BackgroundGenomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, which is especially relevant for the genetic improvement of boreal conifers characterized by long breeding cycles. In the present study, we tested GS in an advanced-breeding population of the boreal black spruce (Picea mariana [Mill.] BSP) for growth and wood quality traits, and concurrently examined factors affecting GS model accuracy.ResultsThe study relied on 734 25-year-old trees belonging to 34 full-sib families derived from 27 parents and that were established on two contrasting sites. Genomic profiles were obtained from 4993 Single Nucleotide Polymorphisms (SNPs) representative of as many gene loci distributed among the 12 linkage groups common to spruce. GS models were obtained for four growth and wood traits. Validation using independent sets of trees showed that GS model accuracy was high, related to trait heritability and equivalent to that of conventional pedigree-based models. In forward selection, gains per unit of time were three times higher with the GS approach than with conventional selection. In addition, models were also accurate across sites, indicating little genotype-by-environment interaction in the area investigated. Using information from half-sibs instead of full-sibs led to a significant reduction in model accuracy, indicating that the inclusion of relatedness in the model contributed to its higher accuracies. About 500 to 1000 markers were sufficient to obtain GS model accuracy almost equivalent to that obtained with all markers, whether they were well spread across the genome or from a single linkage group, further confirming the implication of relatedness and potential long-range linkage disequilibrium (LD) in the high accuracy estimates obtained. Only slightly higher model accuracy was obtained when using marker subsets that were identified to carry large effects, indicating a minor role for short-range LD in this population.ConclusionsThis study supports the integration of GS models in advanced-generation tree breeding programs, given that high genomic prediction accuracy was obtained with a relatively small number of markers due to high relatedness and family structure in the population. In boreal spruce breeding programs and similar ones with long breeding cycles, much larger gain per unit of time can be obtained from genomic selection at an early age than by the conventional approach. GS thus appears highly profitable, especially in the context of forward selection in species which are amenable to mass vegetative propagation of selected stock, such as spruces.

We discuss the general design of the ANTARES code which is intended for simulations in stellar hydrodynamics with radiative transfer and realistic microphysics in 1D, 2D and 3D. We then compare the quality of various numerical methods. We have applied ANTARES in order to obtain high resolution simulations of solar granulation which we describe and analyze. In order to obtain high resolution, we apply grid refinement to a region predominantly occupied by an exploding granule. Strong, rapidly rotating vortex tubes of small diameter (∼ 100 km) generated by the downdrafts and ascending into the photosphere near the granule boundaries evolve, often entering the photosphere from below in an arclike fashion. They essentially contribute to the turbulent velocity field near the granule boundaries.

No abstract

Summary Local adaptation in tree species has been documented through a long history of common garden experiments where functional traits (height, bud phenology) are used as proxies for fitness. However, the ability to identify genes or genomic regions related to adaptation to climate requires the evaluation of traits that precisely reflect how and when climate exerts selective constraints.We combine dendroecology with association genetics to establish a link between genotypes, phenotypes and interannual climatic fluctuations. We illustrate this approach by examining individual tree responses embedded in the annual rings of 233 Pinus strobus trees growing in a common garden experiment representing 38 populations from the majority of its range.We found that interannual variability in growth was affected by low temperatures during spring and autumn, and by summer heat and drought. Among‐population variation in climatic sensitivity was significantly correlated with the mean annual temperature of the provenance, suggesting local adaptation. Genotype–phenotype associations using these new tree‐ring phenotypes validated nine candidate genes identified in a previous genetic–environment association study.Combining dendroecology with association genetics allowed us to assess tree vulnerability to past climate at fine temporal scales and provides avenues for future genomic studies on functional adaptation in forest trees.

Plantation‐grown trees have to cope with an increasing pressure of pest and disease in the context of climate change, and breeding approaches using genomics may offer efficient and flexible tools to face this pressure. In the present study, we targeted genetic improvement of resistance of an introduced conifer species in Canada, Norway spruce (Picea abies (L.) Karst.), to the native white pine weevil (Pissodes strobi Peck). We developed single‐ and multi‐trait genomic selection (GS) models and selection indices considering the relationships between weevil resistance, intrinsic wood quality, and growth traits. Weevil resistance, acoustic velocity as a proxy for mechanical wood stiffness, and average wood density showed moderate‐to‐high heritability and low genotype‐by‐environment interactions. Weevil resistance was genetically positively correlated with tree height, height‐to‐diameter at breast height (DBH) ratio, and acoustic velocity. The accuracy of the different GS models tested (GBLUP, threshold GBLUP, Bayesian ridge regression, BayesCπ) was high and did not differ among each other. Multi‐trait models performed similarly as single‐trait models when all trees were phenotyped. However, when weevil attack data were not available for all trees, weevil resistance was more accurately predicted by integrating genetically correlated growth traits into multi‐trait GS models. A GS index that corresponded to the breeders’ priorities achieved near maximum gains for weevil resistance, acoustic velocity, and height growth, but a small decrease for DBH. The results of this study indicate that it is possible to breed for high‐quality, weevil‐resistant Norway spruce reforestation stock with high accuracy achieved from single‐trait or multi‐trait GS.

Summary Drought intensity and frequency are increasing under global warming, with soil water availability now being a major factor limiting tree growth in circumboreal forests. Still, the adaptive capacity of trees in the face of future climatic regimes remains poorly documented. Using 1481 annually resolved tree‐ring series from 29‐yr‐old trees, we evaluated the drought sensitivity of 43 white spruce (Picea glauca (Moench) Voss) populations established in a common garden experiment. We show that genetic variation among populations in response to drought plays a significant role in growth resilience. Local genetic adaptation allowed populations from drier geographical origins to grow better, as indicated by higher resilience to extreme drought events, compared with populations from more humid geographical origins. The substantial genetic variation found for growth resilience highlights the possibility of selecting for drought resilience in boreal conifers. As a major research outcome, we showed that adaptive genetic variation in response to changing local conditions can shape drought vulnerability at the intraspecific level. Our findings have wide implications for forest ecosystem management and conservation.

Genomic selection (GS) has a large potential for improving the prediction accuracy of breeding values and significantly reducing the length of breeding cycles. In this context, the choice of mating designs becomes critical to improve the efficiency of breeding operations and to obtain the largest genetic gains per time unit. Polycross mating designs have been traditionally used in tree and plant breeding to perform backward selection of the female parents. The possibility to use genetic markers for paternity identification and for building genomic prediction models should allow for a broader use of polycross tests in forward selection schemes. We compared the accuracies of genomic predictions of offspring's breeding values from a polycross and a full-sib (partial diallel) mating design with similar genetic background in white spruce (Picea glauca). Trees were phenotyped for growth and wood quality traits, and genotyped for 4092 SNPs representing as many gene loci distributed across the 12 spruce chromosomes. For the polycross progeny test, heritability estimates were smaller, but more precise using the genomic BLUP (GBLUP) model as compared with pedigree-based models accounting for the maternal pedigree or for the reconstructed full pedigree. Cross-validations showed that GBLUP predictions were 22-52% more accurate than predictions based on the maternal pedigree, and 5-7% more accurate than predictions using the reconstructed full pedigree. The accuracies of GBLUP predictions were high and in the same range for most traits between the polycross (0.61-0.70) and full-sib progeny tests (0.61-0.74). However, higher genetic gains per time unit were expected from the polycross mating design given the shorter time needed to conduct crosses. Considering the operational advantages of the polycross design in terms of easier handling of crosses and lower associated costs for test establishment, we believe that this mating scheme offers great opportunities for the development and operational application of forward GS.

Delta Scuti (δSct) stars are opacity-driven pulsators with masses of 1.5-2.5 M⊙, their pulsations resulting from the varying ionization of helium. In less massive stars such as the Sun, convection transports mass and energy through the outer 30 per cent of the star and excites a rich spectrum of resonant acoustic modes. Based on the solar example, with no firm theoretical basis, models predict that the convective envelope in δSct stars extends only about 1 per cent of the radius, but with sufficient energy to excite solar-like oscillations. This was not observed before the Kepler mission, so the presence of a convective envelope in the models has been questioned. Here we report the detection of solar-like oscillations in the δSct star HD187547, implying that surface convection operates efficiently in stars about twice as massive as the Sun, as the ad hoc models predicted.