Nature Precedings, "a platform for sharing new and preliminary findings with colleagues on a global scale," has published a short article by Gramene staff scientist Charles Chen entitled "The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species".

Gramene users might be interested in the paper “Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines”, by S. Atwell et al., published in Nature, March 24, 2010.

Two recent papers have cited Gramene. In 2009, Yamamoto et al. acknowledged Gramene’s QTL resources in a paper in DNA Research entitled “Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?”, and in 2010, a paper published in BMC Plant Biology entitled “Transcriptional regulatory network triggered by oxidative signals configures the early [...]

The January 14th edition of Nature contains an article describing the whole-genome shotgun sequencing of the soybean genome. It has been “sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly” (Schmutz et al.).

Fahlgren, et al. recently reported an annotation pipeline called  Cache ASsisted Hash Search with Xor logic (CASHX) in the journal RNA (PubMed ID 19307293). The pipeline can map, quantify and manage large quantities of sequence data. The sequence alignments can be done using any size of DNA sequence data for both query sequences and database. [...]

The genome sequencing of Papaya variety called SunUp was reported recently by Ming et al. Nature. 2008 Apr 24;452(7190):991-6 (PMID: 18432245). SunUp was also the first commercial virus-resistant transgenic fruit tree.

The genome (DNA content) of one of the most commonly found ingredient in your salad, the cucumber (Cucumis sativus var. sativus L.), has been sequenced. A report was published in Nature Genetics on November 1, 2009, (PubMed ID 19881527) by the authors Huang, et al., on sequencing the "Chinese long" inbred line 9930 of [...]

Zhang et al. (Plant Phys, Sept 23) report the influence of TLD1/GH3.13 (PlantGeneWiki: GR:0020049) gene on plant architecture and drought tolerance through the isolation of a gain of function rice mutant, tld1-D. TLD1 is a IAA-amido synthetase that conjugates free IAA to amino acids, in turn reducing available free IAA in the plant. Its expression [...]

In a recent report published in the Transgenic Res. 2009 Sep 22., authors Anand and Tyagi, identified a cDNA for the gene encoding the arabinogalactan protein (AGP) . The cDNA (586bp) isolated from the Oryza sativa indica cDNA library was shown to be  expressing preferentially in the inflorescence. The gene is shown to have pollen-specific and [...]

The journal Bioinformatics has published a brief paper on CMap 1.01: A comparative mapping application for the Internet. CMap was originally written for the Gramene project in 2001 and is freely available at the GMOD site.