Plant Biotechnology Journal · 2014 · 69 citations · 62 references
AgriculturePlant BiologyPlant SciencesPlant BiotechnologyPlant GeneticsSeed BiotechnologyAgrobacterium-mediated TransformationCrop NutritionNutritional EnhancementNutritional Trait AssessmentSeed Nutritional CompositionSeed ProteomicsGrain Protein ContentLinoleic Acid ContentOleic Acid ContentOleic Acid EnhancementPhenotypic Characterization Of Transgenic CropsPhenotypic Characterization Of TransgenicsSeed Fatty Acid CompositionTransgenic Yield Traits
Transgenic soya bean (Glycine max) plants overexpressing a seed-specific bacterial phytoene synthase gene from Pantoea ananatis modified to target to plastids accumulated 845 μg β carotene g(-1) dry seed weight with a desirable 12:1 ratio of β to α. The β carotene accumulating seeds exhibited a shift in oil composition increasing oleic acid with a concomitant decrease in linoleic acid and an increase in seed protein content by at least 4% (w/w). Elevated β-carotene accumulating soya bean cotyledons contain 40% the amount of abscisic acid compared to nontransgenic cotyledons. Proteomic and nontargeted metabolomic analysis of the mid-maturation β-carotene cotyledons compared to the nontransgenic did not reveal any significant differences that would account for the altered phenotypes of both elevated oleate and protein content. Transcriptomic analysis, confirmed by RT-PCR, revealed a number of significant differences in ABA-responsive transcripton factor gene expression in the crtB transgenics compared to nontransgenic cotyledons of the same maturation stage. The altered seed composition traits seem to be attributed to altered ABA hormone levels varying transcription factor expression. The elevated β-carotene, oleic acid and protein traits in the β-carotene soya beans confer a substantial additive nutritional quality to soya beans.
62
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell, Lior Pachter, Steven L. Salzberg · Bioinformatics · 2009 · 12.1K citations · Full text
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
Fran Supek, Matko Bošnjak, Nives Škunca et al. · PLoS ONE · 2011 · 7K citations · Full text