ORCID Profile
0000-0003-1353-3765
Current Organisation
University of Tasmania
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Publisher: Springer Science and Business Media LLC
Date: 12-11-2022
DOI: 10.1007/S11295-022-01572-9
Abstract: To understand the potential of forests to adapt to wildfire, we studied the genetic architecture of fire-related structural, damage and recovery traits in a globally important Australian forest tree species, Eucalyptus globulus . Fourteen traits were evaluated in an outcrossed F 2 population in a field trial in Tasmania, Australia, which was burnt by a wildfire 14 years after planting. The trial also included open-pollinated families of the grandparental dwarf and tall ecotypes used to produce the F 2 population. We studied the phenotypic correlations within the F 2 population and performed quantitative trait loci (QTL) analyses using a linkage map comprised of 472 markers. Ecotype comparisons revealed that almost all traits were under genetic control, with trees of the dwarf ecotype significantly more damaged and mainly recovering from lignotubers, whereas tall ecotype trees mainly recovered from epicormic resprouts extending for a variable height up the stem. Within the F 2 , tree size was negatively correlated with fire damage and positively correlated with recovery. Genetic control of fire-related traits was confirmed by the detection of 38 QTL in the F 2 population. These QTL accounted for 4 to 43% of the phenotypic variation in these traits. Several QTL co-located and likely reflect pleiotropic effects. However, many independent QTL were detected, including QTL for crown consumption and trunk scorch, epicormic resprouting, resprout herbivory, and seedling establishment. The QTL detected argue that many genetically controlled mechanisms are responsible for variation in fire damage and recovery.
Publisher: Wiley
Date: 25-10-2022
DOI: 10.1002/TPG2.20269
Abstract: Adaptation constraints within crop species have resulted in limited genetic ersity in some breeding programs and areas where new crops have been introduced, for ex le, for lentil ( Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology‐related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic ersity by introducing new, exotic material. We used a large, 18 site‐year, multienvironment dataset phenotyped for phenology‐related traits across nine locations and over 3 yr along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil ersity panel (324 accessions), which has also been genotyped with an exome capture array. Genome‐wide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering‐time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology‐related traits across the major growing environments for cultivated lentil.
Publisher: Cold Spring Harbor Laboratory
Date: 12-03-2022
DOI: 10.1101/2022.03.10.483676
Abstract: Adaptation constraints within crop species have resulted in limited genetic ersity in some breeding programs and/or areas where new crops have been introduced, e.g., lentil (Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology-related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic ersity by introducing new, exotic material. We used a large, 18 site-year, multi-environment dataset, phenotyped for phenology-related traits across nine locations and over three years, along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil ersity panel (324 accessions) which has also been genotyped with an exome capture array. Genomewide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology-related traits across the major growing environments for cultivated lentil.
Publisher: Springer Science and Business Media LLC
Date: 06-2022
DOI: 10.1007/S11295-022-01558-7
Abstract: The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for ex le is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic ersity, population differentiation and linkage disequilibrium (LD) across the highly disjunct native range of the Australian forest tree Eucalyptus globulus , using 203,337 SNPs genotyped in 136 trees spanning seven races. We found support for four broad genetic groups, with moderate F ST , high allelic ersity and genome-wide LD decaying to an r 2 of 0.2 within 4 kb on average. These results are broadly similar to those reported previously in Eucalyptus species and support the ‘ring’ model of migration proposed for E. globulus . However, two of the races (Otways and South-eastern Tasmania) exhibited a much slower decay of LD with physical distance than the others and were also the most differentiated and least erse, which may reflect the effects of selective sweeps and/or genetic bottlenecks experienced in their evolutionary history. We also show that F ST and rates of LD vary within and between chromosomes across all races, suggestive of recombination outcomes influenced by genomic features, hybridization or selection. The results obtained from studying this species serve to illustrate the genomic effects of population disjunction and further contribute to the characterisation of genomes of woody genera.
Publisher: Springer Science and Business Media LLC
Date: 11-04-2016
Publisher: Springer Science and Business Media LLC
Date: 10-05-2021
DOI: 10.1038/S42003-021-02009-0
Abstract: Corymbia citriodora is a member of the predominantly Southern Hemisphere Myrtaceae family, which includes the eucalypts ( Eucalyptus , Corymbia and Angophora ~800 species). Corymbia is grown for timber, pulp and paper, and essential oils in Australia, South Africa, Asia, and Brazil, maintaining a high-growth rate under marginal conditions due to drought, poor-quality soil, and biotic stresses. To dissect the genetic basis of these desirable traits, we sequenced and assembled the 408 Mb genome of Corymbia citriodora , anchored into eleven chromosomes. Comparative analysis with Eucalyptus grandis reveals high synteny, although the two erged approximately 60 million years ago and have different genome sizes (408 vs 641 Mb), with few large intra-chromosomal rearrangements. C. citriodora shares an ancient whole-genome duplication event with E. grandis but has undergone tandem gene family expansions related to terpene biosynthesis, innate pathogen resistance, and leaf wax formation, enabling their successful adaptation to biotic/abiotic stresses and arid conditions of the Australian continent.
Publisher: Oxford University Press (OUP)
Date: 15-03-2022
DOI: 10.1093/JXB/ERAC107
Abstract: Modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian, and northern temperate, which correspond to the major global production environments. Reproductive phenology plays a key role in lentil adaptation to this erse ecogeographic variation. Here, we dissect the characteristic earliness of the pilosae ecotype, suited to the typically short cropping season of South Asian environments. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering, and we show that DTF6a alone is sufficient to confer early flowering under extremely short photoperiods. Genomic synteny confirmed the presence of a conserved cluster of three florigen (FT) gene orthologues among potential candidate genes, and expression analysis in near-isogenic material showed that the early allele is associated with a strong derepression of the FTa1 gene in particular. Sequence analysis revealed a 7.4 kb deletion in the FTa1–FTa2 intergenic region in the pilosae parent, and a wide survey of & accessions with erse origin showed that the dtf6a allele is predominant in South Asian material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.
Publisher: MDPI AG
Date: 05-04-2022
DOI: 10.3390/F13040575
Abstract: Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 in iduals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2019
Publisher: Springer Science and Business Media LLC
Date: 05-02-2021
Publisher: Springer Science and Business Media LLC
Date: 22-05-2017
Publisher: Oxford University Press (OUP)
Date: 02-06-2022
DOI: 10.1093/AOB/MCAC072
Abstract: The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. S les of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
Publisher: Oxford University Press (OUP)
Date: 06-04-2022
DOI: 10.1093/JXB/ERAC132
Abstract: Change in phenology has been an important component in crop evolution, and selection for earlier flowering through a reduction in environmental sensitivity has helped broaden adaptation in many species. Natural variation for flowering in domesticated pea (Pisum sativum L.) has been noted and studied for decades, but there has been no clear account of change relative to its wild progenitor. Here we examined the genetic control of differences in flowering time between wild P. sativum ssp. humile and a typical late-flowering photoperiodic P. s. sativum accession in a recombinant inbred population under long and short photoperiods. Our results confirm the importance of the major photoperiod sensitivity locus Hr/PsELF3a and identify two other loci on chromosomes 1 (DTF1) and 3 (DTF3) that contribute to earlier flowering in the domesticated line under both photoperiods. The domesticated allele at a fourth locus on chromosome 6 (DTF6) delays flowering under long days only. Map positions, inheritance patterns, and expression analyses in near-isogenic comparisons imply that DTF1, DTF3, and DTF6 represent gain-of-function alleles of the florigen/antiflorigen genes FTa3, FTa1, and TFL1c/LF, respectively. This echoes similar variation in chickpea and lentil, and suggests a conserved route to reduced photoperiod sensitivity and early phenology in temperate pulses.
Publisher: Springer Science and Business Media LLC
Date: 28-10-2022
DOI: 10.1186/S12864-022-08950-6
Abstract: The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F 1 populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes. Our mapping approach used probabilistic error correction of the marker data, followed by an iterative approach based on stringent parameters. This approach proved highly effective in producing high-density maps with robust marker orders and realistic map lengths (1285–4674 markers per map, with sizes ranging from c. 1643–2292 cM, and mean marker intervals of 0.7–2.1 cM). Colinearity was high between parental linkage maps, although there was evidence for a large chromosomal rearrangement (affecting ~ 90 cM) in one of the parental maps. In total, 28 QTL were detected for growth (stem diameter) and wood properties (wood density and fibre properties measured by Silviscan) in the QTL discovery population, with 1–3 QTL of small to moderate effect size detected per trait in each parental map. Four of these QTL were validated in a second, unrelated F 1 population. Results from genomic prediction and analyses of genetic architecture were consistent with those from QTL scans, with wood properties generally having moderate to high genomic heritabilities and predictive abilities, as well as somewhat less complex genetic architectures, compared to growth traits. Despite the economic importance of radiata pine as a plantation forest tree, robust high-density linkage maps constructed from reproducible, sequence-anchored markers have not been published to date. The maps produced in this study will be a valuable resource for several applications, including the selection of marker panels for genomic prediction and anchoring a recently completed de novo whole genome assembly. We also provide the first map-based evidence for a large genomic rearrangement in radiata pine. Finally, results from our QTL scans, genomic prediction, and genetic architecture analyses are informative about the genomic basis of variation in important phenotypic traits.
Publisher: Springer Science and Business Media LLC
Date: 10-03-2018
Publisher: Springer Science and Business Media LLC
Date: 24-08-2017
No related grants have been discovered for Jakob Butler.