The Experts below are selected from a list of 15843 Experts worldwide ranked by ideXlab platform
P M Hayes - One of the best experts on this subject based on the ideXlab platform.
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Background Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL).
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL). Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) Mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic Map was constructed. The assembled RAD-only Map consists of 445 markers with an average interval length of 5 cM, while an integrated Map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total Map lengths are comparable and the order of common markers is identical in both Maps. The same large-effect QTL for reproductive fitness traits were detected with both Maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage Maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic Maps and association Mapping.
Yada Chutimanitsakun - One of the best experts on this subject based on the ideXlab platform.
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Background Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL).
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL). Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) Mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic Map was constructed. The assembled RAD-only Map consists of 445 markers with an average interval length of 5 cM, while an integrated Map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total Map lengths are comparable and the order of common markers is identical in both Maps. The same large-effect QTL for reproductive fitness traits were detected with both Maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage Maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic Maps and association Mapping.
Elena Hidalgo - One of the best experts on this subject based on the ideXlab platform.
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phosphorylation of the transcription factor atf1 at multiple sites by the Map kinase sty1 controls homologous recombination and transcription
Journal of Molecular Biology, 2020Co-Authors: Laura Sanchezmir, Jose Ayte, Rodrigo Fraile, Elena HidalgoAbstract:Transcription factors are often the downstream effectors of signaling cascades. In fission yeast, the transcription factor Atf1 is phosphorylated by the Map kinase Sty1 under several environmental stressors to promote transcription initiation of stress genes. However, Sty1 and Atf1 have also been involved in other cellular processes such as homologous recombination at hotspots, ste11 gene expression during mating and meiosis, or regulation of fbp1 gene transcription under glucose starvation conditions. Using different phospho-mutants of Atf1, we have investigated the role of Atf1 phosphorylation by Sty1 in those biological processes. An Atf1 mutant lacking the Canonical Map kinase phosphorylation sites cannot activate fbp1 transcription when glucose is depleted, but it is still able to induce recombination at ade6.M26 and to induce ste11 after nitrogen depletion; in these last cases, Sty1 is still required, suggesting that additional non-Canonical sites are activating the transcription factor. In all cases, an Atf1 phosphomimetic mutant bypasses the requirement of the Sty1 kinase in these diverse biological processes, highlighting the essential role of the DNA binding factor Atf1 on chromatin remodeling and cell adaptation to nutritional changes. We propose that post-translational modifications of Atf1 by Sty1, either at Canonical or non-Canonical sites, are sufficient to activate some of the functions of Atf1, those involving chromatin remodeling and transcription initiation. However, in the case of fbp1 where Atf1 acts synergistically with other transcription factors, elimination of the Canonical sites is sufficient to hamper some of the interactions required in this complex scenario and to impair transcription initiation.
Rick Nipper - One of the best experts on this subject based on the ideXlab platform.
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Background Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL).
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL). Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) Mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic Map was constructed. The assembled RAD-only Map consists of 445 markers with an average interval length of 5 cM, while an integrated Map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total Map lengths are comparable and the order of common markers is identical in both Maps. The same large-effect QTL for reproductive fitness traits were detected with both Maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage Maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic Maps and association Mapping.
L Cistue - One of the best experts on this subject based on the ideXlab platform.
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Background Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL).
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construction and application for qtl analysis of a restriction site associated dna rad linkage Map in barley
BMC Genomics, 2011Co-Authors: Yada Chutimanitsakun, Eric A Johnson, Rick Nipper, Alfonso Cuestamarcos, L Cistue, Ann Corey, T Filichkina, P M HayesAbstract:Linkage Maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical Map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected Mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage Map construction, employing barley as a model system. Using the published high density EST-based SNP Map in the Oregon Wolfe Barley (OWB) Mapping population as a reference, we created a RAD Map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both Maps for detection of quantitative trait loci (QTL). Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) Mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic Map was constructed. The assembled RAD-only Map consists of 445 markers with an average interval length of 5 cM, while an integrated Map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the Hordeum genome. Total Map lengths are comparable and the order of common markers is identical in both Maps. The same large-effect QTL for reproductive fitness traits were detected with both Maps and the majority of these QTL were coincident with a dwarfing gene (ZEO) and the VRS1 gene, which determines the two-row and six-row germplasm groups of barley. We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage Maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in de novo genome assembly, development of ultra-high density genetic Maps and association Mapping.