Genomic relationship–based genetic parameters and prospects of genomic selection for growth and wood quality traits in Eucalyptus benthamii

Paludeto, João Gabriel Zanon; Grattapaglia, Dário; Estopa, Regiane Abjaud; Tambarussi, Evandro Vagner

doi:10.1007/s11295-021-01516-9

Cited by 13 publications

(8 citation statements)

References 95 publications

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“…Dairy cattle breeding with a longer history of GS is probably the best example where such a comparative assessment has been made, showing significant improvements in genetic gains per unit time in a number of production and fitness traits [47]. In forest trees, simulations based on deterministic models [1] and experimental data [82,83] have shown that GS would have a tremendous impact in terms of improved efficiency in genetic gain per unit time when breeding cycle length is reduced and selection intensity increased.…”

Section: How Has Gs Performed When Benchmarked Against Conventional P...mentioning

confidence: 99%

Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding

Grattapaglia

2022

Forests

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Twelve years have passed since the early outlooks of applying genomic selection (GS) to forest tree breeding, initially based on deterministic simulations, soon followed by empirical reports. Given its solid projections for causing a paradigm shift in tree breeding practice in the years to come, GS went from a hot, somewhat hyped, topic to a fast-moving area of applied research and operational implementation worldwide. The hype cycle curve of emerging technologies introduced by Gartner Inc. in 1995, models the path a technology takes in terms of expectations of its value through time. Starting with a sudden and excessively positive “peak of inflated expectations” at its introduction, a technology that survives the “valley of disappointment” moves into maturity to climb the “slope of enlightenment”, to eventually reach the “plateau of productivity”. Following the pioneering steps of GS in animal breeding, we have surpassed the initial phases of the Gartner hype cycle and we are now climbing the slope of enlightenment towards a wide application of GS in forest tree breeding. By merging modern high-throughput DNA typing, time-proven quantitative genetics and mixed-model analysis, GS moved the focus away from the questionable concept of dissecting a complex, polygenic trait in its individual components for breeding advancement. Instead of trying to find the needle in a haystack, i.e., the “magic” gene in the complex and fluid genome, GS more efficiently and humbly “buys the whole haystack” of genomic effects to predict complex phenotypes, similarly to an exchange-traded fund that more efficiently “buys the whole market”. Tens of studies have now been published in forest trees showing that GS matches or surpasses the performance of phenotypic selection for growth and wood properties traits, enhancing the rate of genetic gain per unit time by increasing selection intensity, radically reducing generation interval and improving the accuracy of breeding values. Breeder-friendly and cost-effective SNP (single nucleotide polymorphism) genotyping platforms are now available for all mainstream plantation forest trees, but methods based on low-pass whole genome sequencing with imputation might further reduce genotyping costs. In this perspective, I provide answers to why GS will soon become the most efficient and effective way to carry out advanced tree breeding, and outline a simple pilot demonstration project that tree breeders can propose in their organization. While the fundamental properties of GS in tree breeding are now solidly established, strategic, logistics and financial aspects for the optimized adoption of GS are now the focus of attentions towards the plateau of productivity in the cycle, when this new breeding method will become fully established into routine tree improvement.

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Section: How Has Gs Performed When Benchmarked Against Conventional P...mentioning

confidence: 99%

Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding

Grattapaglia

2022

Forests

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“…(EUChip60K and Euc72K). In the case of Eucalyptus , the two SNP arrays have been used in a large number of studies (e.g., Telfer et al, 2015 ; Müller et al, 2019 ; Marco de Lima et al, 2019 ; Mhoswa et al, 2020 ; Ballesta et al, 2018 ; Mostert-O'Neill et al, 2020 ; Jurcic et al, 2021 ; Paludeto etal., 2021 ; Valenzuela et al, 2021 ; Tan and Ingvarsson, 2022 ; Duarte et al, 2023 ). Given its multispecies nature, this platform generally provides between 10,000 and 30,000 informative SNPs in all planted species.…”

Section: Introductionmentioning

confidence: 99%

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Aguirre,

Villalba,

García

et al. 2024

Front. Genet.

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Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.

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Section: Introductionmentioning

confidence: 99%

“…However, the increased accessibility of high-density genome sequencing techniques 15 , 17 has enabled the acquisition of genomic information from individuals of interest, allowing breeders to construct the realized relationship matrix (G matrix), which represents the genetic sharing among individuals, and can replace the pedigree-based relationship matrix (A matrix) 18 . Substitution of the A matrix for the G matrix results in the genomic best linear unbiased predictor (GBLUP) method 19 , which can provide more accurate predictions of individual genetic values 14 , 17 . The use of genomic markers represents an enormous opportunity for non-domesticated species, as it allows decomposition of the genetic variance into its additive and non-additive terms, which would not be possible under normal conditions with unknown parents, providing fundamental information to breeders on the genetic control of the traits studied.…”

Section: Introductionmentioning

confidence: 99%

Genomic studies of the additive and dominant genetic control on production traits of Euterpe edulis fruits

Canal

Oliveira

Almeida

et al. 2023

Sci Rep

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In forest genetic improvement programs for non-domesticated species, limited knowledge of kinship can compromise or make the estimation of variance components and genetic parameters of traits of interest unfeasible. We used mixed models and genomics (in the latter, considering additive and non-additive effects) to evaluate the genetic architecture of 12 traits in juçaizeiro for fruit production. A population of 275 genotypes without genetic relationship knowledge was phenotyped over three years and genotyped by whole genome SNP markers. We have verified superiority in the quality of the fits, the prediction accuracy for unbalanced data, and the possibility of unfolding the genetic effects into their additive and non-additive terms in the genomic models. Estimates of the variance components and genetic parameters obtained by the additive models may be overestimated since, when considering the dominance effect in the model, there are substantial reductions in them. The number of bunches, fresh fruit mass of bunch, rachis length, fresh mass of 25 fruits, and amount of pulp were strongly influenced by the dominance effect, showing that genomic models with such effect should be considered for these traits, which may result in selective improvements by being able to return more accurate genomic breeding values. The present study reveals the additive and non-additive genetic control of the evaluated traits and highlights the importance of genomic information-based approaches for populations without knowledge of kinship and experimental design. Our findings underscore the critical role of genomic data in elucidating the genetic control architecture of quantitative traits, thereby providing crucial insights for driving species' genetic improvement.

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Genomic relationship–based genetic parameters and prospects of genomic selection for growth and wood quality traits in Eucalyptus benthamii

Cited by 13 publications

References 95 publications

Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding

Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Genomic studies of the additive and dominant genetic control on production traits of Euterpe edulis fruits

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