Integrating genomic information and productivity and climate-adaptability traits into a regional white spruce breeding program

Tree improvement programs often focus on improving productivity-related traits; however, under present climate change scenarios, climate change-related (adaptive) traits should also be incorporated into such programs. Therefore, quantifying the genetic variation and correlations among productivity and adaptability traits, and the importance of genotype by environment interactions, including defense compounds involved in biotic and abiotic resistance, is essential for selecting parents for the production of resilient and sustainable forests. Here, we estimated quantitative genetic parameters for 15 growth, wood quality, drought resilience, and monoterpene traits for Picea glauca (Moench) Voss (white spruce). We sampled 1,540 trees from three open-pollinated progeny trials, genotyped with 467,224 SNP markers using genotyping-by-sequencing (GBS). We used the pedigree and SNP information to calculate, respectively, the average numerator and genomic relationship matrices, and univariate and multivariate individual-tree models to obtain estimates of (co)variance components. With few site-specific exceptions, all traits examined were under genetic control. Overall, higher heritability estimates were derived from the genomic- than their counterpart pedigree-based relationship matrix. Selection for height, generally, improved diameter and water use efficiency, but decreased wood density, microfibril angle, and drought resistance. Genome-based correlations between traits reaffirmed the pedigree-based correlations for most trait pairs. High and positive genetic correlations between sites were observed (average 0.68), except for those pairs involving the highest elevation, warmer, and moister site, specifically for growth and microfibril angle. These results illustrate the advantage of using genomic information jointly with productivity and adaptability traits, and defense compounds to enhance tree breeding selection for changing climate.Instituto de Recursos BiológicosFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Cappa, Eduardo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Klutsch, Jenifer G. University of Alberta; Department of Renewable Resources; CanadaFil: Sebastian-Azcona, Jaime. University of Alberta; Department of Renewable Resources; CanadaFil: Ratchiffe, Blaise. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Xiaojing, Wei. University of Alberta; Department of Renewable Resources; CanadaFil: Da Ros, Letitia. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Yang, Liu. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados UnidosFil: Benowicz, Andy. Alberta Agriculture and Forestry. Forest Stewardship and Trade Branch; CanadáFil: Sadoway, Shane. Blue Ridge Lumber Inc.; CanadáFil: Mansfield, Shawn D. University of British Columbia. Faculty of Forestry. Department of Wood Science; CanadáFil: Erbilgin, Nadir. University of Alberta; Department of Renewable Resources; CanadaFil: Thomas, Barb R. University of Alberta; Department of Renewable Resources; CanadaFil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canad

Mitigating the downstream effects of excess soil phosphorus through cultivar selection and increased foliar resorption

Elemental phosphorus has been categorized as a non-renewable resource that is crucial to global food security. This is largely due to the transport of phosphorus being dependent on aqueous transfer and therefore an inherent inability to return to upstream ecosystems. It is only through mining and transport of rock phosphate that agricultural land remains productive. Simultaneously, due to agricultural over-fertilization, phosphorus has been characterized as a pollutant in aquatic environments. Diffuse source run-off from high phosphorus soils continues to contribute to downstream eutrophication decades after nutrient management practices have been put into place. A potential solution involves planting high biomass-producing tree species along riparian areas. Trees belonging to the Salicaceae are ideal candidates as they have a wide geographical distribution in Canada and broad-scale applications, ranging from fibre production to biofuel feedstock to uses in phytoremediation. The objective of this thesis was to identify a commercially available tree genotype, be it poplar or willow, well suited for widespread planting in agricultural areas to limit nutrient enrichment of riparian ecosystems. Phenotypic differences in phosphorus storage and allocation were analyzed using ICP-AES and HPLC. Poplar varieties Tristis and Northwest demonstrated the highest capacity for luxury uptake with an estimated 3.7 – 3.9 mg P g-¹ when 2.2 mM soluble phosphate (100N:70P) was applied, with no measurable metabolic consequences. However, the majority of phosphorus was stored in leaves as phosphate and subsequently returned to the environment as autumnal senescence progressed. This led to the exploration of factors limiting phosphate translocation and resorption. Expression of an exogenous phosphate H⁺/H₂PO₄- symporter in poplar led to a small, but significant increase in phosphate resorption and a pronounced increase in sulfate resorption, leading to further questions surrounding anion efflux from the vacuole and the role of the tonoplast in limiting nutrient translocation. If resorption proficiency could be increased under the high nutrient loads found in productive lands, poplar genotypes with luxury consumption could be bred for improved resorption and used to reduce phosphorus entry into riparian ecosystems. Extrapolation of this information to crop species could lead to reduced fertilizer application and improved nutrient management of perennial production systems.Forestry, Faculty ofGraduat

Baseline inventory of the UBC food system : healthy food situation assessment and action plan

Snacks are an integral part of a university student’s diet given that schedules do not always allow enough time for students to sit down for a regular meal. This means that the to-go items that are offered at the main campus locations play a key role in determining student health. At the University of British Columbia campus, UBC Food Services is the primary food provider as they run and maintain several central dining locations such as Totem Park Residence Dining Hall, Place Vanier Residence Dining Hall, Ike’s Café and the Loop. To assess the healthy snack options on campus from a consumer’s perspective, a baseline inventory of all snack items available at the four locations was compiled and a survey of students was administered. Each inventory item was given a categorized as “choose most”, “choose sometimes”, “choose least”, and “not recommended” according to B.C. Food Sales Guidelines and labeling such as whether the snack was gluten-free was recorded. The Loop and Place Vanier had the most items under the ‘choose most’ category, and therefore, had the healthiest choices. Totem Park and Ike’s Cafe showed lower numbers of snack items belonging to the ‘choose most’ category. The combined survey results showed that 59% of consumers felt that the location they frequented had enough healthy options. At several locations, consumers voiced the desire for more vegan options as well as a greater variety of fruit. This was inconsistent with our inventory and led us to conclude that, although UBC Food Services is actively pursuing its local, fair trade, and organic procurement goals, consumers are often unaware of their procurement policies and the nature of the goods they provide. Therefore, our recommendations for UBC Food Services includes increasing the amount of ‘choose most’ options at both Totem and Ike’s Cafe, improving the labeling of dietary facts on snack items to increase awareness among consumers, as well as increasing the number of vegan, gluten-free and lactose-free snack alternatives. Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”Land and Food Systems, Faculty ofUnreviewedUndergraduat

Drought-Induced Regulatory Cascades and Their Effects on the Nutritional Quality of Developing Potato Tubers

Competition for scarce water resources and the continued effects of global warming exacerbate current constraints on potato crop production. While plants’ response to drought in above-ground tissues has been well documented, the regulatory cascades and subsequent nutritive changes in developing tubers have been largely unexplored. Using the commercial Canadian cultivar “Vigor”, plants were subjected to a gradual drought treatment under high tunnels causing a 4 °C increase in the canopy temperature. Tubers were sampled for RNAseq and metabolite analysis. Approximately 2600 genes and 3898 transcripts were differentially expressed by at least 4-fold in drought-stressed potato tubers, with 75% and 69% being down-regulated, respectively. A further 229 small RNAs were implicated in gene regulation during drought. Expression of several small RNA clusters negatively correlated with expression of their six target patatin genes, suggesting involvement in the regulation of storage proteins during drought. The comparison of protein homologues between Solanum tuberosum L. and Arabidopsis thaliana L. indicated that down-regulated genes were associated with phenylpropanoid and carotenoid biosynthesis. As is indicative of reduced flow through the phenylpropanoid pathway, phenylalanine accumulated in drought-stressed tubers. This suggests that there may be nutritive implications to drought stress occurring during the potato tuber bulking phase in sensitive cultivars.Forestry, Faculty ofNon UBCReviewedFacult

Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine

Abstract Background Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias. Results MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP. Conclusions The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.Forestry, Faculty ofNon UBCForest and Conservation Sciences, Department ofWood Science, Department ofReviewedFacultyResearcherOthe