Analysis of the genetic variation in growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa provenances

Guerra, Fernando; Richards, James H.; Fiehn, Oliver; Famula, Randi; Stanton, Brian J.; Shuren, Richard; Sykes, Robert; Davis, Mark F.; Neale, David B.

doi:10.1007/s11295-015-0965-8

Cited by 42 publications

(56 citation statements)

References 51 publications

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“…This pattern in spring phenology contrasts the strongly clinal, negative trend with latitude consistently observed in the autumn phenology of Populus trichocarpa (Evans et al ., ; McKown et al ., ). Although linear trends were observed at Agassiz, this is likely due to a lack of genotypes from northernmost regions (provenances originated from < 54.3°N), indicating that the accessions selected for Agassiz (and planted in other common gardens, see Evans et al ., ; Guerra et al ., ) capture only a portion of the geographical trend in bud‐break across the species. Prior investigations in poplar have shown weak linear patterns between bud‐break and latitude (e.g.…”

Section: Discussionmentioning

confidence: 95%

“…Prior investigations in poplar have shown weak linear patterns between bud‐break and latitude (e.g. Farmer & Reinholt, ; Olson et al ., ; Guerra et al ., ) or no trends (e.g. Hall et al ., ; Luquez et al ., ; Soolanayakanahally et al ., ; Evans et al ., ).…”

Section: Discussionmentioning

confidence: 99%

“…This explanation is plausible for northern P. trichocarpa , but not for earlier bud‐break observed in the southern genotypes, which set bud much later in the autumn than northern genotypes at Totem Field (McKown et al ., ). In addition, the accessions planted at Agassiz also were planted further south in multiple common gardens (see Evans et al ., ; Guerra et al ., ), and bud‐break results from these trials (specifically in genotypes originating from 50 to 54°N) failed to exhibit this effect.…”

Section: Discussionmentioning

confidence: 99%

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Ecological genomics of variation in bud‐break phenology and mechanisms of response to climate warming in Populus trichocarpa

et al. 2018

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Spring bud-break phenology is a critical adaptive feature common to temperate perennial woody plants. Understanding the molecular underpinnings of variation in bud-break is important for elucidating adaptive evolution and predicting outcomes relating to climate change. Field and controlled growth chamber tests were used to assess population-wide patterns in bud-break from wild-sourced black cottonwood (Populus trichocarpa) genotypes. We conducted a genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) derived from whole genome sequencing to test for loci underlying variation in bud-break. Bud-break had a quadratic relationship with latitude, where southern- and northern-most provenances generally broke bud earlier than those from central parts of the species' range. Reduced winter chilling increased population-wide variation in bud-break, whereas greater chilling decreased variation. GWAS uncovered 16 loci associated with bud-break. Phenotypic changes connected with allelic variation were replicated in an independent set of P. trichocarpa trees. Despite phenotypic similarities, genetic profiles between southern- and northern-most genotypes were dissimilar based on our GWAS-identified SNPs. We propose that the GWAS-identified loci underpin the geographical pattern in P. trichocarpa and that variation in bud-break reflects different selection for winter chilling and heat sum accumulation, both of which can be affected by climate warming.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Ecological genomics of variation in bud‐break phenology and mechanisms of response to climate warming in Populus trichocarpa

et al. 2018

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“…Despite the low number of publications in forest tree metabolomics, when compared to other omics studies [66], GC-TOF-MS has been the method of choice for the primary metabolite profiling of forest tree responses to abiotic and biotic stresses [24,25,58,[67][68][69] as well as other plant growth-related processes [17,26,[70][71][72][73][74][75][76][77]. In these forest tree metabolomics studies, as for plant metabolomics in general, primary metabolites for GC-TOF-MS analysis are commonly extracted using the well-established chloroform:methanol:water extraction protocol, with minor optimization variations across studies (e.g., time of extraction, temperature, solvent ratio, or addition order), and further derivatized with N-methyl-N-(trimethylsilyl)trifloracetamide (MSTFA), containing a mixture of fatty acid methyl esters (FAMEs) with different chain length as time standards (i.e., standard for retention time calibration) [2,34,50,63].…”

Section: Gc-ms Metabolite Profilingmentioning

confidence: 99%

Experimental Design and Sample Preparation in Forest Tree Metabolomics

2019

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Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.

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“…Biomass yield and chemical quality of P. trichocarpa cultivars, as well as their improvement, depend on multiple biological and environmental factors [4]. Considerable variation has been observed in P. trichocarpa for complex traits related to growth, phenology, morphology, ecophysiology and wood chemistry [5][6][7][8]. These phenotypes include diameter and height [9,10], bud set and flush [6,11], water-use efficiency (WUE) [12,13], secondary xylem composition [14] and wood metabolome [5].…”

Section: Introductionmentioning

confidence: 99%

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

Guerra

Suren

Holliday

et al. 2019

Preprint

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Background: Populus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to perform GWAS. Results: A GWAS using 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and 813K single nucleotide polymorphisms (SNPs), identified a variable number of significant SNPs in association with the assessed traits. Associated single-markers (q< 0.1) ranged from 3 to 110 per trait. The SNPs had a cumulative effect of up to 40.6% of the phenotypic variation of any given trait. Similarly, multiple-marker analyses detected between 16 and 291 significant windows for the phenotypes. The SNPs resided within genes that encode proteins belonging to different functional classes as well as in intergenic regions. Conclusion: SNP-markers within and proximal to genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies.

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Analysis of the genetic variation in growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa provenances

Cited by 42 publications

References 51 publications

Ecological genomics of variation in bud‐break phenology and mechanisms of response to climate warming in Populus trichocarpa

Ecological genomics of variation in bud‐break phenology and mechanisms of response to climate warming in Populus trichocarpa

Experimental Design and Sample Preparation in Forest Tree Metabolomics

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

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