Tagged: RNA-Seq



How arbuscular mycorrhizal fungi talk to plants before colonisation

Plant roots do not sit alone in the soil. In the earth you will also find various microbes. Lurking in the dirt is Rhizophagus irregularis, an arbuscular mycorrhizal fungus that colonises wheat. In a new study Hui Tian and colleagues investigated if what happened before a fungus makes contact with the wheat roots. There are over 200 species of arbuscular mycorrhizal fungi in the soil, but Rhizophagus irregularis is a particularly useful fungus to examine, as Dr Tian explained. “We chose the fungi Rhizophagus irregularis because this is the only arbuscular mycorrhizal fungal species whose genome data is available up...

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Dunes

Genotypic differentiation in a heterogeneous dune landscape in Arabidopsis lyrata

The role of fine-scale habitat heterogeneity on within-population genetic divergence is studied in North American Arabidopsis lyrata (Brassicaceae) inhabiting a sand dune landscape. Wos and Willi relate site-of-origin variables of maternal seed families with genotypic trait differentiation and gene expression differences to find traits and genes involved in microhabitat adaptation. Multivariate analysis reveals significant environment–trait associations, between distance from trees, relative dune position and the potential of interspecific competition, and plant size and reproductive phenology. Expression analysis on those associations point to the importance of genes involved in stress responses and senescence in microhabitat adaptation.

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rice

Pelota genes regulate root development and defense responses in rice

Seeds of the grass species rice (Oryza sativa) serve as the most widely consumed staple food especially in Asia. One of its major threats is Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight, which could severely reduce the production. Ding et al. identify a rice mutant of OsPELO, whose counterparts in animals are involved in ribosome rescue and meiotic cell division. The mutant shows impaired root development and spotted-leaf phenotype. Surprisingly, the mutant is highly resistant to several Xoo strains. Further transcriptome analysis attributes the enhanced resistance to the systemic pre-activation of defence response.

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Histological analysis of galls induced by Meloidogyne graminicola in resistant rice (Oryza glaberrima TOG5681) roots.

Rice resistance responses to the root-knot nematode Meloidogyne graminicola

Meloidogyne graminicola is responsible for production losses in rice (Oryza sativa) in Asia and Latin America. Petitot et al. assess the cytological and molecular mechanisms underlying nematode resistance identified in African rice (Oryza glaberrima). Rice resistance responses act at several steps along the nematode life-cycle to limit penetration and feeding site development, preventing efficient nematode reproduction. This study provides a novel set of candidate genes for O. glaberrima resistance to nematodes. This paper is part of the Annals of Botany Special Issue on Plant Immunity. It will be free access till June 2017 and after April 2018.

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Molecular inference for induction of phenylalanine, tryptamine and tyrosine pathways that lead to the production of defence-associated hormones and metabolites in wheat following F. pseudograminearum infection in wheat

Resistance responses triggered by Fusarium crown rot in wheat

Fusarium diseases of cereals constitute economically significant constraints in cereal production systems. In this study, transcriptomic analysis using RNA-seq is combined with metabolite analysis to provide novel insights into the interaction between bread wheat and Fusarium pseudograminearum, the predominant causal agent of Fusarium crown rot. Powell et al. show that wheat responds to infection by producing a barrage of secondary metabolites involved in plant defence and enzymes that may function in detoxifying Fusarium virulence factors such as deoxynivalenol. The discoveries presented here will aid future efforts to improve resistance in cereals against Fusarium pathogens. This paper is part of the...

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Legume genomics and next-generation sequencing (Invited Review)

Legume genomics and next-generation sequencing (Invited Review)

The legume family (Leguminosae) consists of approximately 17 000 species and those used as crops provide protein and carbohydrates for over 300 million people world-wide. O’Rourke et al. review how next-generation sequencing technologies and associated bioinformatic analyses have allowed individual researchers to assemble genomes, identify gene-coding regions and study gene expression patterns. To illustrate the power of next-generation sequencing in elucidating gene networks underlying biological processes, they present two example studies: an analysis of gene expression profiles in soybean oil seed development and an analysis of phosphate deficiency altering gene expression patterns to induce cluster root formation in white lupin.

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Molecular genetics of cuticle formation in Prunus

Molecular genetics of cuticle formation in Prunus

During growth, the fruit surface of sweet cherry, Prunus avium, expands rapidly whilst only a relatively small amount of new cuticular material is produced, often leading to the formation of microscopic cracks in the cuticle that can reduce fruit quality. Alkio et al. perform RNA-Seq and bioinformatic analyses to identify genes expressed in the skin of developing fruit, and relate gene expression with cuticle deposition. The results suggest that downregulation of genes involved in cuticle deposition occurs early in fruit development, and a number of candidate genes are proposed for further investigation.

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