Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs

Numerous quantitative trait loci (QTLs) 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 QTLs requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTLs mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTLs mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTLs 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 QTLs were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTLs were used to estimate standard deviations (ô) of independently mapped QTLs projected onto the Ae. tauschii genome sequence. The standard deviations ô 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 QTLs. The hypothesis tests and estimation procedure for were implemented in a web portal for meta-analysis of projected QTLs. Twenty-one QTLs 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.

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