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  1. Artikel ; Online: New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum.

    Honghai Yan / Zichao Ren / Di Deng / Kehan Yang / Chuang Yang / Pingping Zhou / Charlene P Wight / Changzhong Ren / Yuanying Peng

    PLoS ONE, Vol 16, Iss 1, p e

    2021  Band 0240703

    Abstract: The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA ... ...

    Abstract The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids

    Robert G. Latta / Wubishet A. Bekele / Charlene P. Wight / Nicholas A. Tinker

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Band 12

    Abstract: Abstract The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A ...

    Abstract Abstract The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oats. These maps greatly improve coverage from older marker systems. Seven linkage groups in the tetraploid showed much stronger homology and synteny with the A genome diploids than did the other seven, implying an allopolyploid hybrid origin of A. barbata from distinct A and B genome diploid ancestors. Inferred homeologies within A. barbata revealed that the A and B genomes are differentiated by several translocations between chromosomes within each subgenome. However, no translocation exchanges were observed between A and B genomes. Comparison to a consensus map of ACD hexaploid A. sativa (2n = 42) revealed that the A and D genomes of A. sativa show parallel rearrangements when compared to the A genomes of the diploids and tetraploids. While intergenomic translocations are well known in polyploid Avena, our results are most parsimoniously explained if translocations also occurred in the A, B and D genome diploid ancestors of polyploid Avena.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2019-08-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement

    Nicholas A. Tinker / Charlene P. Wight / Wubishet A. Bekele / Weikai Yan / Eric N. Jellen / Nikos Tsardakas Renhuldt / Nick Sirijovski / Thomas Lux / Manuel Spannagl / Martin Mascher

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Band 11

    Abstract: Tinker et al. identified the position and effects of major QTLs relative to a new fully annotated reference genome in five recombinant inbred line populations representing nine diverse oat (Avena sativa) varieties. They also characterized two major ... ...

    Abstract Tinker et al. identified the position and effects of major QTLs relative to a new fully annotated reference genome in five recombinant inbred line populations representing nine diverse oat (Avena sativa) varieties. They also characterized two major chromosome rearrangements that may impact breeding targets affected by QTL that are located in these regions.
    Schlagwörter Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2022-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel: Haplotype‐based genotyping‐by‐sequencing in oat genome research

    Bekele, Wubishet A / Catherine J. Howarth / Charlene P. Wight / Nicholas A. Tinker / Shiaoman Chao

    Plant biotechnology journal. 2018 Aug., v. 16, no. 8

    2018  

    Abstract: In a de novo genotyping‐by‐sequencing (GBS) analysis of short, 64‐base tag‐level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag‐level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat ... ...

    Abstract In a de novo genotyping‐by‐sequencing (GBS) analysis of short, 64‐base tag‐level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag‐level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635‐line diversity panel were used to infer chromosome‐level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high‐resolution genome analysis and genomic selection in oats. A combined genome‐wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component‐based genome‐wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS‐derived markers facilitate genome analysis and genomic selection in oat.
    Schlagwörter Avena sativa ; chromosome mapping ; genes ; genetic markers ; genetic variation ; genome-wide association study ; genomics ; genotyping by sequencing ; haplotypes ; loci ; marker-assisted selection ; oats ; prediction ; sequence analysis ; single nucleotide polymorphism
    Sprache Englisch
    Erscheinungsverlauf 2018-08
    Umfang p. 1452-1463.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 2136367-5
    ISSN 1467-7652 ; 1467-7644
    ISSN (online) 1467-7652
    ISSN 1467-7644
    DOI 10.1111/pbi.12888
    Datenquelle NAL Katalog (AGRICOLA)

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  5. Artikel ; Online: Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat.

    Yung-Fen Huang / Jesse A Poland / Charlene P Wight / Eric W Jackson / Nicholas A Tinker

    PLoS ONE, Vol 9, Iss 7, p e

    2014  Band 102448

    Abstract: Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those ... ...

    Abstract Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 590
    Sprache Englisch
    Erscheinungsdatum 2014-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel: High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

    Yan, Honghai / Axel Diederichsen / Brian Boyle / Catherine J. Howarth / Charlene P. Wight / Eric N. Jellen / Nicholas A. Tinker / Robert G. Latta / Tim Langdon / Wubishet A. Bekele / Yong-Bi Fu / Yuanying Peng / Yuming Wei

    Theoretical and applied genetics. 2016 Nov., v. 129, no. 11

    2016  

    Abstract: KEY MESSAGE : Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena ... ...

    Abstract KEY MESSAGE : Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.
    Schlagwörter chromosome mapping ; chromosome translocation ; chromosomes ; diploidy ; genetic markers ; genome ; haplotypes ; hexaploidy ; oats ; phylogeny ; prediction ; sequence analysis ; tetraploidy
    Sprache Englisch
    Erscheinungsverlauf 2016-11
    Umfang p. 2133-2149.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ZDB-ID 2170-2
    ISSN 1432-2242 ; 0040-5752
    ISSN (online) 1432-2242
    ISSN 0040-5752
    DOI 10.1007/s00122-016-2762-7
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  7. Artikel ; Online: Correction

    Rebekah E. Oliver / Nicholas A. Tinker / Gerard R. Lazo / Shiaoman Chao / Eric N. Jellen / Martin L. Carson / Howard W. Rines / Donald E. Obert / Joseph D. Lutz / Irene Shackelford / Abraham B. Korol / Charlene P. Wight / Kyle M. Gardner / Jiro Hattori / Aaron D. Beattie / Åsmund Bjørnstad / J. Michael Bonman / Jean-Luc Jannink / Mark E. Sorrells /
    Gina L. Brown-Guedira / Jennifer W. Mitchell Fetch / Stephen A. Harrison / Catherine J. Howarth / Amir Ibrahim / Frederic L. Kolb / Michael S. McMullen / J. Paul Murphy / Herbert W. Ohm / Brian G. Rossnagel / Weikai Yan / Kelci J. Miclaus / Jordan Hiller / Peter J. Maughan / Rachel R. Redman Hulse / Joseph M. Anderson / Emir Islamovic / Eric W. Jackson

    PLoS ONE, Vol 8, Iss

    SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species.

    2013  Band 10

    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2013-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
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  8. Artikel ; Online: SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    Rebekah E Oliver / Nicholas A Tinker / Gerard R Lazo / Shiaoman Chao / Eric N Jellen / Martin L Carson / Howard W Rines / Donald E Obert / Joseph D Lutz / Irene Shackelford / Abraham B Korol / Charlene P Wight / Kyle M Gardner / Jiro Hattori / Aaron D Beattie / Åsmund Bjørnstad / J Michael Bonman / Jean-Luc Jannink / Mark E Sorrells /
    Gina L Brown-Guedira / Jennifer W Mitchell Fetch / Stephen A Harrison / Catherine J Howarth / Amir Ibrahim / Frederic L Kolb / Michael S McMullen / J Paul Murphy / Herbert W Ohm / Brian G Rossnagel / Weikai Yan / Kelci J Miclaus / Jordan Hiller / Peter J Maughan / Rachel R Redman Hulse / Joseph M Anderson / Emir Islamovic / Eric W Jackson

    PLoS ONE, Vol 8, Iss 3, p e

    2013  Band 58068

    Abstract: A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular ... ...

    Abstract A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2013-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Correction

    Rebekah E. Oliver / Nicholas A. Tinker / Gerard R. Lazo / Shiaoman Chao / Eric N. Jellen / Martin L. Carson / Howard W. Rines / Donald E. Obert / Joseph D. Lutz / Irene Shackelford / Abraham B. Korol / Charlene P. Wight / Kyle M. Gardner / Jiro Hattori / Aaron D. Beattie / Åsmund Bjørnstad / J. Michael Bonman / Jean-Luc Jannink / Mark E. Sorrells /
    Gina L. Brown-Guedira / Jennifer W. Mitchell Fetch / Stephen A. Harrison / Catherine J. Howarth / Amir Ibrahim / Frederic L. Kolb / Michael S. McMullen / J. Paul Murphy / Herbert W. Ohm / Brian G. Rossnagel / Weikai Yan / Kelci J. Miclaus / Jordan Hiller / Peter J. Maughan / Rachel R. Redman Hulse / Joseph M. Anderson / Emir Islamovic / Eric W. Jackson

    PLoS ONE, Vol 8, Iss

    SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

    2013  Band 10

    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2013-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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