ORCID Profile
0000-0002-2380-3805
Current Organisation
Curtin University
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Publisher: Elsevier BV
Date: 07-2019
Publisher: Informa UK Limited
Date: 18-01-2008
DOI: 10.1080/10495390701807634
Abstract: Availability of the human genome sequence and high similarity between humans and pigs at the molecular level provides an opportunity to use a comparative mapping approach to piggy-BAC the human genome. In order to advance the pig genome sequencing initiative, sequence similarity between large-scale porcine BAC-end sequences (BESs) and human genome sequence was used to construct a comparatively-anchored porcine physical map that is a first step towards sequencing the pig genome. A total of 50,300 porcine BAC clones were end-sequenced, yielding 76,906 BESs after trimming with an average read length of 538 bp. To anchor the porcine BACs on the human genome, these BESs were subjected to BLAST analysis using the human draft sequence, revealing 31.5% significant hits (E < e(-5)). Both genic and non-genic regions of homology contributed to the alignments between the human and porcine genomes. Porcine BESs with unique homology matches within the human genome provided a source of markers spaced approximately 70 to 300 kb along each human chromosome. In order to evaluate the utility of piggy-BACing human genome sequences, and confirm predictions of orthology, 193 evenly spaced BESs with similarity to HSA3 and HSA21 were selected and then utilized for developing a high-resolution (1.22 Mb) comparative radiation hybrid map of SSC13 that represents a fusion of HSA3 and HSA21. Resulting RH mapping of SSC13 covers 99% and 97% of HSA3 and HSA21, respectively. Seven evolutionary conserved blocks were identified including six on HSA3 and a single syntenic block corresponding to HSA21. The strategy of piggy-BACing the human genome described in this study demonstrates that through a directed, targeted comparative genomics approach construction of a high-resolution anchored physical map of the pig genome can be achieved. This map supports the selection of BACs to construct a minimal tiling path for genome sequencing and targeted gap filling. Moreover, this approach is highly relevant to other genome sequencing projects.
Publisher: KARGER
Date: 2008
DOI: 10.1159/000317140
Publisher: Wiley
Date: 22-01-2004
Publisher: Springer Science and Business Media LLC
Date: 15-11-2005
Abstract: In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, bio ersity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP) as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD) than does a di-allelic marker system [1]. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced. Seventeen porcine microsatellite markers were isolated from eleven PAC clones by t argeted o ligonucleotide- m ediated m icrosatellite i dentification (TOMMI), an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT) microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC), average heterozygosity (H T ), and effective allele number (N E ) for the STS-markers were calculated using a s ling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds). Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles) in this heterogeneous s ling. Most of the publicly available (porcine) microsatellite licons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger licons. Indeed, fourteen of the seventeen STS-marker licons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be integrated into multilocus assays covering a broader separation spectrum. Linkage mapping results of the markers indicate their potential immediate use in QTL studies to further dissect trait associated chromosomal regions. The sequencing strategy described in this study provides a targeted, inexpensive and fast method to develop microsatellites from large-insert libraries. It is well suited to generate polymorphic markers for selected chromosomal regions, contigs of overlapping clones and yields sufficient high quality sequence data to develop licons greater than 250 bases.
Publisher: MDPI AG
Date: 03-11-2021
Abstract: In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding.
Publisher: CSIRO Publishing
Date: 28-03-2022
DOI: 10.1071/FP21216
Abstract: Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is one of the most economically devastating diseases in chickpea (Cicer arietinum L.). No complete resistance is available in chickpea to this disease, and the inheritance of partial resistance is not understood. Two hundred F7 recombinant inbred lines (RILs) derived from a cross between a partially resistant variety PBA HatTrick, and a highly susceptible variety Kyabra were characterised for their responses to SSR inoculation. Quantitative trait locus (QTL) analysis was conducted for the area under the disease progress curve (AUDPC) after RIL infection with S. sclerotiorum. Four QTLs on chromosomes, Ca4 (qSSR4-1, qSSR4-2), Ca6 (qSSR6-1) and Ca7 (qSSR7-1), in idually accounted for between 4.2 and 15.8% of the total estimated phenotypic variation for the response to SSR inoculation. Candidate genes located in these QTL regions are predicted to be involved in a wide range of processes, including phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction. This is the first study investigating the inheritance of resistance to S. sclerotiorum in chickpea. Markers associated with the identified QTLs could be employed for marker-assisted selection in chickpea breeding.
Publisher: Wiley
Date: 20-09-2016
DOI: 10.1111/CEA.12795
Abstract: Air pollution can have adverse health effects on asthma sufferers, but the effects vary with geographic, environmental and population characteristics. There has been no long time-series study in Australia to quantify the effects of environmental factors including pollen on asthma hospitalizations. This study aimed to assess the seasonal impact of air pollutants and aeroallergens on the risk of asthma hospital admissions for adults and children in Adelaide, South Australia. Data on hospital admissions, meteorological conditions, air quality and pollen counts for the period 2003-2013 were sourced. Time-series analysis and case-crossover analysis were used to assess the short-term effects of air pollution on asthma hospitalizations. For the time-series analysis, generalized log-linear quasi-Poisson and negative binomial regressions were used to assess the relationships, controlling for seasonality and long-term trends using flexible spline functions. For the case-crossover analysis, conditional logistic regression was used to compute the effect estimates with time-stratified referent selection strategies. A total of 36,024 asthma admissions were considered. Findings indicated that the largest effects on asthma admissions related to PM Findings suggest that children are more vulnerable and the associations between exposure to air pollutants and asthma hospitalizations tended to be stronger in the cool season compared to the warm season, with the exception of ozone. This study has important public health implications and provides valuable evidence for the development of policies for asthma management.
Publisher: Asian Australasian Association of Animal Production Societies
Date: 2003
Publisher: Wiley
Date: 08-10-2021
DOI: 10.1111/PPA.13484
Abstract: The virulence of 57 Australian isolates of Pyrenophora tritici ‐ repentis (Ptr), a necrotrophic fungal pathogen responsible for the major wheat disease tan spot, was assessed through plant infection assays. Isolates collected from the northern, southern, and western wheat‐cropping regions of Australia were evaluated against 16 Australian bread wheat cultivars under controlled growth conditions. Following infection, the wheat panel displayed varying disease symptoms ranging from tiny necrotic specks to spreading chlorotic and necrotic lesions. Analysis of variance indicated that the wheat cultivar exhibited a greater effect on the disease response, explaining 62.7% of the variation, in comparison to the isolate (10.4%). The interaction between the cultivar and the isolate was statistically significant and was attributed to 9.8% of the total variation. All Ptr isolates examined were able to cause disease, but did not display a clear distinction in virulence on the wheat panel investigated, instead showing subtle differences in aggressiveness. Based on the disease responses, there was no obvious pattern between isolate aggressiveness and cropping region. Some cultivars, such as Hydra, exhibited an effective level of resistance in relation to the panel of isolates tested. All 57 Ptr isolates were found to possess the ToxA effector gene and lack the ToxB effector gene. The gene expression level of ToxA was up‐regulated at 3 days postinfection in both ToxA‐sensitive and ‐insensitive cultivars, independent of ToxA– Tsn1 recognition.
Publisher: Springer Science and Business Media LLC
Date: 18-10-2016
DOI: 10.1038/NCOMMS13158
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus ) before the Holocene ( .7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison ( Bison priscus ) and ancestors of modern cattle (aurochs, Bos primigenius ) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
Publisher: Wiley
Date: 23-12-2017
DOI: 10.1111/ZPH.12335
Abstract: Zoonotic diseases transmitted by arthropods and rodents are a major public health concern in China. However, interventions in recent decades have helped lower the incidence of several diseases despite the country's large, frequently mobile population and socio-economic challenges. Increasing globalization, rapid urbanization and a warming climate now add to the complexity of disease control and prevention and could challenge China's capacity to respond to threats of emerging and re-emerging zoonoses. To investigate this notion, face-to-face interviews were conducted with 30 infectious disease experts in four cities in China. The case study diseases under discussion were malaria, dengue fever and haemorrhagic fever with renal syndrome, all of which may be influenced by changing meteorological conditions. Data were analysed using standard qualitative techniques. The study participants viewed the current disease prevention and control system favourably and were optimistic about China's capacity to manage climate-sensitive diseases in the future. Several recommendations emerged from the data including the need to improve health literacy in the population regarding the transmission of infectious diseases and raising awareness of the health impacts of climate change amongst policymakers and health professionals. Participants thought that research capacity could be strengthened and human resources issues for front-line staff should be addressed. It was considered important that authorities are well prepared in advance for outbreaks such as dengue fever in populous subtropical areas, and a prompt and coordinated response is required when outbreaks occur. Furthermore, health professionals need to remain skilled in the identification of diseases for which incidence is declining, so that re-emerging or emerging trends can be rapidly identified. Recommendations such as these may be useful in formulating adaptation plans and capacity building for the future control and prevention of climate-sensitive zoonotic diseases in China and neighbouring countries.
Publisher: Informa UK Limited
Date: 2012
DOI: 10.1080/10495398.2011.630897
Abstract: Growth and carcass traits are of great economic importance in livestock production. A large number of quantitative trait loci (QTL) have been identified for growth and carcass traits on porcine chromosome one (SSC1). A key positional candidate for this chromosomal region is TGFBR1 (transforming growth factor beta type I receptor). This gene plays a key role in inherited disorders at cardiovascular, craniofacial, neurocognitive, and skeletal development in mammals. In this study, 27 polymorphic SNPs in the porcine TGFBR1 gene were identified on the University of Illinois Yorkshire × Meishan resource population. Three SNPs (SNP3, SNP43, SNP64) representing major polymorphic patterns of the 27 SNPs in F1 and F0 in iduals of the Illinois population were selected for analyses of QTL association and genetic ersity. An association analysis for growth and carcass traits was completed using these three representative SNPs in the Illinois population with 298 F2 in iduals and a large commercial population of 1008 animals. The results indicate that the TGFBR1 gene polymorphism (SNP64) is significantly associated (p < 0.05) with growth rates including average daily gains between birth and 56 kg (p = 0.049), between 5.5 and 56 kg (p = 0.024), between 35 and 56 kg (p = 0.021). Significant associations (p < 0.05) were also identified between TGFBR1 gene polymorphisms (SNP3/SNP43) and carcass traits including loin-eye-area (p = 0.022) in the Illinois population, and back-fat thickness (p = 0.0009), lean percentage (p = 0.0023) and muscle color (p = 0.021) in the commercial population. These three SNPs were also used to genotype a erse panel of 130 animals representing 11 pig breeds. Alleles SNP3_T and SNP43_G were fixed in Pietrain and Sinclair pig breeds. SNP64_G allele was uniquely identified in Chinese Meishan pigs. Strong evidence of association (p < 0.01) between both SNP3 and SNP64 alleles and reproductive traits including gestation length and number of corpora lutea were also observed in the Illinois population. This study gives the first evidence of association between the porcine TGFBR1 gene and traits of economic importance and provides support for using TGFBR1 markers for pig breeding and selection programs. The genetic ersities in different pig breeds would be helpful to understand the genetic background and migration of the porcine TGFBR1 gene.
Publisher: Scientific Societies
Date: 09-2021
DOI: 10.1094/PDIS-02-21-0367-RE
Abstract: Sclerotinia sclerotiorum is an important fungal pathogen of chickpea (Cicer arietinum L.), and it can cause yield losses up to 100%. The wild progenitors are much more erse than domesticated chickpea, and this study describes how this relates to S. sclerotiorum resistance. Initially, the pathogenicity of nine Australian S. sclerotiorum isolates was examined on three Cicer lines to develop a robust phenotyping assay, and significant differences in isolate aggressiveness were identified with six isolates being classed as highly aggressive and three as moderately aggressive. We identified two S. sclerotiorum isolates, CU8.20 and CU10.12, to be highly aggressive and moderately aggressive, respectively. A subsequent phenotyping assay was conducted using the two isolates to evaluate 86 wild Cicer accessions (Cicer reticulatum and Cicer echinospermum) and two C. arietinum varieties for resistance to S. sclerotiorum. A subset of 12 genotypes was further evaluated, and subsequently, two wild Cicer accessions with consistently high levels of resistance to S. sclerotiorum were examined using the initially characterized nine isolates. Wild Cicer accessions Karab_084 and Deste_063 demonstrated consistent partial resistance to S. sclerotiorum. There were significant differences in responses to S. sclerotiorum across wild Cicer collection sites. The Cermik, Karabahce, and Destek sites’ responses to the aggressive isolate CU8.20 ranged from resistant to susceptible, highlighting an interaction between isolate genotype and chickpea collection site for sclerotinia stem rot resistance. This is the first evidence of partial stem resistance identified in wild Cicer germplasm, which can be adopted in chickpea breeding programs to enhance S. sclerotiorum resistance in future chickpea varieties.
Publisher: Wiley
Date: 23-12-2017
DOI: 10.1111/ZPH.12335
Abstract: Zoonotic diseases transmitted by arthropods and rodents are a major public health concern in China. However, interventions in recent decades have helped lower the incidence of several diseases despite the country's large, frequently mobile population and socio-economic challenges. Increasing globalization, rapid urbanization and a warming climate now add to the complexity of disease control and prevention and could challenge China's capacity to respond to threats of emerging and re-emerging zoonoses. To investigate this notion, face-to-face interviews were conducted with 30 infectious disease experts in four cities in China. The case study diseases under discussion were malaria, dengue fever and haemorrhagic fever with renal syndrome, all of which may be influenced by changing meteorological conditions. Data were analysed using standard qualitative techniques. The study participants viewed the current disease prevention and control system favourably and were optimistic about China's capacity to manage climate-sensitive diseases in the future. Several recommendations emerged from the data including the need to improve health literacy in the population regarding the transmission of infectious diseases and raising awareness of the health impacts of climate change amongst policymakers and health professionals. Participants thought that research capacity could be strengthened and human resources issues for front-line staff should be addressed. It was considered important that authorities are well prepared in advance for outbreaks such as dengue fever in populous subtropical areas, and a prompt and coordinated response is required when outbreaks occur. Furthermore, health professionals need to remain skilled in the identification of diseases for which incidence is declining, so that re-emerging or emerging trends can be rapidly identified. Recommendations such as these may be useful in formulating adaptation plans and capacity building for the future control and prevention of climate-sensitive zoonotic diseases in China and neighbouring countries.
Publisher: Elsevier BV
Date: 12-2006
DOI: 10.1016/J.GENE.2006.07.009
Abstract: The transforming growth factor beta (TGF beta) family is essential for normal growth and development of different organ systems. Here we describe the isolation and molecular characterization of the full-length cDNA and the determination of the genomic DNA sequence of the porcine TGFBR1 gene. The full-length TGFBR1 cDNA 1813 bp contains an open reading frame (ORF) of 1512 bp encoding a TGFBR1 protein of 503 amino acids with a calculated molecular weight (Mw) of 56.4 kDa. A BAC clone harboring the porcine TGFBR1 gene was isolated and sequenced. The results of genomic and cDNA sequences of the porcine TGFBR1 gene demonstrated that it spans a transcription unit of 62,182 bp consisting of nine exons ranging from 125 to 354 bp, and eight introns ranging from 1003 to 29,441 bp. A shorter porcine TGFBR1 isoform resulting from the alternative splicing of exon 7 in porcine TGFBR1 cDNA was detected. The shorter TGFBR1 isoform contained a 1140 bp ORF encoding 379 amino acids with a calculated Mw of 41.7 kDa. The core promoter of porcine TGFBR1 gene lacks a TATA box but contains GC boxes and CAAT boxes. Multiple transcription initiation and termination sites were identified in untranslated regions (UTR) resulting in the size of 5'-UTR varying from 15 to 62 bp, and the length of 3'-UTR varying from 169 to 228 bp. Quantitative real time PCR results showed that the TGFBR1 transcript was ubiquitously expressed in all tissues examined (i.e. fat, adrenal, brain, spinal cord, muscle, mandibular lymph node, thymus, bone marrow, uterus, spleen, testis, kidney, liver, and ovary). A total of eighty-five gene polymorphisms (77 SNPs and 8 indels) were detected in the porcine TGFBR1 gene by utilizing a panel of DNA from eight ersified pig breeds (Yorkshire, Chinese Meishan, Berkshire, Duroc, H shire, Landrace, Large White and Pietrain). The minor allele frequencies of these nucleotide variations varied from 0.13 to 0.5 with an average of 0.26. In addition, seventeen microsatellites were identified throughout the genomic sequence of the porcine TGFBR1 gene.
Publisher: Wiley
Date: 09-03-2021
DOI: 10.1111/TPJ.15173
Publisher: Asian Australasian Association of Animal Production Societies
Date: 2002
Publisher: Springer Science and Business Media LLC
Date: 31-01-2011
Abstract: Bos primigenius , the aurochs, is the wild ancestor of modern cattle breeds and was formerly widespread across Eurasia and northern Africa. After a progressive decline, the species became extinct in 1627. The origin of modern taurine breeds in Europe is debated. Archaeological and early genetic evidence point to a single Near Eastern origin and a subsequent spread during the diffusion of herding and farming. More recent genetic data are instead compatible with local domestication events or at least some level of local introgression from the aurochs. Here we present the analysis of the complete mitochondrial genome of a pre-Neolithic Italian aurochs. In this study, we applied a combined strategy employing both multiplex PCR lifications and 454 pyrosequencing technology to sequence the complete mitochondrial genome of an 11,450-year-old aurochs specimen from Central Italy. Phylogenetic analysis of the aurochs mtDNA genome supports the conclusions from previous studies of short mtDNA fragments - namely that Italian aurochsen were genetically very similar to modern cattle breeds, but highly ergent from the North-Central European aurochsen. Complete mitochondrial genome sequences are now available for several modern cattle and two pre-Neolithic mtDNA genomes from very different geographic areas. These data suggest that previously identified sub-groups within the widespread modern cattle mitochondrial T clade are polyphyletic, and they support the hypothesis that modern European breeds have multiple geographic origins.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Wiley
Date: 30-08-2006
Publisher: Informa UK Limited
Date: 07-2006
DOI: 10.1080/10495390500461005
Abstract: We isolated and characterized the highly polymorphic tetra-nucleotide microsatellite S0719 on SSC7q14-q15 adjacent to the porcine testis-specific phosphoglycerate kinase 2 (PGK2) gene and assigned it to the USDA-MARC linkage map on SSC7 position 77.5 cM closely linked to markers SW859 (76.3 cM) and SWR2036 (79.0 cM). In a panel of 344 in iduals representing 11 pig breeds (European, Chinese, and North American), a total of 32 alleles were observed, and the overall breeds' calculated PIC (polymorphism information content), HE (heterozygosity), and NE (effective allele number) were 0.94, 0.94, and 16.41. Breed-specific PIC and HE ranged from 0.66 to 0.87, whereas NE was as low as 2.95 and as high as 7.96. Considering the high allelic variation of S0719 within and among pig breeds (79% of the genotyped animals were heterozygous), the marker is useful for in idual animal identification and parentage determination. Finally, S0719 is also a valuable STS marker for fine-mapping QTL on SSC7 as position 77.5 cM is located in 25 QTL intervals.
Publisher: Public Library of Science (PLoS)
Date: 19-01-2012
Publisher: Springer Science and Business Media LLC
Date: 18-10-2016
DOI: 10.1038/NCOMMS13158
Abstract: The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus ) before the Holocene ( .7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison ( Bison priscus ) and ancestors of modern cattle (aurochs, Bos primigenius ) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya).
Publisher: Elsevier BV
Date: 06-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 03-11-2009
Abstract: The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species erged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 in iduals representing 61 Pecoran species. We produced a highly resolved phylogeny for this erse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to lify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of s les within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient s les. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.
Publisher: Informa UK Limited
Date: 07-2006
DOI: 10.1080/10495390500461005
Abstract: We isolated and characterized the highly polymorphic tetra-nucleotide microsatellite S0719 on SSC7q14-q15 adjacent to the porcine testis-specific phosphoglycerate kinase 2 (PGK2) gene and assigned it to the USDA-MARC linkage map on SSC7 position 77.5 cM closely linked to markers SW859 (76.3 cM) and SWR2036 (79.0 cM). In a panel of 344 in iduals representing 11 pig breeds (European, Chinese, and North American), a total of 32 alleles were observed, and the overall breeds' calculated PIC (polymorphism information content), HE (heterozygosity), and NE (effective allele number) were 0.94, 0.94, and 16.41. Breed-specific PIC and HE ranged from 0.66 to 0.87, whereas NE was as low as 2.95 and as high as 7.96. Considering the high allelic variation of S0719 within and among pig breeds (79% of the genotyped animals were heterozygous), the marker is useful for in idual animal identification and parentage determination. Finally, S0719 is also a valuable STS marker for fine-mapping QTL on SSC7 as position 77.5 cM is located in 25 QTL intervals.
Publisher: Wiley
Date: 30-08-2006
Publisher: Wiley
Date: 27-12-2017
DOI: 10.1111/CEA.12841
Publisher: Springer Science and Business Media LLC
Date: 12-2004
DOI: 10.1007/S00335-004-2405-1
Abstract: We have isolated and characterized the porcine testis-specific phosphoglycerate kinase 2 (PGK2) gene, and 1665 bp of full-length PGK2 cDNA were also compiled using modified rapid lification 5'-RACE and 3'-RACE information. The results of genomic and cDNA sequences of the porcine PGK2 gene demonstrated that it is a single-exon intronless gene with a complete open reading frame of 1251 bp encoding a PGK protein of 417 amino acids. Real-time quantitative PCR results showed that PGK2 mRNA was solely expressed in the testis. There was a lower amount of PGK2 expression in the testis of a 10-month-old herniated boar and a very small amount of PGK2 expression in the testis of an 8-week-old cryptorchid piglet compared to an adult boar. Two SNPs in the PGK2 gene (SNP-A: T427C SNP-B: C914A) resulting in amino acid substitutions (SNP-A: Ser102-Pro102 SNP-B: Thr264-Lys264) were detected and genotyped among six pig breeds. The nucleotide C at SNP-A responsible for the amino acid exchange to proline could lead to the loss of a casein kinase II (CK2) phosphorylation site in the PGK2 peptide. Association analyses between PGK2 genotypes and several traits of sperm quantity and quality were performed. The results showed that SNP-B has a positive significant effect on semen volume in the breed Pietrain (p = 0.08), i.e., boars carrying genotype CC revealed an increased volume of 49 ml compared with boars having the genotype AA.
Publisher: Springer Science and Business Media LLC
Date: 31-05-2021
DOI: 10.1007/S00122-021-03865-4
Abstract: Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For ex le, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.
Publisher: Ivyspring International Publisher
Date: 2007
DOI: 10.7150/IJBS.3.153
Abstract: The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.
Publisher: Elsevier BV
Date: 03-2006
Publisher: Wiley
Date: 20-09-2016
DOI: 10.1111/CEA.12795
Abstract: Air pollution can have adverse health effects on asthma sufferers, but the effects vary with geographic, environmental and population characteristics. There has been no long time-series study in Australia to quantify the effects of environmental factors including pollen on asthma hospitalizations. This study aimed to assess the seasonal impact of air pollutants and aeroallergens on the risk of asthma hospital admissions for adults and children in Adelaide, South Australia. Data on hospital admissions, meteorological conditions, air quality and pollen counts for the period 2003-2013 were sourced. Time-series analysis and case-crossover analysis were used to assess the short-term effects of air pollution on asthma hospitalizations. For the time-series analysis, generalized log-linear quasi-Poisson and negative binomial regressions were used to assess the relationships, controlling for seasonality and long-term trends using flexible spline functions. For the case-crossover analysis, conditional logistic regression was used to compute the effect estimates with time-stratified referent selection strategies. A total of 36,024 asthma admissions were considered. Findings indicated that the largest effects on asthma admissions related to PM Findings suggest that children are more vulnerable and the associations between exposure to air pollutants and asthma hospitalizations tended to be stronger in the cool season compared to the warm season, with the exception of ozone. This study has important public health implications and provides valuable evidence for the development of policies for asthma management.
Publisher: Springer Science and Business Media LLC
Date: 2001
DOI: 10.1007/BF03187010
Publisher: Frontiers Media SA
Date: 04-09-2020
Publisher: Cold Spring Harbor Laboratory
Date: 04-03-2020
DOI: 10.1101/2020.03.04.976324
Abstract: The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact breeding had on the genetic ersity of barley released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic ersity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a erse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined dataset and germplasm collection provide a rich source of genetic ersity that can be applied to understanding and improving environmental adaptation and enhanced yields. Today’s gene pool of crop genetic ersity has been shaped during domestication and more recently by breeding. Genetic ersity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic ersity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties. Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic ersity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive ersity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.
Publisher: Elsevier BV
Date: 02-2021
Publisher: Elsevier BV
Date: 08-2004
Publisher: Oxford University Press (OUP)
Date: 27-08-2019
DOI: 10.1093/JXB/ERZ332
Abstract: Using gene-set association test and epistasis analysis, this research achieved higher statistical power with potentially high accuracy, and detected significant genes and gene networks that influence flowering time in barley.
Publisher: Wiley
Date: 15-08-2021
DOI: 10.1002/TPG2.20129
Abstract: Powdery mildew isa major disease of barley ( Hordeum vulgare L.) for which breeders have traditionally relied on dominant, pathogen race‐specific resistance genes for genetic control. Directional selection pressures in extensive monocultures invariably result in such genes being overcome as the pathogen mutates to evade recognition. This has led to a widespread reliance on fungicides and a single broad‐spectrum recessive resistance provided by the mlo gene. The range of resistance genes and alleles found in wild crop relatives and landraces has been reduced in agricultural cultivars through an erosion of genetic ersity during domestication and selective breeding. Three novel major‐effect adult plant resistance (APR) genes from landraces, designated R esistance to B lumeria g raminis f. sp. h ordei ( Rbgh1 to Rbgh3 ), were identified in the terminal regions of barley chromosomes 5HL, 7HS, and 1HS, respectively. The phenotype of the new APR genes showed neither pronounced penetration resistance, nor the spontaneous necrosis and mesophyll cell death typical of mlo resistance, nor a whole epidermal cell hypersensitive response, typical of race‐specific resistance. Instead, resistance was localized to the site of attempted penetration in an epidermal cell and was associated with cell wall appositions and cytosolic vesicle‐like bodies, and lacked strong induction of reactive oxygen species. The APR genes exhibited differences in vesicle‐like body sizes, their distribution, and the extent of localized 3,3‐diaminobenzidine staining in in idual doubled haploid lines. The results revealed a set of unique basal penetration resistance genes that offer opportunities for combining different resistance mechanisms in breeding programs for robust mildew resistance.
Publisher: Frontiers Media SA
Date: 13-05-2022
Abstract: Heat stress is a primary constraint to Australia's barley production. In addition to impacting grain yield, it adversely affects physical grain quality (weight and plumpness) and market value. The incidence of heat stress during grain filling is rising with global warming. However, breeding for new superior heat-tolerant genotypes has been challenging due to the narrow window of sensitivity, the unpredictable nature of heat stress, and its frequent co-occurrence with drought stress. Greater scientific knowledge regarding traits and mechanisms associated with heat tolerance would help develop more efficient selection methods. Our objective was to assess 157 barley varieties of contrasting genetic backgrounds for various developmental, agro-morphological, and physiological traits to examine the effects of heat stress on physical grain quality. Delayed sowing (i.e., July and August) increased the likelihood of daytime temperatures above 30°C during grain-filling. Supplementary irrigation of field trials ensured a reduced impact of drought stress. Heat tolerance appeared to be the primary factor determining grain plumpness. A wide variation was observed for heat tolerance, particularly among the Australian varieties. Genotypic variation was also observed for grain weight, plumpness, grain growth components, stay-green and stem water-soluble carbohydrates (WSC) content, and mobilisation under normal and delayed sown conditions. Compared to normal sowing, delayed sowing reduced duration of developmental phases, plant height, leaf size, head length, head weight, grain number, plumpness, grain width and thickness, stem WSC content, green leaf area retention, and harvest index (HI), and increased screenings, grain length, grain-filling rate (GFR), WSC mobilisation efficiency (WSCME), and grain protein content. Overall, genotypes with heavier and plumper grains under high temperatures had higher GFR, longer grain-filling duration, longer green leaf area retention, higher WSCME, taller stature, smaller leaf size, greater HI, higher grain weight lumpness potentials, and earlier flowering. GFR played a significant role in determining barley grain weight and plumpness under heat-stress conditions. Enhancing GFR may provide a new avenue for improving heat tolerance in barley.
Location: Germany
Location: Australia
No related grants have been discovered for KEFEI CHEN.