by Marie-Claude Boileau | 7 October 2020
Published in Heredity 124: 562–578. https://doi.org/10.1038/s41437-019-0290-3
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.
by Claire Morin | 2 October 2020
Published in ISPRS Journal of Photogrammetry and Remote Sensing 156: 14-26. https://doi.org/10.1016/j.isprsjprs.2019.07.010
Tree mortality is an important forest ecosystem variable having uses in many applications such as forest health assessment, modelling stand dynamics and productivity, or planning wood harvesting operations. Because tree mortality is a spatially and temporally erratic process, rates and spatial patterns of tree mortality are difficult to estimate with traditional inventory methods. Remote sensing imagery has the potential to detect tree mortality at spatial scales required for accurately characterizing this process (e.g., landscape, region). Many efforts have been made in this sense, mostly using pixel- or object-based methods. In this study, we explored the potential of deep Convolutional Neural Networks (CNNs) to detect and map tree health status and functional type over entire regions. To do this, we built a database of around 290,000 photo-interpreted trees that served to extract and label image windows from 20 cm-resolution digital aerial images, for use in CNN training and evaluation. In this process, we also evaluated the effect of window size and spectral channel selection on classification accuracy, and we assessed if multiple realizations of a CNN, generated using different weight initializations, can be aggregated to provide more robust predictions. Finally, we extended our model with 5 additional classes to account for the diversity of landcovers found in our study area. When predicting tree health status only (live or dead), we obtained test accuracies of up to 94%, and up to 86% when predicting functional type only (broadleaf or needleleaf). Channel selection had a limited impact on overall classification accuracy, while window size increased the ability of the CNNs to predict plant functional type. The aggregation of multiple realizations of a CNN allowed us to avoid the selection of suboptimal models and help to remove much of the speckle effect when predicting on new aerial images. Test accuracies of plant functional type and health status were not affected in the extended model and were all above 95% for the 5 extra classes. Our results demonstrate the robustness of the CNN for between-scene variations in aerial photography and also suggest that this approach can be applied at operational level to map tree mortality across extensive territories.
by Marie-Claude Boileau | 2 October 2020
Tour of Grandes-Piles forest nursery and experimental plantations, presented on August 23, 2019 during the 2019 Canadian Forest Genetics Association Conference, August 19 to 23, 2019, Lac-Delage, QC. Guide. Gouvernement du Québec, ministère des Forêts, de la Faune et des Parcs, Direction de la recherche forestière. 29 p.
by Marie-Claude Boileau | 1 October 2020
Published in Tree Seed Working Group News Bulletin 65: 18-20
by Audrey Verreault | 10 September 2020
Published in Forests 11(7): 742. https://doi.org/10.3390/f11070742
Multi-cohort forest management in northern hardwood stands may well be the best way to successfully regenerate tree species of intermediate shade tolerance, such as yellow birch (Betula alleghaniensis Britt.). The creation of large enough gaps in the canopy favors increased light availability within the opening, while soil scarification provides suitable germination seedbeds. Evidence of these methods’ success nonetheless remains mostly the purview of experimental studies rather than operational tests. In Quebec, Canada, the multi-cohort methods promoted include group selection cutting and patch cutting. The present study tested their implementation at an operational scale and over a large territory in both hardwood-dominated and mixedwood stands. We assessed their efficacy in promoting natural regeneration of commercial hardwood trees, notably yellow birch and sugar maple (Acer saccharum Marsh.). We conducted regeneration surveys at 2, 5, 10, and 15 years after harvest. Overall, group selection and patch cuttings were successful in regenerating the target species. Yellow birch, for instance, showed a mean stocking around 60% and a mean sapling density around 3400 stems ha−1 after 15 years. We compared several variables for measuring regeneration in early years, and found that the relative abundance, the stocking based on one stem per sampling unit, and the mean maximum height were good predictors of the relative presence of yellow birch and sugar maple in 15-year-old canopy openings. Using smaller sampling units (6.25 m2 rather than 25 m2) and waiting until year 5 may be more useful for making such predictions. In addition, there was an important turnover in vertical dominance in these openings. Non-commercial woody competitors were frequently dominant in early years but were often replaced by commercial hardwoods, notably yellow birch. We propose certain thresholds for assessing the success of post-harvest regeneration and for evaluating the need for a cleaning treatment.
