ORCID Profile
0000-0002-1273-0348
Current Organisation
NSW Department of Primary Industries
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Springer Science and Business Media LLC
Date: 04-2021
DOI: 10.1007/S11033-021-06372-3
Abstract: Western flower thrips, Frankliniella occidentalis is an economically important agricultural pest. It causes damage by feeding and oviposition or indirectly by plant virus transmission. Australian F. occidentalis are resistant to many insecticides including spinosad and the related chemical spinetoram. Spinetoram resistance to F. occidentalis has been recently reported in three different Australian States, however, mechanisms conferring that resistance have not been investigated. To identify the mechanisms underlying resistance to spinetoram in F. occidentalis, we sequenced the genomic region of nicotinic acetylcholine receptor Foα6 in number of spinosad and spinetoram resistant field-populations. We found that a single nucleotide substitution (G to A) in exon 9 of the α6 subunit was present in resistant strains (G275E) and absent from susceptible. By examining field populations we consider the G275E mutation is the major cause of resistance to spinetoram in Australian F. occidentalis. We developed a real-time PCR diagnostic assay to quickly identify resistant alleles in field-populations. The method was used to test spinetoram resistant F. occidentalis collected from Australian cotton during the 2018-2019. Results show thrips tested carried the G275E mutation and the resistance allele was unusually widely distributed. The wide distribution of G275E mutation was not expected because spinetoram is not extensively used in Australian cotton. We speculate resistance may relate to extensive chemical use in crops nearby such as horticulture where thrips are often targeted for control. Our molecular diagnostic assay can provide timely and precise resistance frequency information that can support sustainable chemical use including spinetoram based IPM.
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/AN12098
Abstract: Residual feed intake (RFI) is a measure of feed efficiency in beef cattle. Young Angus bulls from lines of cattle ergently selected for RFI were used in a gene expression profiling study of the liver. Quantitative real-time PCR (qPCR) assay was used to quantify the differentially expressed genes and the information was used to examine the relationships between the genes and RFI and to classify the bulls into their respective RFI group. Gene expression of 21 genes in liver biopsies from 22 low RFI and 22 high RFI bulls were measured by qPCR. Gene expressions of 14 of the 21 genes were significantly correlated with RFI. The expression of the genes was used in a principal component analysis from which five components were extracted. The five principal components explained 70% of the variation in the dependency structure. The first component was highly correlated (correlation coefficient of 0.69) with RFI. The genes of the glutathione S-transferase Mu family (GSTM1, GSTM2, GSTM4), protocadherin 19 (PCDH19), ATP-binding cassette transporter C4 (ABCC4) and superoxide dismutase 3 (SOD3) are in the xenobiotic pathway and were the key factors in the first principal component. This highlights the important relationship between this pathway and variation in RFI. The second and third principal components were also correlated with RFI, with correlation coefficients of –0.28 and –0.20, respectively. Two of the four important genes of the second principal component work coordinately in the signalling pathways that inhibit the insulin-stimulated insulin receptor and regulate energy metabolism. This is consistent with the observation that a positive genetic correlation exists between RFI and fatness. The important genes in the third principal component are related to the extracellular matrix activity, with low RFI bulls showing high extracellular matrix activity.
Publisher: S. Karger AG
Date: 2006
DOI: 10.1159/000089896
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/AN11266
Abstract: Feed efficiency is an economically important trait in livestock and residual feed intake (RFI) is a commonly used measure of the trait in beef cattle. Residual feed intake is the difference between the actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. It is a heritable trait, and efficient animals have lower RFI values. Several genes have been identified as being differentially expressed in the liver of Angus bulls that have been ergently selected for RFI. The objective of this study was to use genes that are differentially expressed in bulls to classify Angus steers from the same ergent RFI selection lines. Liver s les were collected at slaughter from 40 high RFI and 40 low RFI steers that were ~23 months old, and had just completed a 251-day feedlot feeding period. RNA s les from the livers were assayed by quantitative real-time PCR for 14 genes, which have been identified previously in bulls. Steers were not measured for RFI, hence the estimated breeding values (EBV) for RFI of their parents were used to calculate their mid-parent (average of the two parents) RFI-EBV. Correlation and discriminant analyses were conducted on the normalised quantitative real-time PCR data from the steers. Discriminant analysis was also conducted on the bull data for comparison. In the steers, 8 out of the 14 genes were significantly (P 0.05) correlated with RFI-EBV. Two genes from the glutathione S-transferase mu family (GSTM1 and GSTM2) and the S100 calcium-binding protein A10 (S100A10) had the highest correlations with RFI-EBV, with correlation coefficients of 0.59, 0.44 and 0.36, respectively. Based on the 14 expressed genes, 84% of the steers and 98% of the bulls were correctly classified into their respective RFI selection lines. The results of this study indicate that a high proportion of the genes that were differentially expressed in the original study with bulls were also differentially expressed in this study with steers. The high accuracy in classification obtained in this study shows that the transcriptional approach to the study of the biological processes involved in variation in RFI has great potential for identification of candidate genes.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/AN12398
Abstract: Hormonal growth promotants (HGP) have been used to improve feed conversion ratio (FCR) and growth rates of cattle by modifying protein turnover rates. Residual feed intake (RFI) is correlated with FCR and has been adopted in Australia as a measure of feed efficiency in cattle for the purpose of genetic improvement. Eight genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3) have been previously reported to be highly associated with RFI and could potentially be used to predict RFI in bulls and steers. In this study, expression levels of these genes in liver tissue of 46 cattle were measured by quantitative real-time PCR. These cattle were part of a larger tenderness gene marker experiment consisting of two breeds (Angus and Brahman) two sexes (steers and heifers) and HGP treatments (implanted vs control). Cattle were measured for growth, feed efficiency, body composition and carcass traits. Results showed the expression of these eight genes was significantly correlated with RFI. However, HGP treatment did not affect RFI or the expression of the RFI-associated genes. HGP treatment increased average daily gain by 20%, improved FCR by 18%, and increased rib eye-muscle area by 7.5%. HGP treatment was effective in improving growth rate, presumably by its known action in the protein turnover mechanism. This mechanism has been hypothesised as one of the regulators of RFI. Lack of effect of HGP treatment on RFI does not support this hypothesis.
Publisher: S. Karger AG
Date: 2005
DOI: 10.1159/000085677
Publisher: Public Library of Science (PLoS)
Date: 10-03-2014
Publisher: Oxford University Press (OUP)
Date: 11-2006
Abstract: The first evidence of genetic linkage and sex-specific recombination in the order Crocodylia is reported. This study was conducted using a resource pedigree of saltwater crocodiles consisting of 16 known-breeding pairs (32 adults) and 101 juveniles. A total of 21 microsatellite loci were available for analysis. Ten of the 21 loci showed linkage with 4 linkage groups: 3 pairwise (Cj131/Cj127, CUD68/Cj101, and Cj107/Cp10) and 1 four-locus (Cj122, CUD78, Cj16, and Cj104) being found. Linkage analysis on the 21 loci revealed evidence of sex-specific differences in recombination rates. All 5 nonzero interlocus intervals were longer in females than in males, with the 4-loci linkage group 3-fold longer in females than in males (41.63 cM and 14.1 cM, respectively). This is the first report of sex-specific recombination rates in a species that exhibits temperature-dependent sex determination.
Publisher: Wiley
Date: 24-05-2005
DOI: 10.1111/J.1399-3089.2005.00230.X
Abstract: The Westran pig has been purposely inbred for use in xenotransplantation. The herd originated in the wild from a limited gene pool and has been inbred by repeated full-sib matings for nine generations. The aim of this study was to evaluate the level of inbreeding by functional assays, such as bi-directional MLR and reciprocal skin grafts between herd members, and by genetic analysis using highly polymorphic genetic markers to calculate the level of inbreeding. The MLR between herd members were non-reactive whereas there was a prompt response to third party pig lymphocytes, indicative of a normal immune responsiveness in Westran pigs but isogenicity of the major histocompatibility complex. Skin grafts between male siblings or female sibling skin grafts on male recipients showed prolonged survival but with few exceptions did not survive beyond 100 days suggesting that by the fifth generation the Westran herd was still mismatched at minor histocompatibility antigens. This level of functional inbreeding was confirmed by microsatellite analysis of highly polymorphic markers, which showed that 52 of 53 chromosomally dispersed markers were fixed by the ninth generation. This level of fixation was consistent with 19 to 20 generations of full-sibling inbreeding. The calculated inbreeding coefficient at generation 10 was 0.98159. This analysis confirms that the Westran pig is highly inbred and we propose that analysis of chromosomally dispersed highly polymorphic markers is an accurate and reproducible method for assessing the level of inbreeding of a pig herd.
Publisher: Wiley
Date: 10-2000
DOI: 10.1046/J.1365-2052.2000.00649.X
Abstract: The genetic ersities and relationships of four Chinese indigenous pig breeds and one Australian commercial pig breed have been evaluated using 27 microsatellites recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO). The allele frequencies, effective numbers of alleles and the polymorphic information content have been calculated. Nei's standard genetic distances have been used to construct a UPGMA dendrogram, which has been evaluated by the Bootstrap test. The utility of microsatellites for evaluating genetic ersity of pigs is discussed.
Publisher: Wiley
Date: 29-08-2013
DOI: 10.1111/AEN.12047
Publisher: Asian Australasian Association of Animal Production Societies
Date: 15-12-2016
DOI: 10.5713/AJAS.15.0605
Publisher: Elsevier BV
Date: 05-2016
Publisher: S. Karger AG
Date: 2003
DOI: 10.1159/000075737
Abstract: Conserved segments have been identified by ZOO-FISH between pig chromosome 9 (SSC9) and human chromosomes 1, 7 and 11. To assist in the identification of positional candidate genes for QTL on SSC9, the comparative map was further developed. Primers were designed from porcine EST sequence homologous to genes in regions of human chromosomes 1, 7 and 11. Porcine ESTs were then physically assigned using the INRA somatic cell hybrid panel (INRASCHP) and the high-resolution radiation hybrid panel (IMpRH). Seventeen genes (PEPP3, RAB7L1, FNBP2, MAPKAPK2, GNAI1, ABCB1, STEAP, AKAP9, CYP51A1, SGCE, ROBO4, SIAT4C, GLUL, CACNA1E, PTGS2, C1orf16 and ETS1) were mapped to SSC9, while GUSB, CPSF4 and THG-1 were assigned to SSC3.
Publisher: S. Karger AG
Date: 2003
DOI: 10.1159/000075736
Abstract: ZOO-FISH mapping shows human chromosomes 1, 9 and 10 share regions of homology with pig chromosome 10 (SSC10). A more refined comparative map of SSC10 has been developed to help identify positional candidate genes for QTL on SSC10 from human genome sequence. Genes from relevant chromosomal regions of the public human genome sequence were used to BLAST porcine EST databases. Primers were designed from the matching porcine ESTs to assign them to porcine chromosomes using the INRA somatic cell hybrid panel (INRA-SCHP) and the INRA-University of Minnesota Radiation Hybrid Panel (IMpRH). Twenty-eight genes from HSA1, 9 and 10 were physically mapped: fifteen to SSC10 (ACO1, ATP5C1, BMI1, CYB5R1, DCTN3, DNAJA1, EPHX1, GALT, GDI2, HSPC177, OPRS1, NUDT2, PHYH, RGS2, VIM), eleven to SSC1 (ADFP, ALDHIB1, CLTA, CMG1, HARC, PLAA, STOML2, RRP40, TESK1, VCP and VLDLR) and two to SSC4 (ALDH9A1 and TNRC4). Two anonymous markers were also physically mapped to SSC10 (SWR1849 and S0070) to better connect the physical and linkage maps. These assignments have further refined the comparative map between SSC1, 4 and 10 and HSA1, 9 and 10.
Publisher: Wiley
Date: 03-04-2020
DOI: 10.1111/AEN.12457
Publisher: Wiley
Date: 18-10-2014
DOI: 10.1111/AGE.12092
Abstract: Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between ergent lines of high- and low-RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real-time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency-related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.
Publisher: Wiley
Date: 30-09-2011
DOI: 10.1111/J.1365-2052.2010.02107.X
Abstract: Feed efficiency and growth are the most important traits in pig production, and very few genetic markers have been reported to be associated with feed efficiency. The suppressor of cytokine signalling-2 (encoded by SOCS2) is the main negative regulator of somatic growth, and the knockout of SOCS2 and naturally mutant mice have high-growth phenotypes. Porcine SOCS2 was selected as a primary positional candidate for feed efficiency, because it is located on chromosome 5q, in the vicinity of a Quantitative Trait Locus (QTL) region for food conversion ratio in pigs. Here, we report five single nucleotide polymorphisms identified by sequencing of the promoter region and exon 1. One PCR-RFLP assay was designed for genotyping the polymorphism c.1667A > G (GenBank Accession No AY312266). Association analyses were performed in an Australian mapping resource pedigree population (PRDC-US43) for food conversion ratio, backfat, IGF1 level and growth traits and showed significant effects on average daily gain on test (ADG2) (P < 0.01) and marginal association with food conversion ratio (FCR) (P < 0.08).
Publisher: Springer Science and Business Media LLC
Date: 17-08-2017
Publisher: Springer Science and Business Media LLC
Date: 25-02-2015
Publisher: Wiley
Date: 05-03-2015
Publisher: Oxford University Press (OUP)
Date: 09-2004
Publisher: Wiley
Date: 31-03-2011
DOI: 10.1111/J.1365-2052.2011.02182.X
Abstract: Feed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA-based marker-assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long-oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty-one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker-assisted selection.
Publisher: Elsevier BV
Date: 05-1994
Abstract: Loci containing (GT)n repeats were isolated from three different plasmid libraries with inserts of porcine genomic DNA between 140 and 200, 200 and 300, and 350 and 400 bp. Sequencing showed that the average repeat length and the fraction of perfect repeats were increased in the libraries containing longer inserts (> or = 200 bp). The polymorphism of (GT)n loci containing at least 10 repeat units was analyzed using the polymerase chain reaction and an automated DNA sequencer. Nearly all tested loci are polymorphic and can therefore be used as marker loci for gene mapping and for other applications. The (GT)n loci were categorized into three classes: (1) loci containing the (GT)n repeats associated with a SINE element, (2) loci containing the (GT)n repeats associated with one or more other simple repeats, and (3) loci containing (GT)n as the only detected repetitive element. At most loci of the first class, the (GT)n repeat was in a fixed configuration adjacent to the 3' end of the SINE. The findings support the notion of clustering of different repeat types in the mammalian genome.
Publisher: Wiley
Date: 16-02-2016
DOI: 10.1111/AEN.12190
Publisher: Wiley
Date: 03-01-2013
DOI: 10.1002/PS.3455
Abstract: Aphis gossypii is an important pest of cotton that has developed resistance to many chemicals used for its control. Any lack of understanding of its genetic structure, resistance status and host plant specialisation h ers effective management. Eight microsatellite markers were genotyped for a collection of Australian A. gossypii field isolates from 55 plant species from major Australian cotton-producing regions. The aphid's pirimicarb resistance status linked to the ACE1 (acetylcholinesterase) S431F mutation was determined by PCR-RFLP. Overall, the genetic ersity was low and there were only 13 multilocus genotype (MLG) groups found in a total of 936 aphids, suggesting asexual reproduction. Three MLGs (Aust-01, Aust-02 and Aust-04) represented 78% of all aphids tested. MLGs Aust-01 (41%) and Aust-02 (18%) were linked to the ACE1 S431F mutation and found on cotton and a range of hosts. Aust-04 (19%) hosted mainly on cotton (but also Asteraceae and Malvaceae) was predominantly susceptible to pirimicarb. Given their abundance and widespread occurrence, these three clones were considered to be superclones. The study demonstrated that any strategy to control A. gossypii and manage pirimicarb resistance should target A. gossypii strains of all MLG types residing on any plant species and not just cotton
Publisher: Wiley
Date: 14-08-2019
DOI: 10.1002/PS.5557
Abstract: A major challenge to sustainable agricultural pest control is the rapid evolution of insecticide resistance. This is caused by mechanisms that reduce insecticide efficacy. Understanding the genetic mechanisms of resistance is essential for DNA-based monitoring of resistance in field populations. One such insecticide is indoxacarb, an important selective control option for Helicoverpa armigera in a range of crops including grain, horticulture and cotton. Recently, a strain of H. armigera (GY7-39) resistant to indoxacarb (198-fold) was isolated from field-collected moth. To identify the indoxacarb resistance locus, GY7-39 was backcrossed for six generations to susceptible strain New GR. In each generation, only resistant males were used to cross back to New GR. Genotype-by-sequencing was carried out on 95 H. armigera s les. In total, 13 203 tags with 8697 unique locations on the H. armigera genome were obtained. The indoxacarb resistance locus in strain GY7-39 was mapped to a 2.6 Mbp region on chromosome 16. In this region, two closely linked loci (IndoR1 and IndoR2) were found to be associated with indoxacarb resistant GY7-39. We mapped indoxacarb resistance in GY7-39 to two closely linked loci IndoR1 and IndoR2 in a narrowed 2.6 Mbp region of H. armigera chromosome 16. The results provide essential background data for future genetic investigations including fine mapping of the indoxacarb resistance gene and the eventual development of an effective DNA-based diagnostic to support resistance management. © 2019 Society of Chemical Industry.
Publisher: Wiley
Date: 08-09-2021
DOI: 10.1111/AEN.12570
Abstract: Fall armyworm ( Spodoptera frugiperda ) has recently been detected in Australia. Globally, S. frugiperda is reported to be resistant to insecticides, including those permitted for its control by the Australian Pesticides and Veterinary Medicines Authority. Consequently, an understanding of the insecticide resistance status of newly migrated S. frugiperda into Australia, as well as an ability to accurately identify newly hatched larvae, would facilitate sustainable management. To aid identification, we developed a real‐time polymerase chain reaction diagnostic assay that can identify S. frugiperda species, irrespective of life stage, and distinguish between the rice and corn strains. We then screened S. frugiperda in iduals from Queensland, Western Australia, the Northern Territory and New South Wales for mutations causing target site insensitivity in the acetylcholinesterase (AChE) gene, the voltage‐gated sodium channel gene and the ryanodine receptor gene. In the populations tested, we found that mutation at positions A210S and F290V in AChE were common. These mutations are known to be associated with carbamate and organophosphate resistance in S. frugiperda outside Australia. In contrast, no mutation was found in gene voltage‐gated sodium channel causing pyrethroid resistance or the ryanodine receptor gene associated with diamide resistance. As S. frugiperda is new to Australia, the wide distribution of mutations in the AChE gene associated with organophosphate/carbamate resistance suggests that the original migrated S. frugiperda moths may have carried the mutations from outside Australia. As resistance genes have been detected, it is important to continue to monitor the resistance status of Australian S. frugiperda and further integrate complementary bioassay when available. Finally, as pesticide resistance is possible, it should be additionally considered when making pest management decisions and any spray failure should be followed by a pesticide from a different chemical group.
No related grants have been discovered for Yizhou Chen.