ORCID Profile
0000-0003-1502-5617
Current Organisation
University of Queensland
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Crop and pasture production | Animal reproduction and breeding | Horticultural crop improvement (incl. selection and breeding) | Crop and pasture improvement (incl. selection and breeding)
Publisher: Elsevier BV
Date: 06-2022
Publisher: Frontiers Media SA
Date: 24-12-2021
Abstract: Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked s le analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance.
Publisher: American Society for Horticultural Science
Date: 04-2019
Abstract: Current macadamia breeding programs involve a lengthy and laborious two-stage selection process: evaluation of a large number of unreplicated seedling progeny, followed by replicated trials of clonally propagated elite seedlings. Yield component traits, such as nut-in-shell weight (NW), kernel weight (KW), and kernel recovery (KR) are commercially important, are more easily measured than yield, and have a higher heritability. A genome-wide association study (GWAS) combined with marker-assisted selection offers an opportunity to reduce the time of candidate evaluation. In this study, a total of 281 progeny from 32 families, and 18 of their 29 parents have been genotyped for 7126 single nucleotide polymorphism (SNP) markers. A GWAS was performed using ASReml with 4352 SNPs. We found five SNPs significantly associated with NW, nine with KW, and one with KR. Further, three of the top 10 markers for NW and KW were shared between the two traits. Future macadamia breeding could involve prescreening of in iduals for desired traits using these significantly associated markers, with only predicted elite in iduals continuing to the second stage of selection, thus potentially reducing the selection process by 7 years.
Publisher: Science Alert
Date: 15-12-2006
Publisher: Public Library of Science (PLoS)
Date: 31-08-2018
Publisher: Elsevier BV
Date: 2022
Publisher: Springer Science and Business Media LLC
Date: 03-2019
Publisher: Science Alert
Date: 15-03-2006
Publisher: Science Alert
Date: 15-06-2007
Publisher: Wiley
Date: 11-07-2022
Abstract: Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. However, these techniques are inefficient in plants, which limits their applications for crop breeding programs. Recently, substantial developments have been made to improve the efficiency of these techniques in plants. Several strategies, such as RNA donor templating, chemically modified donor DNA template, and tandem‐repeat homology‐directed repair, are aimed at improving GT. Additionally, improved prime editing gRNA design, use of engineered reverse transcriptase enzymes, and splitting prime editing components have improved the efficacy of prime editing in plants. These emerging strategies and existing technologies are reviewed along with various perspectives on their future improvement and the development of robust precision genome editing technologies for plants.
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2021
DOI: 10.1101/2021.09.08.459545
Abstract: Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the erse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii , being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low ersity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.
Publisher: MDPI AG
Date: 14-08-2022
Abstract: Macadamia pericarps that fail to abscise (‘stick-tights’) are an important trait to select against in breeding as they can harbour pests and diseases. Traditional macadamia breeding cycles are lengthy and expensive due to long juvenilities and large tree sizes. Thus, genome-wide association studies (GWAS) are an important investigative tool to identify candidate trait-linked markers to enable potential reductions in evaluation and selection cycles via marker-assisted selection (MAS) in young seedlings. This study assessed 199 wild macadamia germplasm accessions for stick-tight prevalence across two years. As the number of stick-tights per tree is limited by the number of nuts per tree, we conducted association analyses to identify SNPs linked with the number of stick-tights per tree, and examined whether such SNPs were also associated with, and thus confounded with, the number of nuts per tree. We also assessed associations with the proportion of stick-tights per total number of nuts. Thirty-two SNPs were associated with at least one of the stick-tight traits in one year (p 0.001). Of all such SNPs, only one was associated with the number of nuts per tree (p 0.001), indicating that most associations were not confounded with yield.
Publisher: CABI
Date: 02-07-2021
Publisher: Science Alert
Date: 15-04-2008
Publisher: Springer Science and Business Media LLC
Date: 11-04-2023
DOI: 10.1007/S10681-023-03169-2
Abstract: Husk spot caused by the Pseudocercospora macadamiae fungus induces premature abscission of fruit in many industry standard macadamia cultivars. Fungicides and other management strategies add to farm costs, thus breeding for varietal resistance is important. Genetic parameters of husk spot symptom expression had not previously been estimated. To guide selection methods for field resistance, over 300 open-pollinated seedlings of 32 families and 24 parent genotypes were inoculated, and seven symptom expression traits were evaluated. Narrow-sense and broad-sense heritabilities were estimated, breeding values were predicted, and correlations between breeding values of trait pairs were tested for significance. The traits with the highest heritabilities were necrotic lesion number per fruit ( H 2 = 0.41–0.59 h 2 = 0.21–0.30) and necrotic incidence ( H 2 = 0.19–0.27 h 2 = 0.17–0.24). Breeding values of the two traits were highly correlated (r = 0.98 p 0.001), suggesting that either trait could be used to indirectly select for the other. All genotypes expressed symptoms to some degree, however, breeding values for necrotic traits and symptom-induced premature abscission were low for clones and progeny of cultivar ‘HAES791’. Necrotic trait breeding values were also promising for progeny of cultivar ‘HAES246’ and clones of Australian Macadamia Breeding Program elite selection, ‘BAM263’. Having been identified as potentially partially resistant, these selections can now be further evaluated and used as parents of new progeny populations.
Publisher: MDPI
Date: 03-12-2021
Publisher: Wiley
Date: 12-2021
DOI: 10.1002/PLD3.364
Abstract: Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the erse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii , being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here, we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi‐C, comprising 14 pseudo‐molecules, with a N50 of 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive. Completeness assessment revealed that the assembly covered −97.1% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism, and anti‐microbial proteins. Re‐sequencing of seven other genotypes confirmed low ersity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high‐quality genome also provides a key resource for evolutionary and comparative genomics studies.
Publisher: International Society for Horticultural Science (ISHS)
Date: 10-2020
Publisher: American Society for Horticultural Science
Date: 04-2019
Abstract: The Hawaiian cultivars Keaau (HAES660) and Mauka (HAES741) were selected by the University of Hawaii—released in 1966 and 1977, respectively—and have been used extensively in macadamia orchards throughout the world. Recent molecular evidence suggests that these two cultivars are almost identical genetically however, commercially they have been considered phenotypically different. This study reviews available molecular, historical, and phenotypic evidence to examine the hypothesis that these two cultivars are the same genotype. Phenotypic variability for morphological traits was observed in a replicated trial at Wolvi, QLD. Historical evidence suggests that both ‘HAES660’ and ‘HAES741’ were derived from the same orchard. We identified strong genetic and phenotypic similarities between these cultivars, with variability in some simple traits. This study provides evidence that these two cultivars are isogenic or near isogenic and may have been derived from the same plant source.
Publisher: Science Alert
Date: 15-04-2007
Publisher: MDPI
Date: 02-12-2021
Publisher: Wiley
Date: 2017
Publisher: Scientific Societies
Date: 2023
DOI: 10.1094/PDIS-03-22-0507-RE
Abstract: Husk spot, a fungal disease of macadamia pericarps (Pseudocercospora macadamiae), induces premature abscission in several major commercial cultivars. Breeding for resistance to husk spot is a priority of the Australian macadamia industry. Due to the large tree size of macadamia and high numbers of progeny in breeding populations, inoculating for resistance screening is laborious and time consuming. Previously utilized methods included direct applications of P. macadamiae suspensions and the hanging of bags of diseased husks above developing fruit in tree canopies. In this study, both methods were modified to allow for efficient application in large-scale breeding populations, and their efficacy was evaluated. Two quantities of diseased husk per bag, ‘large’ (75 g) and ‘small’ (30 g), and two concentrations of sprayed P. macadamiae suspensions, ‘stock’ (5 × 10 5 propagules/ml) and ‘dilute’ (2.5 × 10 5 propagules/ml), were tested across two fruiting seasons. Treatments were compared against a control (sterile water) in commercial cultivars A38 and A4. Husk spot incidence and severity produced by small bags were significantly affected by season. A significant season effect was less common for other treatments. All four treatments infected over 50% of target fruit in each season, but the highest husk spot incidence across both seasons (≥85%) was produced from large bags. Overall, the large bags were the most reliable method for infection of target fruit. Results also demonstrate the importance of considering the effect of season when selecting husk spot inoculation methods.
Publisher: Wiley
Date: 25-03-2014
DOI: 10.1111/NPH.12767
Abstract: Tillering determines the plant size of sorghum ( Sorghum bicolor ) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller ( PTT ) and probably represented hormonal effects. Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT . The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences.
Publisher: Springer Science and Business Media LLC
Date: 20-05-2021
DOI: 10.1186/S12864-021-07694-Z
Abstract: Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8 years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8 years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations. Narrow-sense heritability of yield and yield stability was low (h 2 = 0.30 and 0.04, respectively). Prediction accuracy for yield was 0.57 for predictions across related populations and 0.14 when predicted across unrelated populations. Accuracy of prediction of yield stability was high (r = 0.79) for predictions across related populations. Predicted genetic gain of yield using GS in related populations was 474 g/year, more than double that of traditional breeding methods (226 g/year), due to the halving of generation length from 8 to 4 years. The results of this study indicate that the incorporation of GS for yield into the Australian macadamia breeding program may accelerate genetic gain due to reduction in generation length, though the cost of genotyping appears to be a constraint at present.
Publisher: Science Alert
Date: 15-10-2005
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: Elsevier BV
Date: 11-2019
Publisher: Springer Science and Business Media LLC
Date: 04-03-2020
DOI: 10.1186/S12864-020-6575-3
Abstract: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: MDPI AG
Date: 05-10-2023
DOI: 10.3390/SU151914506
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: MDPI AG
Date: 03-06-2020
Abstract: Macadamia is an Australian native rainforest tree that has been domesticated and traded internationally for its premium nuts. Common cultivars rely upon a limited gene pool that has exploited only two of the four species. Introducing a more erse germplasm will broaden the genetic base for future crop improvement and better adaptation for changing environments. This study investigated the genetic structure of 302 accessions of wild germplasm using 2872 SNP and 8415 silicoDArT markers. Structure analysis and principal coordinate analysis (PCoA) assigned the 302 accessions into four distinct groups: (i) Macadamia integrifolia, (ii) M. tetraphylla, and (iii) M. jansenii and M. ternifolia, and (iv) admixtures or hybrids. Assignment of the four species matched well with previous characterisations, except for one M. integrifolia and four M. tetraphylla accessions. Using SNP markers, 94 previously unidentified accessions were assigned into the four distinct groups. Finally, 287 accessions were identified as pure ex les of one of the four species and 15 as hybrids of M. integrifolia and M. tetraphylla. The admixed accessions showed the highest genetic ersity followed by M. integrifolia, while M. ternifolia and M. jansenii accessions were the least erse. Mantel test analysis showed a significant correlation between genetic and geographic distance for M. integrifolia (r = 0.51, p = 0.05) and a positive but not significant correlation for M. tetraphylla (r = 0.45, p = 0.06). This study provides a population genetics overview of macadamia germplasm as a background for a conservation strategy and provides directions for future macadamia breeding.
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: International Society for Horticultural Science (ISHS)
Date: 06-2018
Publisher: Springer Science and Business Media LLC
Date: 03-09-2019
Publisher: CABI
Date: 02-07-2021
Publisher: MDPI AG
Date: 19-07-2021
DOI: 10.3390/AGRICULTURE11070680
Abstract: Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing ersity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased s ling within sites to capture wide genetic ersity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.
Publisher: Science Alert
Date: 15-10-2005
Publisher: Elsevier BV
Date: 2023
Publisher: Elsevier BV
Date: 12-2020
Publisher: MDPI
Date: 29-11-2021
Publisher: Springer Science and Business Media LLC
Date: 28-08-2014
DOI: 10.1007/S00122-014-2377-9
Abstract: A QTL model for the genetic control of tillering in sorghum is proposed, presenting new opportunities for sorghum breeders to select germplasm with tillering characteristics appropriate for their target environments. Tillering in sorghum can be associated with either the carbon supply-demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.
Publisher: Frontiers Media SA
Date: 08-07-2021
DOI: 10.3389/FGENE.2021.661276
Abstract: Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, Crassostrea angulata . The study consisted of 647 oysters: 188 oysters from 57 full-sib families from the first generation and 459 oysters from 33 full-sib families from the second generation. The number per family ranged from two to eight oysters for the first and 12–15 oysters for the second generation. After quality control, a set of 13,048 markers were analyzed to estimate the genetic parameters (heritability and genetic correlation) and predictive accuracy of the genomic selection for these traits. The multi-locus mixed model analysis indicated high estimates of heritability for meat yield traits: 0.43 for soft tissue weight and 0.77 for condition index. The estimated genomic heritabilities were 0.45 for whole weight, 0.24 for cup ratio, and 0.33 for fan ratio and ranged from 0.14 to 0.54 for color traits. The genetic correlations among whole weight, meat yield, and body shape traits were favorably positive, suggesting that the selection for whole weight would have beneficial effects on meat yield and body shape traits. Of paramount importance is the fact that the genomic prediction showed moderate to high accuracy for the traits studied (0.38–0.92). Therefore, there are good prospects to improve whole weight, meat yield, body shape, and color traits using genomic information. A multi-trait selection program using the genomic information can boost the genetic gain and minimize inbreeding in the long-term for this population.
Publisher: Science Alert
Date: 15-06-2007
Publisher: MDPI
Date: 19-01-2020
Publisher: Science Alert
Date: 15-12-2008
Publisher: Springer International Publishing
Date: 2020
Publisher: MDPI
Date: 13-02-2020
Start Date: 2023
End Date: 12-2027
Amount: $5,000,000.00
Funder: Australian Research Council
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