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Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs.
G3 (Bethesda). 2019 03 07; 9(3):841-853.G

Abstract

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 ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] 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 [Formula: see text] 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.

Authors+Show Affiliations

Department of Plant Sciences, University of California, Davis, California.Department of Statistics, Iowa State University, Iowa.Department of Plant Sciences, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California. Department of Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran, and.Department of Biology, Concordia University, Montreal, Quebec, Canada.Department of Plant Sciences, University of California, Davis, California.Department of Statistics, University of California, Davis, California.Department of Plant Sciences, University of California, Davis, California, jdvorak@ucdavis.edu.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

30670607

Citation

Xu, Jiale, et al. "Aegilops Tauschii Genome Sequence: a Framework for Meta-analysis of Wheat QTLs." G3 (Bethesda, Md.), vol. 9, no. 3, 2019, pp. 841-853.
Xu J, Dai X, Ramasamy RK, et al. Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs. G3 (Bethesda). 2019;9(3):841-853.
Xu, J., Dai, X., Ramasamy, R. K., Wang, L., Zhu, T., McGuire, P. E., Jorgensen, C. M., Dehghani, H., Gulick, P. J., Luo, M. C., Müller, H. G., & Dvorak, J. (2019). Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs. G3 (Bethesda, Md.), 9(3), 841-853. https://doi.org/10.1534/g3.118.200921
Xu J, et al. Aegilops Tauschii Genome Sequence: a Framework for Meta-analysis of Wheat QTLs. G3 (Bethesda). 2019 03 7;9(3):841-853. PubMed PMID: 30670607.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs. AU - Xu,Jiale, AU - Dai,Xiongtao, AU - Ramasamy,Ramesh K, AU - Wang,Le, AU - Zhu,Tingting, AU - McGuire,Patrick E, AU - Jorgensen,Chad M, AU - Dehghani,Hamid, AU - Gulick,Patrick J, AU - Luo,Ming-Cheng, AU - Müller,Hans-Georg, AU - Dvorak,Jan, Y1 - 2019/03/07/ PY - 2019/1/24/pubmed PY - 2019/7/10/medline PY - 2019/1/24/entrez KW - QTL database KW - QTL distribution KW - Web portal KW - fusarium head blight KW - meta-QTL KW - probability KW - recombination rate SP - 841 EP - 853 JF - G3 (Bethesda, Md.) JO - G3 (Bethesda) VL - 9 IS - 3 N2 - 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 ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] 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 [Formula: see text] 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. SN - 2160-1836 UR - https://www.unboundmedicine.com/medline/citation/30670607/Aegilops_tauschii_Genome_Sequence:_A_Framework_for_Meta_analysis_of_Wheat_QTLs_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/30670607/ DB - PRIME DP - Unbound Medicine ER -