Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs
Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2019-03-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.118.200921 |
| _version_ | 1818886459938045952 |
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| author | Jiale Xu Xiongtao Dai Ramesh K. Ramasamy Le Wang Tingting Zhu Patrick E. McGuire Chad M. Jorgensen Hamid Dehghani Patrick J. Gulick Ming-Cheng Luo Hans-Georg Müller Jan Dvorak |
| author_facet | Jiale Xu Xiongtao Dai Ramesh K. Ramasamy Le Wang Tingting Zhu Patrick E. McGuire Chad M. Jorgensen Hamid Dehghani Patrick J. Gulick Ming-Cheng Luo Hans-Georg Müller Jan Dvorak |
| author_sort | Jiale Xu |
| collection | DOAJ |
| description | Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations (σ ^ ) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations σ ^ were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for σ ^ were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses. |
| first_indexed | 2024-12-19T16:21:41Z |
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| id | doaj.art-c734d37fadf44a4ab9561187ac92b1d3 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-19T16:21:41Z |
| publishDate | 2019-03-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-c734d37fadf44a4ab9561187ac92b1d32022-12-21T20:14:28ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362019-03-019384185310.1534/g3.118.20092121Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLsJiale XuXiongtao DaiRamesh K. RamasamyLe WangTingting ZhuPatrick E. McGuireChad M. JorgensenHamid DehghaniPatrick J. GulickMing-Cheng LuoHans-Georg MüllerJan DvorakNumerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations (σ ^ ) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations σ ^ were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for σ ^ were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.http://g3journal.org/lookup/doi/10.1534/g3.118.200921QTL distributionmeta-QTLQTL databaseprobabilityWeb portalrecombination ratefusarium head blight |
| spellingShingle | Jiale Xu Xiongtao Dai Ramesh K. Ramasamy Le Wang Tingting Zhu Patrick E. McGuire Chad M. Jorgensen Hamid Dehghani Patrick J. Gulick Ming-Cheng Luo Hans-Georg Müller Jan Dvorak Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs G3: Genes, Genomes, Genetics QTL distribution meta-QTL QTL database probability Web portal recombination rate fusarium head blight |
| title | Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs |
| title_full | Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs |
| title_fullStr | Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs |
| title_full_unstemmed | Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs |
| title_short | Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs |
| title_sort | aegilops tauschii genome sequence a framework for meta analysis of wheat qtls |
| topic | QTL distribution meta-QTL QTL database probability Web portal recombination rate fusarium head blight |
| url | http://g3journal.org/lookup/doi/10.1534/g3.118.200921 |
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