70 research outputs found
Genome-wide analysis of essential oil yield variation in Eucalyptus polybractea
Essential oil found in the leaves of Myrtaceous species, stored
in specialised sub-epidermic secretory cavities, consists mostly
of a large variety of terpenoid compounds. One such oil,
Eucalyptus oil, is produced from a number of “oil mallee”
species with high total foliar oil concentration, high proportion
of the monoterpene 1,8-cineole and the ability to re-sprout with
multiple stems from lignotubers after coppicing. The yield of
foliar oil in such commercially harvested perennial species (e.g.
eucalypts, Tea Trees and Hop) is dependent on complex
quantitative traits such as foliar oil concentration, leafy
biomass accumulation and adaptability. These often show large
natural variation and some are highly heritable, which has
enabled significant gains in oil yield via traditional phenotypic
recurrent selection. However, molecular breeding techniques could
increase gains per unit time by improving the accuracy of
selection and reducing cycle time.
In this thesis I explore the pathway to implementing genomic
selection for essential oil traits in Eucalyptus polybractea
(blue mallee). This begins with a general review of the
challenges of breeding in perennial essential oil crops. I
discuss the potential for applying genomic selection (GS) to
improve oil yield, while noting the factors that affect GS
accuracy and how they may manifest in openpollinated tree
populations. Next, using non-destructive methods I assess traits
relating to oil yield (quantitative and qualitative variation of
foliar essential oils and biomass-related parameters) for their
variability, heritability as well as phenotypic and genetic
interactions in an open-pollinated progeny trial with 40 families
and 480 individuals of E. polybractea. From raw phenotypes I
develop a model that is able to predict future harvest oil yield
performance at the family-level with a rank correlation of r =
0.74. This study shows that relying on oil concentration and
1,8-cineole proportion alone is not ideal for selection of top
performing families for oil yield. Rather a mixture of biomass
related traits, foliar oil concentration, 1,8-cineole proportion
and leaf architecture contribute to family-level oil yield in
varying ways.
To implement genomic selection it is important to understand the
genetic architecture of the trait under selection. To this end I
use whole genome re-sequencing of 480 blue mallees to perform a
GWAS of eleven oil yield traits. I find that allelic variants in
the pathways involved in the biosynthesis of terpenes are not
necessarily the major driver of foliar oil concentration when
viewed at the genome-wide level rather than at candidate-gene
level. I also reveal additional candidate genes that may be
involved in precursor availability for terpene biosynthesis,
terpene transport and the formation of oil secretory cavities.
The GWAS widens our understanding of the genetic basis of
essential oil variation to the genomic scale, while also
providing an informative set of priors for advanced genomic
selection models that make use of such information.
GS models face a problem of over-parameterization when fitting
large numbers of SNPs obtained from whole genome sequencing since
most SNPs are uninformative. Therefore I implement a modified
G-BLUP model that weights specific SNPs according to the trait
genetic architecture. I show that by using curated candidate gene
information the accuracy of prediction for total oil
concentration can be improved by 15-50% over standard G-BLUP.
Finally, this philosophy of partitioning genomic data into parts
to be modelled differently based on a-priori knowledge is well
established in phylogenetics. I explore the effects of different
approaches to partitioning in the context of phylogenetics,
noting that poor partitioning can result in misleading outcomes.
In general, this thesis broadens our understanding of the genetic
basis of quantitative oil traits, and shows how that information
can be used to more accurately predict genetic value in breeding
populations. Specific terpenes are increasingly sought after for
industrial purposes, such as advanced biofuels, so this knowledge
may facilitate increased production of key terpenes through
either plant-based systems or engineered pathway
Selecting optimal partitioning schemes for phylogenomic datasets
BACKGROUND Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. METHODS We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. RESULTS We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. CONCLUSIONS These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.RL would like to acknowledge support from a National Evolutionary Synthesis Centre (NESCent) short-term visitor grant. We would also like to acknowledge support from NESCent to pay for open-access publishing
Accuracy of Genomic Prediction for Foliar Terpene Traits in Eucalyptus polybractea
Unlike agricultural crops, most forest species have not had millennia of improvement through phenotypic selection, but can contribute energy and material resources and possibly help alleviate climate change. Yield gains similar to those achieved in agricultural crops over millennia could be made in forestry species with the use of genomic methods in a much shorter time frame. Here we compare various methods of genomic prediction for eight traits related to foliar terpene yield in Eucalyptus polybractea, a tree grown predominantly for the production of Eucalyptus oil. The genomic markers used in this study are derived from shallow whole genome sequencing of a population of 480 trees. We compare the traditional pedigree-based additive best linear unbiased predictors (ABLUP), genomic BLUP (GBLUP), BayesB genomic prediction model, and a form of GBLUP based on weighting markers according to their influence on traits (BLUP|GA). Predictive ability is assessed under varying marker densities of 10,000, 100,000 and 500,000 SNPs. Our results show that BayesB and BLUP|GA perform best across the eight traits. Predictive ability was higher for individual terpene traits, such as foliar α-pinene and 1,8-cineole concentration (0.59 and 0.73, respectively), than aggregate traits such as total foliar oil concentration (0.38). This is likely a function of the trait architecture and markers used. BLUP|GA was the best model for the two biomass related traits, height and 1 year change in height (0.25 and 0.19, respectively). Predictive ability increased with marker density for most traits, but with diminishing returns. The results of this study are a solid foundation for yield improvement of essential oil producing eucalypts. New markets such as biopolymers and terpene-derived biofuels could benefit from rapid yield increases in undomesticated oil-producing species.Funding for this project was provided by the Australian Research
Council Linkage Program (LP110100184) toWJF, the Rural Industries
Research and Development Corporation (RIRDC), Australia. Support
was also provided by the Center for BioEnergy Innovation (CBI), a
U.S DOE Bioenergy Research Center supported by the DOE office of
science
High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus
Terpenoid based essential oils are economically important commodities, yet beyond their biosynthetic pathways, little is known about the genetic architecture of terpene oil yield from plants. Transport, storage, evaporative loss, transcriptional regulation and precursor competition may be important contributors to this complex trait.
Here, we associate 2.39 M single nucleotide polymorphisms derived from shallow whole genome sequencing of 468 Eucalyptus polybractea individuals with 12 traits related to the overall terpene yield, eight direct measures of terpene concentration and four biomass‐related traits.
Our results show that in addition to terpene biosynthesis, development of secretory cavities where terpenes are both synthesised and stored, and transport of terpenes were important components of terpene yield. For sesquiterpene concentrations, the availability of precursors in the cytosol was important. Candidate terpene synthase genes for the production of 1,8‐cineole and α‐pinene, and β‐pinene, (which made up more than 80% of the total terpenes) were functionally characterised as a 1,8‐cineole synthase and a β / α‐pinene synthase.
Our results provide novel insights of the genomic architecture of terpene yield and we provide candidate genes for breeding or engineering of crops for biofuels or the production of industrially valuable terpenes
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Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.
Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation
A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant.
Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation
High Throughput Screening Technologies in Biomass Characterization
Biomass analysis is a slow and tedious process and not solely due to the long generation time for most plant species. Screening large numbers of plant variants for various geno-, pheno-, and chemo-types, whether naturally occurring or engineered in the lab, has multiple challenges. Plant cell walls are complex, heterogeneous networks that are difficult to deconstruct and analyze. Macroheterogeneity from tissue types, age, and environmental factors makes representative sampling a challenge and natural variability generates a significant range in data. Using high throughput (HTP) methodologies allows for large sample sets and replicates to be examined, narrowing in on more precise data for various analyses. This review provides a comprehensive survey of high throughput screening as applied to biomass characterization, from compositional analysis of cell walls by NIR, NMR, mass spectrometry, and wet chemistry to functional screening of changes in recalcitrance via HTP thermochemical pretreatment coupled to enzyme hydrolysis and microscale fermentation. The advancements and development of most high-throughput methods have been achieved through utilization of state-of-the art equipment and robotics, rapid detection methods, as well as reduction in sample size and preparation procedures. The computational analysis of the large amount of data generated using high throughput analytical techniques has recently become more sophisticated, faster and economically viable, enabling a more comprehensive understanding of biomass genomics, structure, composition, and properties. Therefore, methodology for analyzing large datasets generated by the various analytical techniques is also covered
Evaluation of methods and marker systems in genomic selection of oil palm (Elaeis guineensis Jacq.)
Background
Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits.
Results
The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods.
Conclusion
Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly outperformed other methods, but required parameters optimization for GS implementation
City of Hitchcock Comprehensive Plan 2020-2040
Hitchcock is a small town located in Galveston
County (Figure 1.1), nestled up on the Texas Gulf
Coast. It lies about 40 miles south-east of Houston.
The boundaries of the city encloses an area of
land of 60.46 sq. miles, an area of water of 31.64
sq. miles at an elevation just 16 feet above sea level.
Hitchcock has more undeveloped land (~90% of
total area) than the county combined. Its strategic
location gives it a driving force of opportunities in
the Houston-Galveston Region.The guiding principles for this planning process were Hitchcock’s vision statement and its corresponding goals, which were crafted by the
task force. The goals focus on factors of growth and development including public participation, development considerations,
transportation, community facilities, economic development, parks, and housing and social vulnerabilityTexas Target Communitie
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