ORCID Profile
0000-0003-2589-3928
Current Organisation
Scion
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Publisher: Oxford University Press (OUP)
Date: 06-2019
Abstract: We present an H i study of the galaxy group LGG 351 using Widefield ASKAP L-band Legacy All-sky Blind Survey (WALLABY) early science data observed with the Australian Square Kilometre Array Pathfinder (ASKAP). LGG 351 resides behind the M 83 group at a velocity range (cz) of ∼3500–4800 km s−1 within the rich Hydra-Centaurus overdensity region. We detect 40 sources with the discovery of a tidally interacting galaxy pair and two new H i sources that are not presented in previous optical catalogues. 23 out of 40 sources have new redshifts derived from the new H i data. This study is the largest WALLABY sub-s le to date and also allows us to further validate the performance of ASKAP and the data reduction pipeline askapsoft. Extended H i emission is seen in six galaxies indicating interaction within the group, although no H i debris is found. We also detect H i in a known ultra-faint dwarf galaxy (dw 1328−29), which demonstrates that it is not a satellite of the M 83 group as previously thought. In conjunction with multiwavelength data, we find that our galaxies follow the atomic gas fraction and baryonic Tully–Fisher scaling relations derived from the GALEX Arecibo SDSS Survey. In addition, majority of our galaxies fall within the star formation main sequence indicating inefficiency of gas removal processes in this loose galaxy group.
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Publisher: Springer Science and Business Media LLC
Date: 10-02-2020
DOI: 10.1186/S12863-020-0821-1
Abstract: Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environments was undertaken to assess genotype x environment interaction (GxE) of coast redwood in order to understand the performance of genotypes across environments. The quantitative genetic analysis discovered no GxE between investigated environments for diameter at breast height (DBH). However, no genetic component was detected at one environment possibly due to stressful conditions. The implementation of universal response function allowed for the identification of important environmental factors affecting species productivity. Additionally, this approach enabled us to predict the performance of species across the New Zealand environmental conditions. In combination with quantitative genetic analysis which identified genetically superior material, the URF model can directly identify the optimal geographical regions to maximize productivity. However, the finding of ideally uncorrelated climatic variables for species with narrow ecological litude is rather challenging, which complicates construction of informative URF model. This, along with a small number of tested environments, tended to overfit a prediction model which resulted in extreme predictions in untested environments.
Publisher: Scion
Date: 12-2016
Publisher: Oxford University Press (OUP)
Date: 26-07-2019
Abstract: We present a Wide-field ASKAP L-Band Legacy All-sky Blind surveY (WALLABY) study of the nearby (vsys = 915 km s−1) spiral galaxy IC 5201 using the Australian Square Kilometre Array Pathfinder (ASKAP). IC 5201 is a blue, barred spiral galaxy that follows the known scaling relations between stellar mass, SFR, H i mass, and diameter. We create a four-beam mosaicked H i image cube from 175 h of observations made with a 12-antenna sub-array. The root mean square noise level of the cube is 1.7 mJy beam−1 per channel, equivalent to a column density of $N_{\\rm H\\, \\small {I}}$ = 1.4 × 1020 cm−2 over 25 km s−1. We report nine extragalactic H i detections – five new H i detections including the first velocity measurements for two galaxies. These sources are IC 5201, three dwarf satellite galaxies, two galaxies, and a tidal feature belonging to the NGC 7232/3 triplet and two potential infalling galaxies to the triplet. There is evidence of a previous tidal interaction between IC 5201 and the irregular satellite AM 2220−460. A close fly-by is likely responsible for the asymmetric optical morphology of IC 5201 and warping its disc, resulting in the irregular morphology of AM 2220−460. We quantify the H i kinematics of IC 5201, presenting its rotation curve as well as showing that the warp starts at 14 kpc along the major axis, increasing as a function of radius with a maximum difference in position angle of 20°. There is no evidence of stripped H i, triggered or quenched star formation in the system as measured using DECam optical and GALEX UV photometry.
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.TPLANTS.2018.08.005
Abstract: Phenotyping is the accurate and precise physical description of organisms. Accurate and quantitative phenotyping underpins the delivery of benefits from genetic improvement programs in agriculture. In forest trees, phenotyping at an equivalent precision has been impossible because trees and forests are large, long-lived, and highly variable. These facts have restricted the delivery of genetic gains in forestry compared to other agricultural sectors. We describe a landscape-scale phenotyping platform that integrates remote sensing, spatial information systems, and genomics to facilitate the delivery of greater gains enabling forestry to catch up with other sectors. Combining remote sensing at a range of spatial and temporal scales with genomics will ultimately impact on tree breeding globally.
Publisher: Scion
Date: 12-2014
Publisher: Springer Science and Business Media LLC
Date: 31-01-2015
Publisher: Springer Science and Business Media LLC
Date: 1992
DOI: 10.1007/BF00196245
Publisher: Public Library of Science (PLoS)
Date: 09-07-2015
Publisher: Oxford University Press (OUP)
Date: 04-10-2018
Publisher: Elsevier BV
Date: 07-2001
Publisher: Oxford University Press (OUP)
Date: 29-10-2019
Publisher: Elsevier BV
Date: 09-2017
Publisher: Informa UK Limited
Date: 2002
Publisher: Springer Science and Business Media LLC
Date: 06-07-2018
Publisher: Cambridge University Press (CUP)
Date: 2022
DOI: 10.1017/PASA.2022.43
Abstract: We present the Widefield ASKAP L-band Legacy All-sky Blind surveY (WALLABY) Pilot Phase I H i kinematic models. This first data release consists of H i observations of three fields in the direction of the Hydra and Norma clusters, and the NGC 4636 galaxy group. In this paper, we describe how we generate and publicly release flat-disk tilted-ring kinematic models for 109/592 unique H i detections in these fields. The modelling method adopted here—which we call the WALLABY Kinematic Analysis Proto-Pipeline (WKAPP) and for which the corresponding scripts are also publicly available—consists of combining results from the homogeneous application of the FAT and 3DBarolo algorithms to the subset of 209 detections with sufficient resolution and $S/N$ in order to generate optimised model parameters and uncertainties. The 109 models presented here tend to be gas rich detections resolved by at least 3–4 synthesised beams across their major axes, but there is no obvious environmental bias in the modelling. The data release described here is the first step towards the derivation of similar products for thousands of spatially resolved WALLABY detections via a dedicated kinematic pipeline. Such a large publicly available and homogeneously analysed dataset will be a powerful legacy product that that will enable a wide range of scientific studies.
Publisher: Springer Science and Business Media LLC
Date: 30-05-2013
Publisher: Springer Science and Business Media LLC
Date: 27-06-2018
Publisher: Springer Science and Business Media LLC
Date: 02-2013
Publisher: Oxford University Press (OUP)
Date: 11-10-2022
DOI: 10.1093/G3JOURNAL/JKAC245
Abstract: The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark. Genetic parameters from different genomic prediction methods—single-trait best linear unbiased prediction based on a marker-based relationship matrix (genomic best linear unbiased prediction), multitrait single-step genomic best linear unbiased prediction, which integrated the marker-based and pedigree-based relationship matrices (single-step genomic best linear unbiased prediction) and the single-trait generalized ridge regression—were compared to equivalent single- or multitrait pedigree-based approaches (ABLUP). The influence of the statistical distribution of data on the genetic parameters was assessed. Results indicated that the heritability estimates were increased nearly 2-fold with genomic models compared to the equivalent pedigree-based models. Predictive accuracy of the single-step genomic best linear unbiased prediction was higher than the ABLUP for most traits. Allowing for heterogeneity in marker effects through the use of generalized ridge regression did not markedly improve predictive ability over genomic best linear unbiased prediction, arguing that most of the chemical traits are modulated by many genes with small effects. Overall, the traits with low pedigree-based heritability benefited more from genomic models compared to the traits with high pedigree-based heritability. There was no evidence that data skewness or the presence of outliers affected the genomic or pedigree-based genetic estimates.
Publisher: Springer Science and Business Media LLC
Date: 07-2020
Publisher: Springer Science and Business Media LLC
Date: 22-10-2018
DOI: 10.1038/S41437-018-0159-X
Abstract: Published online: 6 July 2018 This article was originally published under standard licence, but has now been made available under a [CC BY 4.0] license. The PDF and HTML versions of the paper have been modified accordingly.
Publisher: Springer Science and Business Media LLC
Date: 07-05-2016
Publisher: Canadian Science Publishing
Date: 02-2019
Abstract: Progeny testing of resistance to needle loss caused by Cyclaneusma minus (cyclaneusma needle cast) has been included in the needle disease resistance strategy of Pinus radiata D. Don in New Zealand since the late 1970s. Data on progeny trials, two in the North Island of New Zealand and one in Tasmania, Australia, were available to estimate heritability between trait genetic correlations and genotype × environment interaction. Resistance to cyclaneusma needle cast had moderate estimates of heritability (0.25 to 0.46) at all sites. Genetic correlations between the assessed traits indicated that selection for faster early growth, i.e., tree height at age 4 years and diameter at breast height at age 6 years, favours trees that are prone to Cyclaneusma infection, while a favourable genetic association between resistance to cyclaneusma needle cast and productivity was evident at a later assessment at age 9 years. No significant genotype × environment interaction was found for resistance to cyclaneusma needle cast however, stability of genotypes across a wider range of environments and with a high genetic connectedness requires more research. Considerable genetic improvement can be achieved for resistance to cyclaneusma needle cast and indirect selection for the trait should be pursued by selecting for productivity and culling susceptible genotypes from breeding.
Publisher: Frontiers Media SA
Date: 10-07-2020
Publisher: Scion
Date: 24-02-2017
Publisher: Canadian Science Publishing
Date: 12-2015
Abstract: Realised genetic gain for radiata pine (Pinus radiata D. Don) was estimated using data from 46 installations of three series of block-plot trials spanning a wide range of site types throughout New Zealand. These trials contained 63 unique seedlots with different levels of genetic improvement. Realised genetic gain was quantified using two measures of productivity: site index and 300 Index (a measure of volume productivity). The level of genetic improvement of each seedlot was determined by its GF Plus rating, a genetic rating system based on breeding values used for New Zealand radiata pine. There was a positive relationship between GF Plus rating and both productivity measures. Differences of 25% in total standing volume at age 30 years and of 5.6% in site index were found between unimproved (GF Plus 9.9) and highly improved (GF Plus 25) seedlots. Each unit increase in GF Plus rating was associated with a 1.51% increase in volume growth rate. In absolute terms, the magnitude of the increase was greater on more productive sites compared with less productive sites, although in percentage terms, it varied little between sites or regions. Quantification of genetic gain in this manner enables it to be easily incorporated into existing growth and yield simulators.
Publisher: MDPI AG
Date: 18-12-2020
DOI: 10.3390/F11121356
Abstract: Bark stripping by mammals is a major problem for conifer forestry worldwide. In Australia, bark stripping in the exotic plantations of Pinus radiata is mainly caused by native marsupials. As a sustainable management option, we explored the extent to which natural variation in the susceptibility of P. radiata is under genetic control and is thus amenable to genetic improvement. Bark stripping was assessed at ages four and five years in two sister trials comprising 101 and 138 open-pollinated half-sib families. A third younger trial comprising 74 full-sib control-pollinated families was assessed at two and three years after planting. Significant additive genetic variation in bark stripping was demonstrated in all trials, with narrow-sense heritability estimates between 0.06 and 0.14. Within sites, the amount of additive genetic variation detected increased with the level of bark stripping. When strongly expressed across the two sister trials, the genetic signal was stable (i.e., there was little genotype × environment interaction). No significant non-additive effect (specific combining ability effect) on bark stripping was detected in the full-sib family trial, where it was estimated that up to 22.1% reduction in bark stripping might be achieved by selecting 20% of the less susceptible families. Physical traits that were genetically correlated, and likely influenced the amount of bark removed from the trees by the marsupials, appeared to depend upon tree age. In the older trials, these traits included bark features (presence of rough bark, rough bark height, and bark thickness), whereas in the younger trial where rough bark was not developed, it was the presence of obstructive branches or needles on the stem. In the younger trial, a positive genetic correlation between prior height and bark stripping was detected, suggesting that initially faster growing trees exhibit more bark stripping than slower growing trees but later develop rough bark faster and became less susceptible. While the presence of unexplained genetic variation after accounting for these physical factors suggests that other explanatory plant traits may be involved, such as chemical traits, overall the results indicate that selection for reduced susceptibility is possible, with potential genetic gains for deployment and breeding.
Publisher: Frontiers Media SA
Date: 07-01-2021
Abstract: Phenotyping in idual trees to quantify interactions among genotype, environment, and management practices is critical to the development of precision forestry and to maximize the opportunity of improved tree breeds. In this study we utilized airborne laser scanning (ALS) data to detect and characterize in idual trees in order to generate tree-level phenotypes and tree-to-tree competition metrics. To examine our ability to account for environmental variation and its relative importance on in idual-tree traits, we investigated the use of spatial models using ALS-derived competition metrics and conventional autoregressive spatial techniques. Models utilizing competition covariate terms were found to quantify previously unexplained phenotypic variation compared with standard models, substantially reducing residual variance and improving estimates of heritabilities for a set of operationally relevant traits. Models including terms for spatial autocorrelation and competition performed the best and were labelled ACE (autocorrelation-competition-error) models. The best ACE models provided statistically significant reductions in residuals ranging from −65.48% for tree height ( H ) to −21.03% for wood stiffness ( A ), and improvements in narrow sense heritabilities from 38.64% for H to 14.01% for A . In idual tree phenotyping using an ACE approach is therefore recommended for analyses of research trials where traits are susceptible to spatial effects.
Publisher: Springer Science and Business Media LLC
Date: 2003
Publisher: Scion
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 21-10-2016
Publisher: Springer Science and Business Media LLC
Date: 17-07-2008
Publisher: Canadian Science Publishing
Date: 08-2010
DOI: 10.1139/X10-095
Abstract: Detailed radial measurements of wood properties, taken at breast height, were obtained from control pollinated seedlings and a selection of 13 year old radiata pine ( Pinus radiata D. Don) clones. Using these data the key objectives of this study were to determine (i) the magnitude of mean clonal variation in modulus of elasticity (MOE) and properties affecting MOE (density and microfibril angle (MFA)) and (ii) whether there is a significant age × clone interaction for these traits. All wood properties were significantly affected by the main and interactive effects of age and clone. There was a relatively linear increase in both MOE and density with tree age, while MFA declined linearly with tree age. Values of density and MOE erged between the clonal extremes from age 3 to age 12. After erging markedly up to age 6, differences in MFA between clonal extremes remained relatively constant to age 12. At age 12, values for density, MFA, and MOE varied between clonal extremes by, respectively, 194 kg·m –3 (465–659 kg·m –3 ), 11.3° (9.6–20.9°), and 11.2 GPa (10.4–21.6 GPa). The seedling material had a relatively intermediate ranking, across the age range, for all traits considered.
Publisher: Cambridge University Press (CUP)
Date: 2023
DOI: 10.1017/PASA.2023.28
Abstract: We investigate the ersity in the sizes and average surface densities of the neutral atomic hydrogen (H i ) gas discs in $\\sim$ 280 nearby galaxies detected by the Widefield ASKAP L-band Legacy All-sky Blind Survey (WALLABY). We combine the uniformly observed, interferometric H i data from pilot observations of the Hydra cluster and NGC 4636 group fields with photometry measured from ultraviolet, optical, and near-infrared imaging surveys to investigate the interplay between stellar structure, star formation, and H i structural parameters. We quantify the H i structure by the size of the H i relative to the optical disc and the average H i surface density measured using effective and isodensity radii. For galaxies resolved by $ $ $1.3$ beams, we find that galaxies with higher stellar masses and stellar surface densities tend to have less extended H i discs and lower H i surface densities: the isodensity H i structural parameters show a weak negative dependence on stellar mass and stellar mass surface density. These trends strengthen when we limit our s le to galaxies resolved by $ $ 2 beams. We find that galaxies with higher H i surface densities and more extended H i discs tend to be more star forming: the isodensity H i structural parameters have stronger correlations with star formation. Normalising the H i disc size by the optical effective radius (instead of the isophotal radius) produces positive correlations with stellar masses and stellar surface densities and removes the correlations with star formation. This is due to the effective and isodensity H i radii increasing with mass at similar rates while, in the optical, the effective radius increases slower than the isophotal radius. Our results are in qualitative agreement with previous studies and demonstrate that with WALLABY we can begin to bridge the gap between small galaxy s les with high spatial resolution H i data and large, statistical studies using spatially unresolved, single-dish data.
Publisher: Public Library of Science (PLoS)
Date: 22-09-2017
Publisher: Wiley
Date: 03-03-2021
DOI: 10.1111/COBI.13671
Abstract: Decades of research and policy interventions on bio ersity have insufficiently addressed the dual issues of bio ersity degradation and social justice. New approaches are therefore needed. We devised a research and action agenda that calls for a collective task of revisiting bio ersity toward the goal of sustaining erse and just futures for life on Earth. Revisiting bio ersity involves critically reflecting on past and present research, policy, and practice concerning bio ersity to inspire creative thinking about the future. The agenda was developed through a 2‐year dialogue process that involved close to 300 experts from erse disciplines and locations. This process was informed by social science insights that show bio ersity research and action is underpinned by choices about how problems are conceptualized. Recognizing knowledge, action, and ethics as inseparable, we synthesized a set of principles that help navigate the task of revisiting bio ersity. The agenda articulates 4 thematic areas for future research. First, researchers need to revisit bio ersity narratives by challenging conceptualizations that exclude ersity and entrench the separation of humans, cultures, economies, and societies from nature. Second, researchers should focus on the relationships between the Anthropocene, bio ersity, and culture by considering humanity and bio ersity as tied together in specific contexts. Third, researchers should focus on nature and economies by better accounting for the interacting structures of economic and financial systems as core drivers of bio ersity loss. Finally, researchers should enable transformative bio ersity research and action by reconfiguring relationships between human and nonhuman communities in and through science, policy, and practice. Revisiting bio ersity necessitates a renewed focus on dialogue among bio ersity communities and beyond that critically reflects on the past to channel research and action toward fostering just and erse futures for human and nonhuman life on Earth.
Publisher: Public Library of Science (PLoS)
Date: 30-09-2019
Publisher: Scion
Date: 18-11-2014
Publisher: Elsevier BV
Date: 08-2019
Publisher: Springer Science and Business Media LLC
Date: 09-05-2017
Publisher: Oxford University Press (OUP)
Date: 05-07-2021
Abstract: We present sofia 2, the fully automated 3D source finding pipeline for the WALLABY extragalactic H i survey with the Australian SKA Pathfinder (ASKAP). sofia 2 is a reimplementation of parts of the original sofia pipeline in the c programming language and makes use of OpenMP for multithreading of the most time-critical algorithms. In addition, we have developed a parallel framework called sofia-X that allows the processing of large data cubes to be split across multiple computing nodes. As a result of these efforts, sofia 2 is substantially faster and comes with a much reduced memory footprint compared to its predecessor, thus allowing the large WALLABY data volumes of hundreds of gigabytes of imaging data per epoch to be processed in real time. The source code has been made publicly available to the entire community under an open-source licence. Performance tests using mock galaxies injected into genuine ASKAP data suggest that in the absence of significant imaging artefacts sofia 2 is capable of achieving near-100 per cent completeness and reliability above an integrated signal-to-noise ratio (SNR) of about 5–6. We also demonstrate that sofia 2 generally recovers the location, integrated flux, and w20 line width of galaxies with high accuracy. Other parameters, including the peak flux density and w50 line width, are more strongly biased due to the influence of the noise on the measurement. In addition, very faint galaxies below an integrated SNR of about 10 may get broken up into multiple components, thus requiring a strategy to identify fragmented sources and ensure that they do not affect the integrity of any scientific analysis based on the sofia 2 output.
Publisher: Canadian Science Publishing
Date: 2004
DOI: 10.1139/X03-181
Abstract: Computer simulation is the only realistic method of evaluating alternative methods of breeding hybrid forest trees. Empirical tests would be very long term and expensive. This paper describes the development of a simulation program, called XSIM, which generates two different but closely related outcrossing tree species. The genetic correlation between performance in each parental species and performance in the resulting hybrid can be set, in addition to the amounts and types of variances in each parental species. The breeding strategies available for testing include conventional reciprocal recurrent selection, reciprocal recurrent selection with forward selection, recurrent selection within each pure species, and the creation of a synthetic species. XSIM allows the strategies to be compared using the same base populations, equivalent selection intensities, and comparable mating patterns. Innovative best linear unbiased prediction procedures allow all ancestral and current progeny generation data, from both parental species and the hybrid, to be analysed together. The theoretical basis for the simulation is given, and genetic and statistical models are described. In summary, XSIM allows rigorous comparisons of the strategies in terms of genetic gain per time and provides useful insight into hybrid forest tree breeding.
Publisher: Oxford University Press (OUP)
Date: 28-02-2023
Abstract: Galaxy morphology in atomic hydrogen (H i) and in the ultraviolet (UV) are closely linked. This has motivated their combined use to quantify morphology over the full H i disc for both H i and UV imaging. We apply galaxy morphometrics: concentration, asymmetry, gini, M20 and multimode-intensity-deviation statistics to the first moment-0 maps of the WALLABY Survey of galaxies in the hydra cluster centre. Taking advantage of this new H i survey, we apply the same morphometrics over the full H i extent on archival GALEX FUV and NUV data to explore how well H i truncated, extended ultraviolet disc (XUV) and other morphological phenomena can be captured using pipeline WALLABY data products. Extended H i and UV discs can be identified relatively straightforward from their respective concentration. Combined with WALLABY H i, even the shallowest GALEX data are sufficient to identify XUV discs. Our second goal is to isolate galaxies undergoing ram-pressure stripping in the H i morphometric space. We employ four different machine learning techniques, a decision tree, a k-nearest neighbour, a support-vector machine, and a random forest. Up to 80 per cent precision and recall are possible with the random forest giving the most robust results.
Publisher: MDPI AG
Date: 12-07-2021
DOI: 10.3390/F12070904
Abstract: The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining an optimal mating design that maintains a large effective population size. We utilised “genotyping-by-sequencing” (GBS) in combination with bioinformatics tools developed specifically for GBS data to recover genetic relatedness, with a focus on parent-offspring relationships in a Eucalyptus nitens breeding population as well as recognition of in iduals representing other Eucalyptus species and putative hybrids. We found a clear advantage on using tools specifically designed for data of highly variable sequencing quality when recovering genetic relatedness. The parent-offspring relatedness showed a significant response to data filtering from 0.05 to 0.3 when the standard approach (G1) was used, while it oscillated around 0.4 when the specifically designed method (G5) was implemented. Additionally, comparisons with commonly used tools demonstrated vulnerability of the relatedness estimates to incorrect imputation of missing data when shallow sequencing information and genetically distant in iduals are present in the population. In turn, these biased imputed genotypes negatively affected the estimation of genetic relatedness between parents and offspring. Careful filtering for both genetic outliers and shallowly sequenced markers led to improvements in estimations of genetic relatedness. Alternatively, a method that avoided missing data imputation and took sequence depth into consideration improved the accuracy of parent-offspring relationship coefficients where sequencing data quality was highly variable.
Publisher: Elsevier BV
Date: 06-2009
Publisher: Springer Science and Business Media LLC
Date: 24-10-2019
DOI: 10.1186/S12863-019-0778-0
Abstract: Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance rogeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree. The use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased. Consideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation.
Publisher: Springer Science and Business Media LLC
Date: 11-05-2020
DOI: 10.1186/S12870-020-02403-6
Abstract: Many conifer breeding programs are paying increasing attention to breeding for resistance to needle disease due to the increasing importance of climate change. Phenotyping of traits related to resistance has many biological and temporal constraints that can often confound the ability to achieve reliable phenotypes and consequently, reliable genetic progress. The development of next generation sequencing platforms has also enabled implementation of genomic approaches in species lacking robust reference genomes. Genomic selection is, therefore, a promising strategy to overcome the constraints of needle disease phenotyping. We found high accuracy in the prediction of genomic breeding values in the disease-related traits that were well characterized, reaching 0.975 for genotyped in iduals and 0.587 for non-genotyped in iduals. This compared well with pedigree-based accuracies of up to 0.746. Surprisingly, poorly phenotyped disease traits also showed very high accuracy in terms of correlation of predicted genomic breeding values with pedigree-based counterparts. However, this was likely caused by the fact that both were clustered around the population mean, while deviations from the population mean caused by genetic effects did not appear to be well described. Caution should therefore be taken with the interpretation of results in poorly phenotyped traits. Implementation of genomic selection in this test population of Pinus radiata resulted in a relatively high prediction accuracy of needle loss due to Dothistroma septosporum compared with a pedigree-based approach. Using genomics to avoid biological/temporal constraints where phenotyping is reliable appears promising. Unsurprisingly, reliable phenotyping, resulting in good heritability estimates, is a fundamental requirement for the development of a reliable prediction model. Furthermore, our results are also specific to the single pathogen mating-type that is present in New Zealand, and may change with future incursion of other pathogen varieties. There is no doubt, however, that once a robust genomic prediction model is built, it will be invaluable to not only select for host tolerance, but for other economically important traits simultaneously. This tool will thus future-proof our forests by mitigating the risk of disease outbreaks induced by future changes in climate.
Publisher: Scion
Date: 02-07-2014
Publisher: Canadian Science Publishing
Date: 12-2019
Abstract: Despite recent developments in molecular markers, most forest tree breeding programmes do not use them routinely. One way to integrate markers would be to use them for pedigree reconstruction after a simplified mating design through polymix or open-pollinated breeding. Thanks to the latest developments in the POPSIM simulator, various breeding strategies, including some based on paternity recovery, were evaluated with specified constraints on the level of ersity over breeding cycles. These simulations were carried out in two case studies: the French Pinus pinaster (Ait.) and the New Zealand Eucalyptus nitens (H. Dean & Maiden) Maiden breeding programmes. The Pinus pinaster case study produced lower genetic gain for the polymix breeding strategy with paternity recovery compared with double-pair mating or optimal-contribution strategies. However, the polymix breeding strategy could be of interest if the mating design is faster to complete. In the Eucalyptus nitens case study, pedigree recovery was shown to be a mandatory step to controlling the erosion of ersity over breeding cycles. In both cases, the strategies based on pedigree reconstruction were applicable with a limited level of genotyping. Finally, these simulations allow some general recommendations to be drawn to help breeders when designing a strategy for forest tree breeding.
Publisher: Public Library of Science (PLoS)
Date: 10-12-2018
Publisher: Scion
Date: 12-04-2016
Publisher: Wiley
Date: 02-2003
Publisher: Frontiers Media SA
Date: 06-03-2020
Publisher: Springer Science and Business Media LLC
Date: 25-10-2012
Publisher: Cambridge University Press (CUP)
Date: 2022
DOI: 10.1017/PASA.2022.50
Abstract: We present WALLABY pilot data release 1, the first public release of H i pilot survey data from the Wide-field ASKAP L-band Legacy All-sky Blind Survey (WALLABY) on the Australian Square Kilometre Array Pathfinder. Phase 1 of the WALLABY pilot survey targeted three $60\\,\\mathrm{deg}^{2}$ regions on the sky in the direction of the Hydra and Norma galaxy clusters and the NGC 4636 galaxy group, covering the redshift range of $z \\lesssim 0.08$ . The source catalogue, images and spectra of nearly 600 extragalactic H i detections and kinematic models for 109 spatially resolved galaxies are available. As the pilot survey targeted regions containing nearby group and cluster environments, the median redshift of the s le of $z \\approx 0.014$ is relatively low compared to the full WALLABY survey. The median galaxy H i mass is $2.3 \\times 10^{9}\\,{\\rm M}_{{\\odot}}$ . The target noise level of $1.6\\,\\mathrm{mJy}$ per 30 ′′ beam and $18.5\\,\\mathrm{kHz}$ channel translates into a $5 \\sigma$ H i mass sensitivity for point sources of about $5.2 \\times 10^{8} \\, (D_{\\rm L} / \\mathrm{100\\,Mpc})^{2} \\, {\\rm M}_{{\\odot}}$ across 50 spectral channels ( ${\\approx} 200\\,\\mathrm{km \\, s}^{-1}$ ) and a $5 \\sigma$ H i column density sensitivity of about $8.6 \\times 10^{19} \\, (1 + z)^{4}\\,\\mathrm{cm}^{-2}$ across 5 channels ( ${\\approx} 20\\,\\mathrm{km \\, s}^{-1}$ ) for emission filling the 30 ′′ beam. As expected for a pilot survey, several technical issues and artefacts are still affecting the data quality. Most notably, there are systematic flux errors of up to several 10% caused by uncertainties about the exact size and shape of each of the primary beams as well as the presence of sidelobes due to the finite deconvolution threshold. In addition, artefacts such as residual continuum emission and bandpass ripples have affected some of the data. The pilot survey has been highly successful in uncovering such technical problems, most of which are expected to be addressed and rectified before the start of the full WALLABY survey.
Publisher: Public Library of Science (PLoS)
Date: 12-10-2018
Publisher: Springer Science and Business Media LLC
Date: 2003
Publisher: Oxford University Press (OUP)
Date: 10-04-2017
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S12864-019-6420-8
Abstract: Non-key traits (NKTs) in radiata pine ( Pinus radiata D. Don) refer to traits other than growth, wood density and stiffness, but still of interest to breeders. Branch-cluster frequency, stem straightness, external resin bleeding and internal checking are ex les of such traits and are targeted for improvement in radiata pine research programmes. Genomic selection can be conducted before the performance of selection candidates is available so that generation intervals can be reduced. Radiata pine is a species with a long generation interval, which if reduced could significantly increase genetic gain per unit of time. The aim of this study was to evaluate the accuracy and predictive ability of genomic selection and its efficiency over traditional forward selection in radiata pine for the following NKTs: branch-cluster frequency, stem straightness, internal checking, and external resin bleeding. Nine hundred and eighty-eight in iduals were genotyped using exome capture genotyping by sequencing (GBS) and 67,168 single nucleotide polymorphisms (SNPs) used to develop genomic estimated breeding values (GEBVs) with genomic best linear unbiased prediction (GBLUP). The documented pedigree was corrected using a subset of 704 SNPs. The percentage of trio parentage confirmed was about 49% and about 50% of parents were re-assigned. The accuracy of GEBVs was 0.55–0.75 when using the documented pedigree and 0.61–0.80 when using the SNP-corrected pedigree. A higher percentage of additive genetic variance was explained and a higher predictive ability was observed when using the SNP-corrected pedigree than using the documented pedigree. With the documented pedigree, genomic selection was similar to traditional forward selection when assuming a generation interval of 17 years, but worse than traditional forward selection when assuming a generation interval of 14 years. After the pedigree was corrected, genomic selection led to 37–115% and 13–77% additional genetic gain over traditional forward selection when generation intervals of 17 years and 14 years were assumed, respectively. It was concluded that genomic selection with a pedigree corrected by SNP information was an efficient way of improving non-key traits in radiata pine breeding.
Publisher: Oxford University Press (OUP)
Date: 05-01-2019
DOI: 10.1093/MNRAS/STZ017
Abstract: We report on neutral hydrogen (H i) observations of the NGC 7232 group with the Australian Square Kilometre Array Pathfinder (ASKAP). These observations were conducted as part of the Wide-field ASKAP L-Band Legacy All-sky Blind surveY (WALLABY) Early Science program with an array of 12 ASKAP antennas equipped with Phased Array Feeds, which were used to form 36 beams to map a field of view of 30 deg2. Analysing a subregion of the central beams, we detect 17 H i sources. Eleven of these detections are identified as galaxies and have stellar counterparts, of which five are newly resolved H i galaxy sources. The other six detections appear to be tidal debris in the form of H i clouds that are associated with the central triplet, NGC 7232/3, comprising the spiral galaxies NGC 7232, NGC 7232B, and NGC 7233. One of these H i clouds has a mass of MH i ∼ 3 × 108 M⊙ and could be the progenitor of a long-lived tidal dwarf galaxy. The remaining H i clouds are likely transient tidal knots that are possibly part of a diffuse tidal bridge between NGC 7232/3 and another group member, the lenticular galaxy IC 5181.
Publisher: Canadian Science Publishing
Date: 05-2006
DOI: 10.1139/X06-014
Abstract: The potential for breeding Pinus radiata D. Don to improve wood stiffness (modulus of elasticity, MoE) was examined by obtaining pith-to-bark cores from trees at breast height in two independent genetic trials. The effectiveness of early selection for stiffness and indirect selection on the component traits, microfibril angle (MfA) and wood density, was determined as well as the age-related changes in the genetic variation of these traits. The first trial comprised 50 open-pollinated families in the central North Island, New Zealand. The second trial comprised 20 control-pollinated families in New South Wales, Australia. The genetic control of MfA, density, and MoE was found to be high in the corewood and moderate in the outerwood. Estimated genetic correlations suggested that early selection for most traits would be successful but could be carried out slightly earlier at the New Zealand site than at the Australian site. To maximize gain in the corewood, selection for MoE and MfA would be most effective around rings 4-8. There were no adverse correlations between MoE and MfA or density, implying that selection for MoE would also improve MfA and density.
Publisher: Frontiers Media SA
Date: 30-10-2020
Start Date: 2012
End Date: 2014
Funder: Ministry of Primary Industries
View Funded ActivityStart Date: 2014
End Date: 2017
Funder: Australian Research Council
View Funded ActivityStart Date: 2012
End Date: 2013
Funder: Ministry of Agriculture, Forestry
View Funded Activity