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.

The recent fire history of northern Quebec biomes (54 000 km2), including the northern Boreal Forest, the southern and northern Forest—Tundra, and the Shrub Tundra, was documented by examining size and dates of 20th century wildfires using tree ring techniques. Results showed that pronounced south—north differences in fire properties existed, corresponding to climate and vegetation gradients. Fire frequency per biome decreased south—north from closed forest (0.7 fire/yr) to Shrub Tundra (0.4 fire/yr). Average fire size decreased south—north by 100—fold from °8000 ha in the northern Boreal Forest to 80 ha in the Shrub Tundra, while modal fire size was <50 ha in each of the four biomes. Most fires (>80%) of the northern Forest—Tundra and the Shrub Tundra were <100 ha, and fires >100 000 ha occurred only in the northern Boreal Forest and the southern Forest—Tundra. Less than 35% of all mapped fires in the Boreal Forest were <50 ha, but >30% were >1000 ha. From south to north, the fire—free interval per biome was, respectively, °2.6, 0.6, 0.6, and 2.2 yr, the Boreal Forest data being overestimated. The largest burned areas were recorded in the 1950s throughout the biomes, most likely associated with longlasting drier and warmer conditions. The fire rotation period per biome, based on the percentage of burned areas during the 1920—1984 period (or 1930—1984 in Tundra), increased south—north by 100—fold from 100 yr in the northern Boreal Forest to 9320 yr in the Shrub Tundra. The fire rotation period around the tree line, i.e., 20 km south and north of the present tree line, was estimated to be >7800 yr. Biome boundaries have developed and are maintained in response to fire by the ability of spruce to seed and regenerate. Stability of northernmost conifer sites is maintained by (1) the inability of patchy shrub and conifer cover in the northern Forest—Tundra and Shrub Tundra to carry fire and (2) failure of trees to produce viable seeds in these two biomes. Present data suggest that the area is characterized by a much higher fire frequency than expected from the fire weather index and from calculated frequencies typical of vegetation—type studies. It is concluded that size of the study area is a key element in the determination of regional fire regimes. Finally, the ecological significance of the natural fire rotation and postfire regeneration in northern environments is discussed in a paleoecological perspective.

The northernmost jack pine (Pinus banksiana Lamb.) populations in northern Quebec are located at the boreal forest–forest tundra boundary, along the Grande rivière de la Baleine, where they colonize the sandy terraces affected by recurrent fires. The recent fire history in the study area, as deduced from fire scar and age structure data, spans a 216-year period from 1773 to 1988. Forest fires occurred on the sites at intervals averaging 40 to 80 years. The analysis of 19 coniferous stands (jack pine and black spruce (Picea mariana (Mill.) Bsp)) indicated that forest communities younger than 67 years old were open jack pine – Cladina mitis or jack pine – black spruce – C. mitis woodlands, while the oldest stands, more than 132 years old, were dominated by jack pine, black spruce, and Cladina stellaris. Stands less than 67-years-old had an age structure almost normally distributed and regeneration often occurred within less than 30 years after fire in both species, while most stands older than 132 years had a multiaged structure. In sites with a prolonged fire-free interval, jack pine was overgrown by black spruce. Spruce woodlands have developed on sites where the organic layer was relatively thick and continuous and they are the end result of the postfire successional process. However, at several sites both conifer species showed an ability to regenerate in prolonged absence of fire disturbance, particularly in open sites with exposed mineral substrates. At the regional scale, fire frequency during the last 200 years has been high enough to prevent pine exclusion at its range limit. The key requirement for the long-term maintenance of jack pine populations is that fires return at intervals shorter than the average life-span of individual trees. It is concluded that the northernmost jack pine populations are able to maintain and regenerate under present fire conditions. Key words: fire, subarctic, jack pine, postfire regeneration, boreal forest.

BackgroundThe genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the genomic architecture of adaptive traits in black spruce, which is a widely distributed conifer of the North American boreal forest. As an alternative to the usual candidate gene approach, a candidate SNP approach was developed for association testing.ResultsA genetic map containing 231 gene loci was used to identify QTL that were related to budset timing and to tree height assessed over multiple years and sites. Twenty-two unique genomic regions were identified, including 20 that were related to budset timing and 6 that were related to tree height. From results of outlier detection and bulk segregant analysis for adaptive traits using DNA pool sequencing of 434 genes, 52 candidate SNPs were identified and subsequently tested in genetic association studies for budset timing and tree height assessed over multiple years and sites. A total of 34 (65%) SNPs were significantly associated with budset timing, or tree height, or both. Although the percentages of explained variance (PVE) by individual SNPs were small, several significant SNPs were shared between sites and among years.ConclusionsThe sharing of genomic regions and significant SNPs between budset timing and tree height indicates pleiotropic effects. Significant QTLs and SNPs differed quite greatly among years, suggesting that different sets of genes for the same characters are involved at different stages in the tree’s life history. The functional diversity of genes carrying significant SNPs and low observed PVE further indicated that a large number of polymorphisms are involved in adaptive genetic variation. Accordingly, for undomesticated species such as black spruce with natural populations of large effective size and low linkage disequilibrium, efficient marker systems that are predictive of adaptation should require the survey of large numbers of SNPs. Candidate SNP approaches like the one developed in the present study could contribute to reducing these numbers.