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In Print: Last Week's Microarray Papers of Note: Jul 1, 2014


A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.
DNA Res. 2014 Jun 27. [Epub ahead of print]
Iehisa J, et al.

The authors developed a microarray-based polymorphism detection system using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808.Quantitative trait locus analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map.

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study.
Nat Methods. 2014 Jun 29. [Epub ahead of print]
Mestdagh P, et al.

The authors systematically compared 12 commercially available platforms, including Affymetrix and Agilent Technologies microarrays and NanoString Technologies' nCounter assays, for analysis of microRNA expression. They measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA, human serum samples and synthetic spikes from microRNA family members with varying homology. They found that each method has its strengths and weaknesses, and believe their results could guide the informed selection of a quantitative microRNA gene expression platform for specific study goals.

Genomic prediction for rust resistance in diverse wheat landraces.
Theor Appl Genet. 2014 Jun 26. [Epub ahead of print]
Daetwyler H, et al.

In this study, the authors assessed the accuracy of genomic estimated breeding values for rust resistance in 206 hexaploid wheat landraces from the Watkins collection of phenotypically diverse wheat genotypes from 32 countries. The landraces were genotyped for 5,568 SNPs using an Illumina iSelect 9K bead chip assay and phenotyped for field-based leaf rust, stem rust, and stripe rust responses across multiple years. Investigation of the impact of genetic relatedness between validation and reference lines on accuracy of genomic prediction showed that accuracy will be higher when each validation line had at least one close relationship to the reference lines.