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Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH: 0.429, and WGR: 0.513) or design (HT: 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918-1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits' heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.

The ascomycete fungi Dothistroma septosporum (Dorogin) M. Morelet and D. pini Hulbary are both responsible for Dothistroma needle blight disease (DNB) on pines. Using a DNA-barcoding approach, we c...

Refining and modifying experimental procedures play a vital role in improving methodology while also reducing animal distress. In this study, we asked if an increase in feed time duration affects discrimination in an operant go/no-go task. Specifically, we used zebra finches’ sexually dimorphic distance calls as acoustic stimuli to test whether there were any significant differences in performance on an operant discrimination task requiring zebra finches to classify calls according to the sex of the producer when a key experimental parameter, feed time duration, was increased from 1 second to 2 seconds. We found no differences in learning speed (trials to criterion) between birds that were given 1 sec or 2 sec of food access following a correct go response. Our results indicate doubling food access duration did not impact the speed of acquisition of distance call discrimination in zebra finches. These findings suggest that we can provide twice as much time for zebra finches to access food, potentially improving animal welfare, with no impact on experimental outcomes.

Additional file 1.

Refining and modifying experimental procedures play a vital role in improving methodology while also reducing animal distress. In this study, we asked if an increase in feed time duration affects discrimination in an operant go/no-go task. Specifically, we used zebra finches' sexually dimorphic distance calls as acoustic stimuli to test whether there were any significant differences in performance on an operant discrimination task requiring zebra finches to classify calls according to the sex of the producer when a key experimental parameter, feed time duration, was increased from 1 s to 2 s. We found no differences in learning speed (trials to criterion) between birds that were given 1 s or 2 s of food access following a correct go response. Our results indicate doubling food access duration did not impact the speed of acquisition of distance call discrimination in zebra finches. These findings suggest that we can provide twice as much time for zebra finches to access food, potentially improving animal welfare, with no impact on experimental outcomes.

Survival and growth of Siberian larch (SL, Larix sibirica Ledeb.) were compared with those of three conifer species native to Alberta, Canada: lodgepole pine (LP; Pinus contorta var. latifolia Engelm. ex S. Watson), white spruce (WS, Picea glauca (Moench) Voss), and jack pine (JP, Pinus banksiana Lamb.) at 12, 10, and 3 trial locations, respectively. The average data age was 18 years (range: 3 to 27 years). Survival of SL averaged 4.2% and 6.5% worse than LP and WS, respectively, while it was 5% better than JP. SL grew 25%, 94%, and 23% taller than LP, WS, and JP, respectively. Stem forking rates were similar between SL and LP, WS, and JP. The best seed sources for Alberta were mature trees established in Alberta and Saskatchewan of unknown initial provenances. The Russian Altai Mountain source grew well at high elevations, while the Finnish Raivola performed well in the northern, low-elevation area. Open-pollinated progeny tests of 58 families planted in five diverse locations yielded individual-tree narrow-sense heritabilities and family mean heritabilities for height at age 15 of 0.15 and 0.59, respectively. The type B between-site genetic correlation was 0.44, indicating a strong genotype × environment interaction. SL has performed well in Alberta, and its growth can be further improved by selection and breeding from appropriate seed sources.

Many current tree improvement programs are incorporating assisted gene flow strategies to match reforestation efforts with future climates. This is the case for the lodgepole pine (Pinus contorta var. latifolia), the most extensively planted tree in western Canada. Knowledge of the structure and origin of pathogen populations associated with this tree would help improve the breeding effort. Recent outbreaks of the Dothistroma needle blight (DNB) pathogen Dothistroma septosporum on lodgepole pine in British Columbia and its discovery in Alberta plantations raised questions about the diversity and population structure of this pathogen in western Canada. Using genotyping-by-sequencing on 119 D. septosporum isolates from 16 natural pine populations and plantations from this area, we identified four genetic lineages, all distinct from the other DNB lineages from outside of North America. Modeling of the population history indicated that these lineages diverged between 31.4 and 7.2 thousand years ago, coinciding with the last glacial maximum and the postglacial recolonization of lodgepole pine in western North America. The lineage found in the Kispiox Valley from British Columbia, where an unprecedented DNB epidemic occurred in the 1990s, was close to demographic equilibrium and displayed a high level of haplotypic diversity. Two lineages found in Alberta and Prince George (British Columbia) showed departure from random mating and contemporary gene flow, likely resulting from pine breeding activities and material exchanges in these areas. The increased movement of planting material could have some major consequences by facilitating secondary contact between genetically isolated DNB lineages, possibly resulting in new epidemics.

Creation of second generation Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) hybrids based on parents from geographically distant locations did not appreciably increase variance in height, frost damage and bud break. New and favorable trait combinations between height and the two adaptive traits were found in the F2 populations. Increased genetic variance and new trait combinations can improve selection efficiency in terms of selection response and increased adaptability. This project tested a novel method for generating higher genetic variance and new trait combinations in Douglas-fir populations. Parents from Southern British Columbia (BC), Washington (WA), Oregon (OR), and Northern BC (NBC) were crossed within each provenance; then selections from BC were crossed with the other sources to create three F1 interpopulation generations. Unrelated random selections from the same F1 population were subsequently crossed to produce three F2 populations. The parental, F1 and F2 generations were concurrently grown in three field tests and were evaluated for height, frost damage, and bud break date. Significant segregation variances were found only in the BCxNBC cross for height in two sites and frost damage in one site and in the BCxOR cross for bud break in one site. In the BCxNBC cross, correlations between breeding values for height and frost damage changed from 0.71 in F1 to − 0.04 in F2 and between height and bud break from − 0.71 to − 0.26. In the BC-OR cross, correlations between height and bud break changed from − 0.71 in F1 to − 0.49 in F2. Our results suggest that creation of wide-cross hybrids may not be very effective in increasing segregation variance in traditional tree improvement programs but in some cases may be considered to increase diversity of trait combinations.

Clonal replicates of Chamaecyparis nootkatensis (D. Don) Spach rooted cuttings (ramets) originating from pruned donor hedges (ortets) were grown for 3 years in a completely randomized common garden in southwestern British Columbia. Ramets were cut when ortets were 3, 7, 11, and 15 years old; selected ramets were also serially propagated for one, two, or three cycles, 4 years apart. Serial propagation and physiological and chronological aging effects of ortets on ramets were evaluated for photosynthetic and gas exchange parameters, rooting, height, biomass, and cold hardiness. Genotypic variation typically exceeded treatment differences. Excepting several genotypes, serial propagation had no significant effect on aging for pruned plants. Some genotypes had crooked or plagiotropic growth. These differences strengthened with ortet age, but serial propagation effects varied with genotype. Rooting success was similar across treatments. Detrimental effects of ortet aging were detected only at age 15. Clonal rooting differences were obscured by age 7; 15-year-old material had the lowest rooting success and smallest individuals. Serially propagated ramets from 15-year-old ortets had smaller shoots. No consistent trends were caused by age or serial propagation for other traits. Serial propagation can successfully mass produce tested elite yellow-cedar planting stock up to age 15.

Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) zygotic seedlings and seedlings produced through somatic embryogenesis were grown in a field test on southern Vancouver Island, British Columbia. The two stock types were compared in a number of adaptive attributes evaluated during two growing seasons (1999 and 2000). The attributes were related to gas exchange, water relations, phenology, and fall frost hardiness. In both years, somatic and zygotic seedlings had similar rates of net photosynthesis in optimum and reduced light conditions, similar mesophyll conductance, and dark respiration rates. Small differences (P [Formula: see text] 0.05) were found for water relation attributes measured on irrigated plants: intrinsic water use efficiency (WUEi), transpiration (E), stomatal conductance (gwv) and midday xylem water potential (Ψ). Somatic seedlings had marginally higher E and gwv and lower Ψ in 2000 and lower WUEi in 1999 and 2000. Zygotic seedlings had higher WUEi because of their lower gwv while maintaining the same rates of net photosynthesis as somatic seedlings. There were no differences between somatic and zygotic seedlings in frost hardiness throughout the fall. Zygotic and somatic seedlings had similar timing of spring bud break pointing to a comparable level of spring frost hardiness in both stock types. Findings from this study indicate that somatic and zygotic seedlings had a similar pattern of physiological performance throughout 2 years of assessment.

Genetic structure (variance among and within populations) and geographic pattern of variations in growth and frost hardiness of mountain hemlock (Tsuga mertensiana (Bong.) Carr.) populations from coastal British Columbia (BC) were examined. Populations fell into two main groups — south coast (16 sources) and north coast (two sources). Height growth of greenhouse grown seedlings was measured during the first growing season on a weekly basis whereas frost hardiness and branch water content were evaluated during the fall at monthly intervals. Significant differences among the populations were found in maximum instantaneous growth rate, height at the end of the growing season and in October and November frost hardiness. There were no differences in date of maximum growth rate, branch water content and September frost hardiness. Most of the genetic variance was found within populations: 77% for height, maximum growth rate and November frost hardiness and 87% for October frost hardiness. Geographic trends were identified using multiple linear regression and canonical correlation analyses based on population means and latitude, longitude and elevation of the population origin. The uneven distribution of sources limited the extrapolation, but some general trends appeared. Maximum instantaneous growth rates increased with latitude, elevation and decreased with longitude (R2=0.64) and consequently were negatively correlated with the length of the growing season in the seed collection sites. Both populations from the north coast developed frost hardiness earlier than any population from the south coast. The relationship between climate coldness and growth rates has potential implications for seed transfer guidelines. Due to their higher growth rates, plants from higher altitudes may accomplish the same amount of growth within a shorter period compared to plants from lower altitudes when both are transferred north. Results of the frost hardiness tests indicate that seed transfer along the British Columbia coast of more than 3° northward will considerably increase chances of frost damage in plantations.

Patterns of genetic variation for adaptive and quantitative attributes in mountain hemlock ( Tsuga mertensiana (Bong.)) seedlings from British Columbia were examined at the population (provenance) and family levels. The population and family levels were represented by 12 provenances and 10 families from a single location, respectively. The adaptive attributes were related to gas exchange (net photosynthesis, transpiration rate, intercellular-to-ambient CO 2 concentration ratio, mesophyll conductance, stomatal conductance, and photosynthetic water use efficiency) and the quantitative traits were related to biomass allocation (height, root collar diameter, root dry weight, shoot dry weight and harvest index). Univariate and multivariate analyses of the studied attributes indicated the presence of significant differences at both, the population and family levels. Although the populations differed significantly in all studied traits, a relatively small portion (5–15%) of the total variation was attributed to among populations. On account of the observed large intra-population variation, no trends between the studied traits and geography were detected when data from individual seedlings were used; however, significant trends were detected on population means for the majority of gas-exchange attributes. Population-level analyses indicated lack of appreciable relationship between the quantitative and adaptive attributes. Intra-population analyses produced high narrow-sense heritabilities for the majority of the attributes studied. The observed high intra-population variation that is accompanied with high genetic control over the studied attributes present an opportunity for genetic improvement. On the other hand, the observed significant differences among populations represent a challenge for gene conservation efforts as well as to the methods deployed to exploit these variations.

Fifteen microsatellite markers have been isolated from western hemlock [Tsuga heterophylla (Raf.) Sarg] genomic DNA and six of these markers were optimized for use in mountain hemlock [Tsuga mertensiana (Bong) Carr.]. The mean expected heterozygosity (HE) was 0.88 and 0.89 for western hemlock and mountain hemlock, respectively. Allelic diversity was high for both hemlock species, ranging from 7 to 15 alleles per locus for western hemlock and 5–30 alleles per locus for mountain hemlock. The allelic variation identified in this project will allow monitoring of changes in genetic variation as a result of selection pressure in breeding programs.

Patterns of genetic variations in adaptive and quantitative attributes of Sitka alder, Alnus sinuata Rydb., were examined at the population level. The following traits were studied: germination, frost hardiness, bud break, characteristics related to gas exchange (photosynthesis, dark respiration, stomatal conductance, transpiration, carboxylation efficiency, stomatal sensitivity to vapor pressure deficit and intrinsic water use efficiency) and characteristics related to biomass allocation (height, stem diameter, shoot dry weight, root dry weight, height growth rate and number and size of major stems per plant). The number of examined populations was 29, all but one from British Columbia. There were large genetic differences among the populations in all measured traits except for spring frost hardiness and stomatal sensitivity to vapor pressure deficit. Population genetic structure (variance within and between populations) was investigated: inter-population variations accounted for 13-31% and 26-61%) for gas exchange and biomass related variables, respectively. The populations differed significantly in fall and winter cold resistance, though the differences were less pronounced in maximum hardiness than were found for the timing of frost hardiness development. On 11 November, 1996 65% of the total variation in frost injury index was explained by the differences between the populations, while on 15 December, 1996 33%) of the total variance was due to the population effect. The observed patterns of large genetic variations in Sitka alder populations represent a challenge for gene conservation efforts in high elevation ecosystems. Based on univariate (multiple linear regression) and mulitvariate methods (canonical correlations and cluster analysis), geographic patterns of variation were found for most traits. Variations related to geography were particularly strong in fall frost hardiness (R2 = 0.62), shoot dry weight (R = 0.64), growth rate in July (R = 0.70), ratio of root dry weight to total dry weight (R2 = 0.67) and net photosynthetic rate (R2 = 0.52). Most of the variation was due to latitude and distance from the coast. Seedlings generated from northern seed sources were in general more frost hardy, smaller and allocated more carbon to roots compared to shoots. Plants from the interior wet belt were frost hardy to the same levels as coastal seedlings suggesting that snow cover plays a role in Sitka alder adaptation to low temperatures. Rate of photosynthesis (A) increased largely with the distance from the coast and, to a lesser degree, with elevation and latitude implying that an inverse relationship exists between A and the length of the growing season. Interior populations had higher A due to higher carboxylation efficiency and stomatal conductance (gs). As a result of higher gs, plants from more xeric interior regions tend to have lower water use efficiency. Productivity was negatively correlated with A and positively with water use efficiency. Speed of germination did not affect the plant size after one growing season and was independent from the germination completeness. Strong positive correlation was found between timing of frost hardiness development and spring bud break.