Genome-wide investigation and analysis of NAC transcription factor family in Populus tomentosa and expression analysis under salt stress.

The NAC transcription factor family is one of the largest families of TFs in plants, and members of NAC gene family play important roles in plant growth and stress response. Recent release of the haplotype-resolved genome assembly of P. tomentosa provide a platform for NAC protein genome-wide analysis. A total of 270 NAC genes were identified and a comprehensive overview of the PtoNAC gene family is presented, including gene promoter, structure and conserved motif analyses, chromosome localization and collinearity analysis, protein phylogeny, expression pattern, and interaction analysis. The results indicate that protein length, molecular weight, and theoretical isoelectric points of the NAC TF family vary, while gene structure and motif are relatively conserved. Chromosome mapping analysis showed that the P. tomentosa NAC genes are unevenly distributed on 19 chromosomes. The interchromosomal evolutionary results indicate 12 pairs of tandem and 280 segmental duplications. Segmental duplication is possibly related to amplification of P. tomentosa NAC gene family. Expression patterns of 35 PtoNAC genes from P. tomentosa subgroup were analysed under high salinity, and seven NAC genes were induced by this treatment. Promoter and protein interaction network analyses showed that PtoNAC genes are closely associated with growth, development, and abiotic and biotic stress, especially salt stress. These results provide a meaningful reference for follow-up studies of the functional characteristics of NAC genes in the mechanism of stress response and their potential roles in development of P. tomentosa.

Effect of clonal testing on the efficiency of genomic evaluation in forest tree breeding.

Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree-(BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus providing additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods.

Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3-40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31-0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation (r=0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04-0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.

A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

Development and characterization of microsatellite loci in western larch (Larix occidentalis Nutt.).

Western larch (Larix occidentalis Nutt.) is an important ecological and commercial species in the Pacific Northwest. We isolated nine microsatellite loci with variable polymorphism ranging from five to 19 alleles per locus. Observed and expected heterozygosities averaged 0.42 and 0.64 and ranged from 0.11 to 0.83 and from 0.48 to 0.80, respectively. These markers, along with those already existing, will be useful for the species' gene resource management activities.

Genetic evaluation of alternative silvicultural systems in coastal montane forests: western hemlock and amabilis fir.

Genetic diversity and mating system were quantified for shelterwood, patch cut and green tree-retention silvicultural systems, and compared to adjacent old-growth. This is a component of a larger study conducted in montane old-growth forests of coastal British Columbia to evaluate the feasibility and ecological consequences of alternative silvicultural systems. The experiment includes replicated treatments representing a range of overstory removal adjacent to old-growth and clearcut areas. Based on 22 electrophoretically assayed loci, the effects of silvicultural systems on genetic parameters of amabilis fir (Abies amabilis and western hemlock (Tsuga heterophylla were assessed by comparing an average number of alleles per locus, the percent polymorphic loci, and observed and expected heterozygosity between parental populations and naturally regenerated progeny as well as among treatments. Genetic variation in natural regeneration was greater than in parental populations, especially for low-frequency alleles. Silvicultural treatments caused no significant differences in amabilis fir genetic-diversity parameters, while the shelterwood system resulted in lower observed and expected heterozygosity in western hemlock. Nei's genetic distance revealed that all parental populations were extremely similar. The two species had contrasting mating system dynamics with amabilis fir producing higher levels of correlated paternity and inbreeding with wider variation among individual tree outcrossing-rate estimates. Western hemlock had significant levels of correlated paternity only for the green tree and shelterwood treatments demonstrating family structuring inversely related to stand density. Inbreeding in western hemlock was significant but lower than that observed for amabilis fir with a J-shaped distribution for individual tree multilocus outcrossing-rate estimates. The pollination and dispersal mechanisms of the two species represent the most-likely factors causing these differences. Artificial regeneration may be utilized to augment the genetic resources of natural ingress.

Sexual reproduction in the white pine weevil (Pissodes strobi [Peck] [Coleoptera: Curculionidae]): implications for population genetic diversity.

Controlled mating experiments in the white pine weevil (Pissodes strobi [Peck]) indicated that female weevils either stored sperm or fertilized eggs from one season to the next, and were able to colonize Sitka spruce (Picea sitchensis [Bong.] Carr.) trees without additional mating events. This was interpreted as being beneficial for the insect, in that population establishment in a new habitat could be initiated by dispersing previously mated females without participation of the male. This makes colonization and population/outbreak development more likely as it reduces the need for mate searching in the second season. Paternity identification, based on microsatellite molecular markers, established that the progeny produced in year 2 by females mated only in year 1, were often fathered by more than one male. Multiple paternity, coupled with a lack of parthenogenesis, which was also demonstrated herein, may help to account for the high degree of genetic diversity evidenced in this species.

Inheritance of null alleles for microsatellites in the white pine weevil (Pissodes strobi [Peck] [Coleoptera: Curculionidae]).

Four families of the white pine weevil (Pissodes strobi) produced by controlled breeding were used to study the mode of inheritance at four microsatellite loci. The results confirmed the Mendelian segregation of all loci. Three of the four loci showed the presence of null alleles. The observed high polymorphism of P. strobi microsatellites increased their usefulness for paternity determination. The presence of null alleles predicates the need to redesign primers before using them in population genetics studies where pedigree is unknown.

Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci.

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.

Geographic pattern of genetic variation in photosynthetic capacity and growth in two hardwood species from British Columbia.

Geographic patterns of intraspecific variations in traits related to photosynthesis and biomass were examined in two separate common garden experiments using seed collected from 26 Sitka alder (Alnus sinuata Rydb.) and 18 paper birch (Betula papyrifera Marsh.) populations from climatically diverse locations in British Columbia, Canada. Exchange rates of carbon dioxide and water vapour were measured on 2-year-old seedlings to determine the maximum net instantaneous photosynthetic rate, mesophyll conductance, stomatal conductance, and photosynthetic water use efficiency. Height, stem diameter, root and shoot dry mass and fall frost hardiness data were also obtained. Mean population maximum photosynthetic rate ranged from 10.35 to 14.57 µmol CO2 m-2 s-1 in Sitka alder and from 14.76 to 17.55 µmol CO2 m-2 s-1 in paper birch. Based on canonical correlation analyses, populations from locations with colder winters and shorter (but not necessarily cooler) summers had higher maximum photosynthetic rates implying the existence of an inverse relationship between leaf longevity and photosynthetic capacity. Significant canonical variates based on climatic variables derived for the seed collection sites explained 58% and 41% of variation in the rate of photosynthesis in Sitka alder and paper birch, respectively. Since growing season length is reflected in date of frost hardiness development, an intrinsic relationship was found between photosynthetic capacity and the level of fall frost hardiness. The correlation was particularly strong for paper birch (r=-0.77) and less strong for Sitka alder (r=-0.60). Mean population biomass accumulation decreased with increased climate coldness. These patterns may be consequential for evaluation of the impact of climate change and extension of the growing season on plant communities.

Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia.

Concerns over the reductionist nature of the domestication of forest-tree species focus on the possibility of potential genetic erosion during this process. To address these concerns, genetic diversity assessments in a breeding zone the Province of British Columbia "interior" spruce (Picea glauca x engelmanni) program was conducted using allozyme markers. Genetic-variation comparisons were made between natural and production (seed orchard) populations as well as seed and seedling crops produced from the same breeding zone's seed orchard. The natural population sample consisted of a total of 360 trees representing three stands within each of three watersheds present in the Shuswap-Adams low-elevation zone of interior British Columbia. Small amounts of genetic differentiation were observed among the nine natural populations (4%) and this was attributable to extensive gene flow (N(m) = 7). Consequently, the sum of these nine populations was considered as a baseline for the genetic variation present in the breeding zone. The comparisons between the seed orchard and the breeding zone produced a similar percentage of polymorphic loci (%P = 64.7%) while the expected hetrozygosity (H(e)) (0.207 vs 0.210) and the average number of alleles per locus (2.7 vs 2.4) were slightly lower in the seed orchard. A total of seven natural populations' rare alleles (P < 0.007) were not present in the orchard population, while one allele was unique to the orchard. The %P increased to 70.6% in the seedlot, but dropped to the natural populations level (64.7%) in the plantation. The observed increase in %P was a result of pollen contamination in the orchard. It is suspected that the reduction in the plantation was caused by an unintentional selection in the nursery. Simulated roguing in the orchard did not drastically reduce H(e) even if up to 50% of the orchard's clones were rogued. However, roguing was associated with a reduction in the average number of alleles per locus (i.e., sampling effect).

Evaluation of the tree-improvement delivery system: factors affecting genetic potential.

Possible causes of the genetic erosion that occurs during the fragmented phases of the tree-improvement delivery system are reviewed. The impacts of intentional and unintentional directional selection during phenotypic selection, seed production (with its associated reproductive-phenology asynchrony, fecundity differential and varying propensity to inbreeding), seed processing and storage, and seedling production are evaluated. In general, genetic diversity and heterozygosity parameters of seed orchards are higher or similar to those observed in their natural-population counterparts. However, parental contribution to the resultant seed orchard seed crops is consistently asymmetrical, and this is a major cause of genetic erosion. In most cases, less than 20% of an orchard's clones contribute 80% of the cone crop, thus reducing the effective population size. Because seed germination of coniferous tree species is under strong maternal genetic control, the combined effects of differences in reproductive output and germination, as well as of management practices (e.g., simulated long-term storage of seed showed that loss of viability during storage is genotype specific), cause unintentional directional selection during seedling production. This review confirms the need for genetic monitoring of each phase of the tree-improvement delivery system, so that practical solutions can be developed to alleviate genetic erosion.

Estimation of relationship coefficients among progeny derived from wind-pollinated orchard seeds.

Statistical analyses of trees produced from wind-pollinated seeds to determine levels of additive variance need to be adjusted to compensate for the relationships among the progeny. The assumption that the coefficient of relationship among the progeny is 0.25 will lead to inaccurate estimation of the additive variance if the relationships among the progeny are not entirely half-sib. Foreign pollen intrusion into the orchard pollen cloud, selfing, and reproductive phenology variation (i.e., mating proportion differences) among the parent trees may lead to varying proportions of self, self-half, half-sib, and full-sib relationships among the progeny. The variance of the coefficient of relationship from 0.25 for two coniferous seed orchards subjected to simulated selfing and foreign pollen problems illustrate the need for caaution when estimation techniques are employed.

Inheritance of chloroplast and mitochondrial DNA in Picea and composition of hybrids from introgression zones.

The cloning of white spruce (Picea glauca) mitochondrial DNA homologous to the cytochrome oxidase II and ATPaseα genes of maize is described. These probes were used to define restriction fragment length polymorphisms which distinguish the white, Engelmann (P. engelmannii) and Sitka spruce (P. sitchensis) populations that occur in British Columbia. Analysis of progeny from crosses between the species revealed that mitochondrial DNA was maternally inherited in all cases (32 progeny from five independent crosses). The inheritance of chloroplast DNA was determined using a probe described previously; in this case, all progeny exhibited paternal inheritance (27 progeny from four crosses). Mitochondrial and chloroplast probes were used to test trees from zones of introgression between coastal (Sitka) and interior spruces (white and Engelmann). In most cases mitochondria and chloroplasts within individuals were contributed by different species. The data shows that there is a significant Sitka spruce component in trees east of the coastal watershed in British Columbia.

Effective number of pollen parents in clonal seed orchards.

A method for quantifying mating behavior in clonal seed orchards of forest tree species is presented. It involves the estimation of effective numbers of pollen parents from seed samples collected from individual ramets in such orchards. These effective numbers are variance effective numbers for populations of male gametes that are successful in uniting with ovules to produce viable seed. Three such effective numbers are defined for clonal seed orchards:N p (a) for male gamete populations for ramets within clones,N p (b) for male gamete populations for clones, andN p (c) for male gamete populations for entire orchards. Estimators for these effective numbers and for standardized variances of allele frequencies in the male gametic populations are presented. Expressions are also given for the confidence intervals for each of the three effective numbers. Estimates of these parameters and the corresponding confidence intervals for two seed orchards are presented and interpreted.

Classifying seedlots of Picea sitchensis and P. glauca in zones of introgression using restriction analysis of chloroplast DNA.

Chloroplast DNA (cpDNA) restriction analysis was used to classify five reforestation seedlots as to species. The material included two Sitka spruce (Picea sitchensis (Bong.) Carr.), one white spruce (P. glauca (Moench) Voss) from interior British Columbia, and two putative hybrid seedlots from the coast-interior introgression zone in British Columbia. The cpDNA patterns generated by Bam-HI and Bc1-I from individual trees of Sitka spruce, white spruce, western white spruce (P. glauca var. albertiana (S. Brown)), and Engelmann spruce (P. engelmanni (Parry)) were species-specific. They were used as reference patterns for comparisons. In addition, two controlled crosses between white and Sitka spruce were analyzed to demonstrate the paternal inheritance of cpDNA in spruces. The cpDNA restriction patterns for the five seedlots were obtained from composite samples of seedlings from each lot and compared to the typical cpDNA patterns of each species. Restriction patterns for the two Sitka spruce seedlots agreed with those from the Sitka spruce tree, while patterns for the white spruce seedlots from British Columbia agreed with those from the white spruce tree, lacking evidence of any Engelmann spruce component in the sample. On the other hand, one putative hybrid seedlot showed cpDNA patterns similar to white spruce while the other showed fragments unique to both Sitka and white spruce, indicating that this was a hybrid seedlot. The analysis of cpDNA restriction polymorphism has proven to be an effective tool for classifying seedlots in regions of introgression. To our knowledge, these results provide the first demonstration of the use of cpDNA analysis for solving practical forestry problems.

Evaluation of interclonal elemental-profile variation in Sitka spruce seed.

Elemental profiles of seeds collected from four ramets in each of 10 clones growing in a 12-year-old Sitka spruce [Picea sitchensis (Bong.) Carr.] seed orchard were determined by X-ray energy-dispersive spectrometry. The data collected from the resultant spectra were used to assess differences among clones and among ramets of a single clone and to determine the mechanism governing the observed differences. The spectra were shown to be different from each other and were specific to each clone. Results from analyses of variance (ANOVA) indicated that the clonal differences accounted for the majority of variation (77%), while among ramets within clones differences rated second (17%). Broad-sense heritability estimates were highly significant and ranged from 0.46 to 0.95. The multivariate analyses conducted on the data further emphasized the results obtained from ANOVA and a high degree of success (90%) was achieved in classifying seed samples to their source clone. Results support the hypothesis that the elemental uptake and assimilation of minerals of Sitka spruce is under genetic control.

The nature of inbreeding in a seed orchard of Douglas fir as shown by an efficient multilocus model.

The amounts of self-fertilization versus consanguineous matings (as measured by effective selfing) was estimated in a seed orchard of Douglas-fir, using progeny array data at six allozyme loci. The orchard is family structured, consisting several grafts (clones) and/or open-pollinated (o-p) progeny from each of several 'plus-trees'. Population-wide selfing rates were found to be 7% for the o-p trees and 2% for the cloned trees. Estimates of mating system parameters for individual trees showed this difference for average outcrossing rate t (1) still largely remained when outcrossingpollen gene frequency p was not allowed to vary among trees and (2) disappeared when p was allowed to vary among trees. Under this joint t and p estimation, o-p trees showed both significant variation of t (based upon a one-way ANOVA grouped by common plus-tree) and significant regressions of p on ovule genotype (indicative of consanguineous matings); cloned trees showed neither. This higher rate of consanguineous mating for o-p trees might be explained by the larger and more variable size of o-p families in the orchard. Estimates of outcrossing rate t and outcrossingpollen gene frequency p were based upon a multilocus model which makes full use of the information in the data. The increased information it gives over 'observed outcross' models is equivalent to adding 30-50% more loci, and it gives enough degrees of freedom to jointly estimate t and p for individual trees (individual progeny arrays) under certain conditions. In addition, inclusion of megagametophyte data nearly doubles the information about the mating system of individual trees.

Associations between Allozyme Genotypes and Quantitative Traits in Douglas-Fir [PSEUDOTSUGA MENZIESII (Mirb.) Franco].

Effects of maternal genotypes for eight enzyme loci on seven quantitative traits in 41 half-sib families were determined. Heritability estimates for the quantitative traits were highly significant and ranged from 0.57 to 0.86. Only six of 112 comparisons (56 comparisons for each of the genotypes and 56 for homozygous versus heterozygous contrasts) were statistically significant (P < 0.05). None of these significant comparisons could be associated with either a particular allele or a particular genotype. No heterotic effects were observed when the homozygous genotypes were compared with the heterozygous ones. Because the quantitative traits are highly correlated, a discriminant function analysis was performed to obtain the two most important canonical variates that accounted for 75% of the variance in the quantitative traits. There were no significant associations among enzyme loci and the two canonical variates. I conclude that, in this study, enzyme genotypic differences do not influence the quantitative traits to a major extent.