Papers by Matthew Hamilton
Aquaculture International
In 2017, the base population of a family-based silver carp (Hypophthalmichthys molitrix) genetic ... more In 2017, the base population of a family-based silver carp (Hypophthalmichthys molitrix) genetic improvement program was spawned in Bangladesh. This program aims to improve the growth rate of silver carp under polyculture production systems, through direct selection on the primary trait of harvest-age weight. The objective of this study was to quantify genetic variation in, and genetic correlations between, harvest-age weight (assessed on 8012 fish from 184 families) and a set of secondary traits (assessed on 1603 fish from 175 families). Secondary traits examined included feeding and digestive system traits (i.e. gill raker sponginess and gut length as a ratio of standard length), a morphometric trait (i.e. extent of overlap of pectoral and pelvic fins) and health traits (i.e. presence of Lernaea and prevalence of red spots — sites of inflammation/haemorrhaging). Despite not being under direct selection, genetic change in secondary traits is possible across generations in closed ge...
Journal of Heredity, 2020
Optimal contributions approaches to parental selection in closed breeding populations aim to maxi... more Optimal contributions approaches to parental selection in closed breeding populations aim to maximize genetic gains, while restraining long-term inbreeding. The adoption of optimal contribution selection (OCS) in highly fecund outcrossing species presents a number of challenges not applicable to species of low fecundity (e.g., livestock) for which they were developed. This is particularly true if overlapping-generations or rolling-front breeding strategies are applied, in which case the number of individuals per family in juvenile (i.e., sexually immature) age groups is not necessarily known but is likely to be large. In these circumstances, conventional OCS procedures must be modified or a large number of dummy individuals defined, making computations onerous. Here, an approach to OCS is presented that involves the use of “between-family relationship matrices” instead of “between-individual relationship matrices.” The method is applicable to breeding programs involving highly fecun...
Annals of Forest Science, 2020
& Key message Radial variation of wood properties affects product recovery from veneer logs. In E... more & Key message Radial variation of wood properties affects product recovery from veneer logs. In Eucalyptus nitens, the radial variation in wood density, microfibril angle and modulus of elasticity was described using non-linear models. The timing of radial change was trait-dependent, and the age at which thresholds for structural products were reached differed between sites. & Context Eucalyptus nitens is widely planted in cool temperate regions of the world. While mainly grown for pulpwood, rotarypeeled veneer is becoming important. Threshold levels of wood stiffness are required for using this veneer for structural purposes. Stiffness is determined by wood density and microfibril angle, which improve with tree age. The nature of this radial variation affects the recovery of suitable veneer and profitability of the plantation resource. & Aims We model the radial variation of these veneer-critical wood properties and determine whether it varies with growing conditions. & Methods We used logs from three 20-22-year-old Tasmanian plantations. Radial variations in wood density, microfibril angle and modulus of elasticity (measuring stiffness) were assessed using SilviScan. Eight linear and non-linear models were examined using cambial age as the independent variable. & Results The increases in wood density and modulus of elasticity with age were modelled by sigmoidal functions and the decrease in microfibril angle modelled by an asymptotic function. The timing of radial change was trait-dependent, and the mean ages at which thresholds for structural products were reached between sites. & Conclusion Radial variation varied among sites and will likely impact the recovery of structural grade veneer from plantations.
Aquaculture, 2021
Silver carp (Hypophthalmichthys molitrix) is an important aquaculture species in Bangladesh and g... more Silver carp (Hypophthalmichthys molitrix) is an important aquaculture species in Bangladesh and globally. Multiple introductions have been made of this exotic species to Bangladesh since 1969. Accordingly, the genetic composition of the species in the country is complex and imperfectly understood. In 2015-16, WorldFish sourced silver carp individuals from 21 Bangladeshi hatcheries as 'candidate founders' of a family-based genetic improvement program. In total, 544 candidate founders were sampled, of which 220 from 17 hatcheries were ultimately spawned as the 'actual founders' of the WorldFish Silver Carp Genetic Improvement Program (WSCGIP) population. The extent of relatedness among candidate founders was unknown when they were sourced from hatcheries. Candidate founders were genotyped using the DArTseq platformwith a total of 15,102 single nucleotide polymorphisms (SNPs) and 13,504 silicoDArT markers obtainedand genetic affinities among hatcheries examined. Based on unsupervised k-means clustering and hatchery-identified origins, each hatchery was assigned to one of six genetic groups to enable the adoption of genetic group models in pedigree-based analyses. Within genetic groups, sibship was assigned using COLONY software, and a pedigree constructed and validated against genomic relationships generated from 2007 SNPs retained after quality control. The mean pedigree-derived additive genetic relationship between actual founders was small (0.0093), indicating that relationships between actual founders are unlikely to have a meaningful impact on future parent selection, mating decisions or rates of inbreeding.
Genetics Selection Evolution, 2019
Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in ... more Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in Bangladesh from which approximately 900 individuals were retained as 'candidate founders' of a breeding population. These fish were fin-clipped and genotyped using the DArTseq platform to obtain, 3048 single nucleotide polymorphisms (SNPs) and 4726 silicoDArT markers. Using SNP data, individuals that shared no putative parents were identified using the program COLONY, i.e. 140, 47 and 23 from the Halda, Jamuna and Padma rivers, respectively. Allele frequencies from these individuals were considered as representative of those of the river populations, and genomic relationship matrices were generated. Then, half-sibling and full-sibling relationships between individuals were assigned manually based on the genomic relationship matrices. Many putative half-sibling and full-sibling relationships were found between individuals from the Halda and Jamuna rivers, which suggests that catla sampled from rivers as spawn are not necessarily representative of river populations. This has implications for the interpretation of past population genetics studies, the sampling strategies to be adopted in future studies and the management of broodstock sourced as river spawn in commercial hatcheries. Using data from individuals that shared no putative parents, overall multi-locus pairwise estimates of Wright's fixation index (F ST) were low (≤ 0.013) and the optimum number of clusters using unsupervised K-means clustering was equal to 1, which indicates little genetic divergence among the SNPs included in our study within and among river populations.
Frontiers in Genetics, 2019
Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt pro... more Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full-and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise F ST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.
The New phytologist, Jan 22, 2018
The extent to which spatial structuring of host resistance in wild plant populations reflects dir... more The extent to which spatial structuring of host resistance in wild plant populations reflects direct pathogen imposed selection is a subject of debate. To examine this issue, genetic susceptibility to an exotic and co-evolved native fungal pathogen were compared using two Australian host tree species. Damage to common host germplasm of Corymbia citriodora subsp. variegata (CCV) and Eucalyptus globulus, caused by recently introduced (Austropuccinia psidii) and native (Quambalaria pitereka and Teratosphaeria sp.) pathogens was evaluated in common-garden experiments. There was significant additive genetic variation within host species for susceptibility to both the exotic and native pathogens. However, susceptibility to A. psidii was not genetically correlated with susceptibility to either native pathogen, providing support for pathogen specific rather than general mechanisms of resistance. Population differentiation (Q ) for susceptibility to the native pathogens was greater than neut...
Annals of Forest Science, 2017
& Key message Multiple lines of evidence suggest acoustic wave velocity (AWV) would provide a rap... more & Key message Multiple lines of evidence suggest acoustic wave velocity (AWV) would provide a rapid and efficient method to indirectly select for superior pulp yield in Eucalyptus globulus breeding programs. & Context Eucalyptus globulus is one of the most widely planted hardwood species in temperate regions of the world and is primarily grown for pulpwood. & Aims To determine if acoustic wave velocity (AWV) can be used to indirectly select for kraft pulp yield in E. globulus. & Methods Genetic group effects, additive and non-additive variance components, and genetic correlations were estimated for AWV and pulpwood traits, including Kraft pulp yield. In a separate trial, the relative position of quantitative trait loci (QTL) for these traits was compared. & Results Estimated narrow-sense heritabilities for AWV and pulp yield were both 0.26, and these traits were strongly genetically correlated (0.84). Furthermore, co-located QTL for these traits were identified. Further evidence that AWV could be used to indirectly select for pulp yield was provided by the ranking of genetic groups-Otways and King Island had the highest AWV and pulp yield and Strzelecki and Tasmania the lowest. There was no evidence of dominance variation in wood property traits. & Conclusion Together, these findings suggest that AWV could be used as a selection criterion for kraft pulp yield in E. globulus breeding programs.
Annals of Forest Science, 2015
& Key message Log-end splitting is one of the single most important defects in veneer logs. We sh... more & Key message Log-end splitting is one of the single most important defects in veneer logs. We show that log-end splitting in the temperate plantation species Eucalyptus nitens varies across sites and within-tree log position and increases with time in storage. & Context Log-end splitting is one of the single most important defects in veneer logs because it can substantially reduce the recovery of veneer sheets. Eucalyptus nitens can develop log-end splits, but factors affecting log-end splitting in this species are not well understood.
Annals of Forest Science, 2014
& Key message High levels of percentage green veneer recovery can be obtained from temperate euca... more & Key message High levels of percentage green veneer recovery can be obtained from temperate eucalypt plantations. Recovery traits are affected by site and log position in the stem. Of the post-felling log traits studied, outof-roundness was the best predictor of green recovery. & Context Eucalyptus globulus and Eucalyptus nitens are widely planted in temperate regions of the globe but few studies of rotary peeling have been documented. & Aims This study aims to examine differences among sites and log positions in post-felling log traits and green veneer recovery traits and determine the extent to which log traits explain variation in recovery traits. & Methods Log traits and green rotary-peeled veneer recovery traits from six temperate eucalypt plantations were studied. Selected plantations encompassed different age, site productivity, silvicultural and species classes in southeastern Australia. Differences in log and recovery traits among sites and between lower and upper logs were examined, as was the extent to which log traits explained variation in recovery traits. & Results Differences among sites for percentage recovered green veneer were non-significant, despite significant differences for peelable billet volume, roundup loss, residual core diameter and all post-felling log traits: small end diameter, sweep, taper, out-of-roundness, end splitting and dynamic modulus of elasticity (MOE dyn). The lower log exhibited more sweep, taper and out-of-roundness but lower MOE dyn and less recovered green veneer. Out-of-roundness was the best predictor of recovery traits (R 2 =13-21 %, P<0.001). & Conclusion Recovered green veneer was high across all sites and log positions (78 % overall).
Canadian Journal of Forest Research, 2015
The cost of harvesting short-rotation plantation eucalypts can be in excess of AU$2500·ha−1. Desp... more The cost of harvesting short-rotation plantation eucalypts can be in excess of AU$2500·ha−1. Despite this high cost, the extent to which harvesting productivity is affected by tree genetics is not well understood. We address this issue in a study of two 10-year-old genetic field trials of Eucalyptus globulus Labill. in Australia. Standing-tree traits analysed were survival, diameter at breast height, basal area, and stem straightness and forking. Harvest traits analysed were volume, time, and productivity. Genetic group and within-group genetic variation (additive and dominance), stand-level family variation, phenotypic and genetic correlations, and the effects of inbreeding were estimated for these traits. The different scenarios studied showed that plantation harvest productivity was affected by tree genetics to some degree but was mainly affected through positive covariation with stem diameter. Harvest productivity is thus unlikely to have been adversely affected by past selectio...
Forests, 2014
Previous studies in Eucalyptus nitens have revealed favourable genetic correlations exist between... more Previous studies in Eucalyptus nitens have revealed favourable genetic correlations exist between acoustic wave velocity (AWV) in standing trees and modulus of elasticity (MOE), which can determine the suitability of trees for structural timber and/or engineered wood products. This study investigates the strength and stability of genetic variation in standing tree AWV across a range of environments in Tasmania, where there are a number of large plantation estates and breeding trials. Trees under study were from open-pollinated progeny trials established in 1993. Across sites, for standing tree AWV the ranking of E. nitens races did not change and within-race additive genetic correlations were strong (0.61 to 0.99). Heritabilities (0.16 to 0.74) and coefficients of additive genetic variation (2.6 to 4.8) were moderate for this trait. Correlations between standing tree AWV and both basic density and diameter at breast height (DBH) were favourable. Results indicate that there is potential to improve MOE in E. nitens through the exploitation of genetic variation in AWV among and within races, the expression of genetic variation in AWV is relatively stable across different growing environments, and past selection for basic density and growth in pulpwood breeding programs is unlikely to have adversely affected MOE.
Annals of Forest Science, 2010
• If selective breeding is to be successful, significant genetic variation must be present in the... more • If selective breeding is to be successful, significant genetic variation must be present in the traits targeted for improvement (i.e. "objective traits"). • This study aimed to quantify genetic variation in Eucalyptus globulus pulpwood and sawn-timber objective traits (rotation-age whole-tree volume, survival, whole-tree basic density, sawn-board Janka hardness and sawn-board internal checking) and estimate additive genetic correlations between these and inexpensively-assessed "selection traits". • Significant genetic variation was identified in all objective traits at the subrace and/or family within subrace level. • Selection-age diameter at breast height (1.3 m, DBH) was strongly genetically correlated with rotation-age volume (0.78) and survival (0.82). Subrace and additive genetic correlations of selectionage Pilodyn penetration with rotation-age 12-×-12-mm-sample basic density (-0.70 and-0.75 respectively) and whole-tree basic density (-0.83 and-0.91 respectively) were also strong. • No significant subrace or additive genetic correlation between wood-sample gross shrinkage and sawn-board internal checking was detected. However, subrace and additive genetic correlations of sawn-board Janka hardness with Pilodyn penetration (-0.75 and-0.58 respectively) and sample gross shrinkage (-0.77 and-0.73 respectively) were significantly different from zero. • These findings suggest that genetic improvement of the examined objective traits is possible through selective breeding, although none of the assessed selection traits were strongly correlated with internal checking.
Eucalypts are amongst the most planted hardwoods in the world (Doughty 2000). They are native to ... more Eucalypts are amongst the most planted hardwoods in the world (Doughty 2000). They are native to Australia and islands to its north (Ladiges et al. 2003) where they occupy diverse ecological habitats ranging from sea level to the alpine tree line, from high rainfall to semi-...
New Zealand Journal of Forestry Science
Eucalyptus nitens is a significant plantation species in temperate regions of the world, with bre... more Eucalyptus nitens is a significant plantation species in temperate regions of the world, with breeding occurring in Australia, Chile, South Africa and New Zealand. We reviewed published genetic parameters from over 100 field trials and calculated average values for key growth, wood property, tree architecture and fitness traits. Average heritabilities for growth traits (e.g. 2 op h =0.26 for diameter) were generally lower than those for wood property traits (e.g. 2 op h =0.51 for basic density). However, this trend was reversed in average additive genetic coefficients of variation (e.g. CV a =13.3% for diameter and 4.5% for basic density). Inter-age genetic correlations for stem diameter ranged from 0.68 to 1.00 but were not available for important wood property traits (e.g. basic density, cellulose content and pulp yield). The few inter-site genetic correlations reported were on average positive and strong (e.g. g r =0.70 for diameter). The average genetic correlation between diame...
Near-infrared calibrations for wood density and modulus of elasticity for Eucalyptus nitens from Tasmania (Australia)
Eucalyptus nitens is widely planted in temperate regions of the world and the second most planted... more Eucalyptus nitens is widely planted in temperate regions of the world and the second most planted eucalypt in Australia. There are 208,000 ha planted on the island of Tasmania, mainly for pulpwood, but 10% of the estate has been thinned and pruned for timber and veneer production. However, these plantations are yet to be harvested commercially for these products, and a better understanding of their wood characteristics is required. Wood density and modulus of elasticity (MOE) are key traits that affect the value of E. nitens timber and veneer products. Large-scale assessment of the plantation resource for these traits requires the development of cost-effective sampling techniques for studying within- and between-tree variation. We developed near-infrared (NIR) calibration models for density and MOE based on 1-mm interval scans of the radial face of intact, air-dried wood samples. The reference data for the model development were obtained from SilviScan assessment at the same scale. ...
Tree Genetics & Genomes, 2008
Eucalyptus nitens plantations are generally established for pulpwood production but an increasing... more Eucalyptus nitens plantations are generally established for pulpwood production but an increasing area is being managed for solid wood. Genetic variation in, and correlations among, three Kraft pulpwood traits (diameter at breast height, basic density and near-infrared-predicted cellulose content) and three 12-mm wood-core shrinkage traits (recoverable collapse, net shrinkage and gross shrinkage) were examined, utilising data from two 9-year-old firstgeneration progeny trials in Tasmania. These trials contained approximately 400 open-pollinated families (over 100 of which were sampled for wood properties) representing three central-Victorian E. nitens races. Significant genetic variation at the race and/or within-race level was identified in all traits. Within races, relative levels of additive genetic variation were higher for shrinkage traits, although narrowsense heritabilities were lower and the expression of genetic variation less stable across sites than for other wood property traits. Heterogeneous intertrait genetic correlations were identified across sites between growth and some wood property traits. However, where significant, genetic correlations indicated that within-race selection for growth would adversely affect core basic density and all core shrinkage traits. Furthermore, results based on cores suggested that within-race selection for higher basic density would favourably impact on cellulose content and collapse but selection for either higher basic density or cellulose content would adversely affect net shrinkage. Most within-race genetic variation in gross shrinkage appeared to be due to genetic variation in collapse. The implications of these results for sawn timber breeding will depend on the strength of genetic correlations between core traits and rotation-age objective traits and objective trait economic weights.
Annals of Forest Science, 2011
& Introduction There is increasing interest in managing Eucalyptus nitens plantations for sawn ti... more & Introduction There is increasing interest in managing Eucalyptus nitens plantations for sawn timber production. & Aims This study aimed to determine the potential for genetic improvement of traits affecting green sawn board recovery in plantation-grown E. nitens. & Methods The study was undertaken on an E. nitens progeny trial. All trees were measured for diameter at breast height (DBH) and stem straightness, and 560 trees were selected for timber processing. Assessment was made of survival, log and green sawn board volume, log taper, and both upper and lower log end splitting. Genetic variation in and between these traits was estimated. & Results Genetic differences among races were significant for DBH at years 9 and 14, stem straightness, log taper and green sawn board volume. Within-race, narrow-sense heritabilities were significant for DBH, stem straightness, log volume, and both upper and lower log end splitting. Positive and significant additive genetic correlations were observed between DBH at all ages and survival, stem straightness and log volume. Significant adverse genetic correlations were shown between upper log end splitting and DBH at years 9 and 14. & Conclusion These findings showed that harvest-age stem straightness and log volume objective traits in E. nitens are amenable to genetic improvement and that selection for early-age DBH in breeding programmes should improve harvest-age survival, stem diameter and straightness, as well as log and green sawn board volume. However, these improvements are likely to be countered to some extent by increased end splitting of logs from larger trees.
Annals of Forest Science, 2007
Wood discs were sampled from 6 heights up the stem of 248 trees representing 10 subraces and 116 ... more Wood discs were sampled from 6 heights up the stem of 248 trees representing 10 subraces and 116 families grown in an E. globulus base-population progeny trial. The lower stem had the least favourable wood properties for kraft pulpwood and most solidwood applications: bark was thickest, basic density was lowest and kino, decay and shrinkage traits were greatest at or below 12% of tree height. Significant genetic differences at the subrace level were revealed in diameter, bark thickness, basic density, decay and gross shrinkage and at the family within subrace level in diameter, basic density and decay. However, subrace-by-height-category interactions in bark thickness, basic density, decay and gross shrinkage indicated that differences among subraces were dependent on height in these traits. Examination of longitudinal trends revealed some evidence that the zone of thick basal bark extended further up the stem in thicker-barked subraces and that the Southern Tasmania subrace might be less effective than other subraces in restricting the longitudinal spread of decay after infection. wood properties / Eucalyptus globulus / longitudinal variation / within-tree variation / genetic variation Résumé-Les variations longitudinales intra-arbre des propriétés papetières et du bois varient entre les génotypes d'Eucalyptus globulus. Des disques de bois ont été prélevés à 6 hauteurs différentes dans 248 arbres représentant 10 provenances et 116 familles d'un dispositif de provenancedescendance d'E. globulus. La partie inférieure des troncs présente les propriétés du bois les moins bonnes pour la pâte Kraft et la plupart des utilisations du bois massif : l'écorce est plus épaisse, l'infradensité plus faible tandis que le lino, la dégradation biologique et les retraits sont plus importants jusqu'à 12 % de la hauteur des tiges. Des différences génétiques significatives ont été établies au niveau provenance pour le diamètre, l'épaisseur d'écorce, l'infradensité et la dégradation biologique et au niveau famille dans une provenance pour l'infradensité et la dégradation biologique. Cependant, pour ces propriétés, les interactions provenance par catégorie de hauteur, pour l'épaisseur d'écorce, l'infradensité, la dégradation biologique et le retrait total, indiquent que les différences entre provenances dépendent de la hauteur. L'analyse des variations longitudinales fait apparaître que la longueur de la bille de pied ayant une écorce plus épaisse est plus importante pour les provenances présentant des écorces épaisses et que les provenances de sud de la Tasmanie pourraient être moins efficaces que les autres pour limiter la diffusion des pourritures après infection. propriétés du bois / variation longitudinale / variation intra arbre / variation génétique / Eucalyptus globulus
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Papers by Matthew Hamilton