Spruce Population Genomics

Bousquet, Jean; Gérardi, Sébastien; Lafontaine, Guillaume de; Jaramillo‐Correa, Juan P.; Pavy, Nathalie; Prunier, Julien; Lenz, P.; Beaulieu, Jean

doi:10.1007/13836_2021_96

Cited by 11 publications

(13 citation statements)

References 258 publications

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“…Thus, multi‐data analyses of physiological, genetic, and genomic nature under broad temporal and environmental scales are likely worthwhile options to better comprehend the quantitative genetics of the response to drought stress in tree species (Depardieu et al, 2021 ; Opgenoorth & Rellstab, 2021 ). This is especially feasible given that extensive genomic resources and common garden long‐term experiments are now accessible for many tree species, including spruces (Bousquet et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi‐site polycross test

Laverdière

Lenz

Nadeau

et al. 2022

Evolutionary Applications

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With climate change, increasingly intense and frequent drought episodes will be affecting water availability for boreal tree species, prompting tree breeders and forest managers to consider adaptation to drought stress as a priority in their reforestation efforts. We used a 19-year-old polycross progeny test of the model conifer white spruce (Picea glauca) replicated on two sites affected by distinct drought episodes at different ages to estimate the genetic control and the potential for improvement of drought response in addition to conventional cumulative growth and wood quality traits. Drought response components were measured from dendrochronological signatures matching drought episodes in wood ring increment cores. We found that trees with more vigorous growth during their lifespan resisted better during the current year of a drought episode when the drought had more severe effects. Phenotypic data were also analyzed using genomic prediction (GBLUP) relying on the genomic relationship matrix of multi-locus gene SNP marker information, and conventional analysis (ABLUP) based on validated pedigree information. The accuracy of predicted breeding values for drought response components was marginally lower than that for conventional traits and comparable between GBLUP and ABLUP. Genetic correlations were generally low and nonsignificant between drought response components and conventional traits, except for resistance which was positively correlated to tree height. Heritability estimates for the components of drought response were slightly lower than for conventional traits, but similar single-trait genetic gains could be obtained. Multi-trait genomic selection simulations indicated that it was possible to improve simultaneously for all traits on both sites while sacrificing little on gain in tree height. In a context of rapid climate change, our results suggest that with careful phenotypic assessment, drought response may be considered in multi-trait improvement of white spruce, with accelerated screening of large numbers of candidates and selection at young age with genomic selection.

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Section: Discussionmentioning

confidence: 99%

Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi‐site polycross test

Laverdière

Lenz

Nadeau

et al. 2022

Evolutionary Applications

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“…In the mountainous landscape of western North America, high diversity of spruce species is found where they have adapted to a variety of climates, including glaciations of the Pleistocene repeatedly reshaping their geographic distributions (Jaramillo‐Correa et al., 2009). Genomics has been key to better understanding the evolutionary biology of spruces, characterizing their genetic diversity in relation to response to biotic and abiotic factors, and providing tools to accelerate spruce breeding programs (Bousquet et al., 2021). In the context of climate change, the search for ecologically relevant markers has taken increasing relevance in the past years and several large‐scale studies have contributed to better understanding some of the linkages between the genetic diversity of spruce species and climate (Hornoy et al., 2015; Yeaman et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

Gagalova

Coombe

et al. 2022

The Plant Journal

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SUMMARY Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non‐synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga‐genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

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“…Comparing the performance of GS across studies is difficult because of the different methods used to estimate prediction accuracy in forest trees ( Bousquet et al., 2021 ; Calleja-Rodriguez et al., 2021 ). However, several studies in spruce used similar CV schemes to those used here and calculated the predictive ability ( PA BV ) or accuracy ( PACC BV as

) of breeding values using additive models ( Table 5 ).…”

Section: Discussionmentioning

confidence: 99%

“…In GS, a population in which individuals are both phenotyped and genotyped is used to train a model, which is then used to predict the genetic merit of young genotyped, but unphenotyped, offspring. Selections from a large number of genotyped candidates should translate into higher selection intensities, while preserving genetic diversity in improved varieties, or allowing for efficient multi-trait selection strategies ( Bouvet et al., 2020 ; Lenz et al., 2020b ; Bousquet et al., 2021 ; Cappa et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce

et al. 2023

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IntroductionGenomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains.MethodsUsing two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models.ResultsWhile wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely.DiscussionThis study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.

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Spruce Population Genomics

Cited by 11 publications

References 258 publications

Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi‐site polycross test

Breeding for adaptation to climate change: genomic selection for drought response in a white spruce multi‐site polycross test

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce

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