], and therefore, these findings should be interpreted with caution. Overall, all target traits had pedigree-based heritability estimates from low to moderate (h 2 = 0.08-0.34), which are in accordance with the range usually expected for forest tree growth, flowering and stem quality related traits, including E. cladocalyx [28,29,[51][52][53][54].…”

Section: Heritability Estimatessupporting

confidence: 78%

“…The following quantitative traits were measured in 17 years-old trees: diameter at breast height (DBH), total tree height (HT), first bifurcation height (BHT), wood density (WD), stem straightness (STR) and slenderness index (SLD). The BHT was rated on a scale of five levels, in which a value of 1 is assigned to trees with a loss of the central axis in the first fifth of the tree's height, a value of 2 indicates that a loss of the central axis occurs in the second fifth of the tree, a value of 3 indicates that a loss of the central axis occurs in the third fifth of the tree, a value of 4 implies a loss of the central axis in the fourth fifth of the tree's height, and a value of 5 implies that a loss of the central axis in the last fifth of the tree height or does not show loss of the apical axis (modified scale by Bush et al [54]). WD was measured indirectly according to Valenzuela et al [28].…”

Section: Plant Materials and Phenotypic Evaluationmentioning

confidence: 99%

“…a corresponds to polygenic effects, with a~N(0, σ 2 a A), and Z is the incidence matrix related to polygenic effects. The coefficients of relationship matrix were adjusted according to Bush et al [54]. Finally, ε is the residual vector, ε~N(0,σ 2 e I n ).…”

Section: Genomic Prediction Modelsmentioning

confidence: 99%

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Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

Ballesta

Bush

Silva

et al. 2020

Plants

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High-throughput genotyping techniques have enabled large-scale genomic analysis to precisely predict complex traits in many plant species. However, not all species can be well represented in commercial SNP (single nucleotide polymorphism) arrays. In this study, a high-density SNP array (60 K) developed for commercial Eucalyptus was used to genotype a breeding population of Eucalyptus cladocalyx, yielding only ~3.9 K informative SNPs. Traditional Bayesian genomic models were investigated to predict flowering, stem quality and growth traits by considering the following effects: (i) polygenic background and all informative markers (GS model) and (ii) polygenic background, QTL-genotype effects (determined by GWAS) and SNP markers that were not associated with any trait (GSq model). The estimates of pedigree-based heritability and genomic heritability varied from 0.08 to 0.34 and 0.002 to 0.5, respectively, whereas the predictive ability varied from 0.19 (GS) and 0.45 (GSq). The GSq approach outperformed GS models in terms of predictive ability when the proportion of the variance explained by the significant marker-trait associations was higher than those explained by the polygenic background and non-significant markers. This approach can be particularly useful for plant/tree species poorly represented in the high-density SNP arrays, developed for economically important species, or when high-density marker panels are not available.

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Section: Heritability Estimatessupporting

confidence: 78%

Section: Plant Materials and Phenotypic Evaluationmentioning

confidence: 99%

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Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

Ballesta

Bush

Silva

et al. 2020

Plants

Self Cite

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“…Por outro lado, essas espécies podem ser trabalhadas para condições climáticas mais amenas visando inicialmente melhorar a sobrevivência das mesmas. Na Austrália, o E. cladocalyx e o E. occidentalis foram trabalhadas para formação de pomares para a produção de sementes melhoradas (BUSH et al, 2015;HARWOOD, 2011). O principal objetivo foi o desenvolvimento de materiais com alta tolerância à seca.…”

Section: E Argophloia E Brookeriana E Cladocalyx E Crebra E unclassified

Sobrevivência e crescimento inicial de espécies de eucalipto em diferentes condições climáticas

Silva¹,

Lee²,

Miranda³

et al. 2017

Sci. For.

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“…Estes autores encontraram herdabilidades (h²) em torno de 0,30 tanto para DAP como para altura (H). Bush et al (2015) utilizaram informação de parentesco baseada em marcadores moleculares para cálculo de parâmetros genéticos em progênies de meios-irmãos em E. cladocalyx e encontraram h²'s iguais a 0,18 e 0,36 para DAP e H, respectivamente (utilizando parentesco via marcadores), e valores iguais a 0,36 e 0,53 utilizando informação de famílias. Valores de h²'s mais baixos como aos desses dois trabalhos são tipicamente encontrados em populações iniciais ou intermediárias de melhoramento , contrastando por este motivo, com os valores de h²'s dos testes clonais apresentados neste trabalho (resultados descritos a seguir).…”

Section: Tabela 2 Comparação Do Ajuste Dos 4 Modelos Utilizadosunclassified

Acurácia preditiva de testes clonais de Eucalyptus spp. utilizando efeitos aditivos do parentesco e validação cruzada

Resende¹,

Resende²,

Silva³

et al. 2017

Sci. For.

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ResumoO uso de extensos plantios clonais é uma prática consenso nas empresas florestais. No entanto, os modelos estatísticos e o tamanho das parcelas utilizadas na seleção dos clones superiores ainda é uma questão entre os melhoristas florestais. Com base em 11 experimentos contendo parcelas semelhantes aos plantios comerciais e 63 clones, este trabalho objetivou avaliar o uso de informação de pedigree, heterogeneidade genética entre ambientes e a possibilidade de redução de parcelas, a fim de otimizar a predição do incremento médio anual (IMA) realizando validação cruzada entre ambientes. Os ambientes proporcionaram altas herdabilidades no sentido-restrito (entre 0,65 a 0,95) e forte alteração dos rankings entre experimentos. A inclusão de parentesco e variâncias genéticas particulares para cada ambiente ao modelo é um procedimento eficiente na melhoria das acurácias realizadas. Além disso, 4 a 16 plantas avaliadas por parcela é uma quantidade confiável para predizer a produtividade dos talhões florestais. Palavras AbstractLarge clonal planting is a practice already established by the timber companies. However, statistical models, the plot size used in selection of superior clones is still a topic of discussion between forest breeders. Based on 11 trials containing plots similar to commercial plantations and 63 clones, this study aimed to evaluate the use of pedigree information, genetic heterogeneity between environments and the possibility of plot reduction in order to optimize the predictive accuracies of the mean annual increment (MAI) performing cross-validation between environments. All trials showed high narrow-sense heritabilities (from 0.65 to 0.95) and a strong change of clonal rankings was verified. It was observed that the inclusion of pedigree information and particular genetic variances for each trial on model is an effective procedure to increase the predictive accuracies. Moreover, between 4-16 trees evaluated per plot is a reliable size for the prediction of forest stands.

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Genetic parameter estimates informed by a marker-based pedigree: a case study with Eucalyptus cladocalyx in southern Australia

Cited by 18 publications

References 32 publications

Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

Sobrevivência e crescimento inicial de espécies de eucalipto em diferentes condições climáticas

Acurácia preditiva de testes clonais de Eucalyptus spp. utilizando efeitos aditivos do parentesco e validação cruzada

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