Recherche

Geraldes, Armando; DiFazio, Steve P.; Slavov, Gancho T.; Ranjan, Priya; Muchero, Wellington; Hannemann, Jan; Gunter, Lee E.; Wymore, Ann M.; Grassa, Christopher J.; Farzaneh, Nima; Porth, Ilga; Mckown, Athena D.; Skyba, Oleksandr; Li, Eryang; Fujita, Miki; Klápště, Jaroslav; Martin, Joel; Schackwitz, Wendy; Pennacchio, Christa; Rokhsar, Daniel; Friedmann, Michael C.; Wasteneys, Geoffrey O.; Guy, Robert D.; El-Kassaby, Yousry A.; Mansfield, Shawn D.; Cronk, Quentin C. B.; Ehlting, Juergen; Douglas, Carl J.; Tuskan, Gerald A. — 2013-01-16 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.

Brar, Simren; Tsui, Clement K. M.; Dhillon, Braham; Bergeron, Marie-Josée; Joly, David L.; Zambino, P. J.; El-Kassaby, Yousry A.; Hamelin, Richard C. — 2016-05-14 White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.

Ratcliffe, Blaise; El-Dien, Omnia Gamal; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; Jaquish, Barry; El-Kassaby, Yousry A. — 2015-05-27 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.

Tsui, Clement Kin-Ming; Farfan, Lina; Roe, Amanda D.; Rice, Adrianne V.; Cooke, Janice E. K.; El-Kassaby, Yousry A.; Hamelin, Richard C. — 2015-06-17 Over 18 million ha of forests have been destroyed in the past decade in Canada by the mountain pine beetle (MPB) and its fungal symbionts. Understanding their population dynamics is critical to improving modeling of beetle epidemics and providing potential clues to predict population expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal symbionts of MPB that aid the beetle to colonize and kill their pine hosts. We investigated the genetic structure and demographic expansion of L. longiclavatum in populations established within the historic distribution range and in the newly colonized regions. We identified three genetic clusters/populations that coincide with independent geographic locations. The genetic profiles of the recently established populations in northern British Columbia (BC) and Alberta suggest that they originated from central and southern BC. Approximate Bayesian Computation supports the scenario that this recent expansion represents an admixture of individuals originating from BC and the Rocky Mountains. Highly significant correlations were found among genetic distance matrices of L. longiclavatum, G. clavigera, and MPB. This highlights the concordance of demographic processes in these interacting organisms sharing a highly specialized niche and supports the hypothesis of long-term multipartite beetle-fungus co-evolutionary history and mutualistic relationships.

Liu, Yang; Erbilgin, Nadir; Ratcliffe, Blaise; Klutsch, Jennifer G.; Wei, Xiaojing; Ullah, Aziz; Cappa, Eduardo Pablo; Chen, Charles; Thomas, Barb R.; El-Kassaby, Yousry A. — 2022-10-09 <p>Whilst droughts, intensified by climate change, have been affecting forests worldwide, pest epidemics are a major source of uncertainty for assessing drought impacts on forest trees. Thus far, little information has documented the adaptability and evolvability of traits related to drought and pests simultaneously. We conducted common-garden experiments to investigate how several phenotypic traits (i.e., height growth, drought avoidance based on water-use efficiency inferred from δ¹³C, and pest resistance based on defense traits) interact in five mature lodgepole pine populations established in four progeny trials in western Canada. The relevance of interpopulation variation in climate sensitivity highlighted that seed-source warm populations had greater adaptive capability than cold populations. In test sites, warming generated taller trees with higher δ¹³C and increased the evolutionary potential of height growth and δ¹³C across populations. We found, however, no pronounced gradient in defenses and their evolutionary potential along populations or test sites. Response to selection was weak in defenses across test sites, but high for height growth, particularly at warm test sites. Response to selection of δ¹³C varied depending on its selective strength relative to height growth. We conclude that warming could promote the adaptability and evolvability of growth response and drought avoidance with limited evolutionary influence from pest (biotic) pressures.</p>

Liu, Yang; Erbilgin, Nadir; Cappa, Eduardo Pablo; Chen, Charles; Ratcliffe, Blaise; Wei, Xiaojing; Klutsch, Jennifer G.; Ullah, Aziz; Azcona, Jaime Sebastian; Thomas, Barb R.; El-Kassaby, Yousry A. — 2022-12-28 We selected five lodgepole pine populations, representing a total of 224 maternal half-sib families, grown in four progeny test sites (> 35 yrs) located along various climatic gradients in central Alberta, Canada. Across the four progeny test sites, we chose a total of 1,490 trees for phenotyping. Height growth (m) was measured at age 35-yr with a clinometer. Carbon isotope ratio (δ13C, in ‰) analysis was performed at Alberta Innovates in Victoria, using outside slabs cut and ground from the 5 mm increment cores taken from the north side of each tree at approximately breast height (1.3 m) at age 35. Samples were analyzed using an established method on a MAT253 Mass Spectrometer with Conflo IV interface and a Fisons NA1500 EA. We assessed the severity of WGR infection in the test sites by a qualitative scoring system with discrete categories ranging from no gall symptoms to deceased (four tiers) for all trees sampled at age 36-yr. We also investigated these trees’ suitability to MPB. Host tree suitability to the beetles was evaluated by quantifying defense chemicals (mainly monoterpenes) using a Gas Chromatography/Flame Ionization Detector based on cambial tissues collected by a hole punch when trees were actively growing, coinciding with MPB flight in western Canada. Then, chemical profiling was performed to test against MPB performance based on laboratory bioassays. A cutoff of four categories was used to classify trees with different MPB suitability levels. In addition, we performed dendrochronological analysis to calculate drought resistance indices based on changes in tree-ring width before and after drought event.

Liu, Yang; El-Kassaby, Yousry A. — 2021-06-28 Natural selection on fitness-related traits can be temporally heterogeneous among populations. As climate changes, understanding population-level responses is of scientific and practical importance. We examined 18 phenotypic traits associated with phenology, biomass, and ecophysiology in 403 individuals of natural Populus trichocarpa populations, growing in a common garden. Compared with tree origin settings, propagules likely underwent drought exposures in the common garden due to significantly low rainfall during the years of measurement. All study traits showed population differentiation reflecting adaptive responses due to local genetic adaptation. Phenology and biomass traits were strongly under selection and showed plastic responses between years, co-varying with latitude. While phenological events (e.g., bud set and growth period) and biomass were under positive directional selection, post-bud set period, particularly from final bud set to the onset of leaf drop, was selected against. With one exception to water-use efficiency, ecophysiology traits were under negative directional selection. Moreover, extended phenological events jointly evolved with source niches under increased temperature and decreased rainfall exposures. High biomass coevolved with climatic niches of high temperature; low rainfall promoted high photosynthetic rates evolution. This work underpins that P. trichocarpa is likely to experience increased fitness (height gain) by evolving toward extended bud set and growth period, abbreviated post-bud set period, and increased drought resistance, potentially constituting a powerful mechanism for long-lived tree species in surviving unpredictably environmental extremes (e.g., drought).

Liu, Yang; El-Kassaby, Yousry A. — 2020-01-06 Faculty Background: Natural selection on fitness-related traits can be temporally heterogeneous among populations. As climate changes, understanding population-level responses is of scientific and practical importance. We examined 18 phenotypic traits associated with phenology, biomass, and ecophysiology in 403 individuals of natural Populus trichocarpa populations, growing in a common garden. Results: Compared with tree origin settings, propagules likely underwent drought exposures in the common garden due to significantly low rainfall during the years of measurement. All study traits showed population differentiation reflecting adaptive responses due to local genetic adaptation. Phenology and biomass traits were strongly under selection and showed plastic responses between years, co-varying with latitude. While phenological events (e.g., bud set and growth period) and biomass were under positive directional selection, post-bud set period, particularly from final bud set to the onset of leaf drop, was selected against. With one exception to water-use efficiency, ecophysiology traits were under negative directional selection. Moreover, extended phenological events jointly evolved with source niches under increased temperature and decreased rainfall exposures. High biomass coevolved with climatic niches of high temperature; low rainfall promoted high photosynthetic rates evolution. Conclusions: This work underpins that P. trichocarpa is likely to experience increased fitness (height gain) by evolving toward extended bud set and growth period, abbreviated post-bud set period, and increased drought resistance, potentially constituting a powerful mechanism for long-lived tree species in surviving unpredictably environmental extremes (e.g., drought). See correction doi 10.1186/s12862-021-01884-9 at http://hdl.handle.net/2429/79273 Forestry, Faculty of Forest and Conservation Sciences, Department of Reviewed http://creativecommons.org/licenses/by/4.0/

El-Kassaby, Yousry A.; Cappa, Eduardo P.; Chen, Charles; Ratcliffe, Blaise; Porth, Ilga M. — 2023-12-18 <p>Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingences and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: 1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, 2) generates unprecedented resolution of genealogical relationships among tested individuals, and 3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method's superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.</p>

Tsui, Clement Kin Ming; Roe, Amanda D.; El-Kassaby, Yousry A.; Rice, Adrianne V.; Massoumi Alamouti, Sepideh; Sperling, Felix A. H.; Cooke, Janice E. K.; Bohlmann, Jörg; Hamelin, Richard C. — 2011-09-13 We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect–fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north–south differentiation of MPB and G. clavigera populations points to the fungal pathogen’s dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus–beetle association is important for the modelling and prediction of MPB epidemics.

Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápste, Jaroslav; Chen, Charles; Porth, Ilga; El-Kassaby, Yousry A. — 2015-05-15 Background: Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost. Results: Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3. Conclusions: The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

Xia, Qijing; Zhang, Hongbin; Lv, Dong; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 1 https://creativecommons.org/licenses/by/4.0/legalcode

Xia, Qijing; Zhang, Hongbin; Lv, Dong; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 2 https://creativecommons.org/licenses/by/4.0/legalcode

Xia, Qijing; Zhang, Hongbin; Lv, Dong; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 3 https://creativecommons.org/licenses/by/4.0/legalcode

Zhou, Chengcheng; Bo, Wenhao; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 1. https://creativecommons.org/licenses/by/4.0/legalcode

Zhou, Chengcheng; Bo, Wenhao; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 2. https://creativecommons.org/licenses/by/4.0/legalcode

Zhou, Chengcheng; Bo, Wenhao; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 3. https://creativecommons.org/licenses/by/4.0/legalcode

Zhou, Chengcheng; Bo, Wenhao; El-Kassaby, Yousry A.; Li, Wei — 2024 Supplementary Material 4. https://creativecommons.org/licenses/by/4.0/legalcode

Xu, Xinyu; Xu, Lianhuan; Yang, Zirui; Chen, Lei; Wang, Yiqing; Ren, Hui; Zhang, Zehuang; El-Kassaby, Yousry A.; Wu, Shasha — 2024 Supplementary Material 5 https://creativecommons.org/licenses/by/4.0/legalcode