Genetic determination of stomatal patterning in winter wheat (Triticum aestivum L.), bioRxiv, 2018-12-11

Leaf stomata are microscopic pores mediating plant-environment interactions. Their role in carbon uptake and transpiration make them prime candidates for improving water use efficiency (WUE). Stomatal density (SD), the number of stomata per unit area, has been shown to be negatively correlated with WUE. However, little is known about the genetic basis of SD in wheat (Triticum aestivum L.), and to what extant genetic variation exists in contemporary wheat germplasm. Here, we evaluated stomatal patterning over two growing seasons in a set of 333 wheat lines, representing the European winter wheat germplasm. Stomatal patterning was mainly determined by two underlying traits, the distance between files of stomata and the distance between stomata within a file. By haplotype association mapping, quantitative trait loci for SD were consistently detected in both seasons on wheat chromosomes (CHR) 2A, 3A and 7B. The single nucleotide polymorphism markers most significantly associated with SD coincided with the genes INDUCER OF CBF EXPRESSION 1 (ICE1) and STOMATAL CYTOKINESIS-DEFECTIVE 1 (SCD1) on CHR 3A, and genes involved in ethylene and auxin signaling on CHR 2A and 7B, respectively. Our study unlocks the phenotypic and genotypic variation for stomatal patterning traits in contemporary wheat germplasm. It provides gene targets for functional validation and practical tools to manipulate SD using marker-assisted selection for crop improvement.

biorxiv plant-biology 100-200-users 2018

Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer, bioRxiv, 2018-09-29

ABSTRACTFungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of plant pathogens. Disease outcomes are often defined not only by the main pathogen but are influenced by diverse microbial communities known as the microbiome at sites of infection. Here we present the first use of whole genome shot-gun sequencing with a portable DNA sequencing device as a method for the detection of fungal pathogens from wheat (Triticum aestivum) in a standard molecular biology laboratory. The data revealed that our method is robust and applicable to the diagnosis of fungal diseases including wheat stripe rust (caused by Puccinia striiformis f. sp. tritici), septoria tritici blotch (caused by Zymoseptoria tritici) and yellow leaf spot (caused by Pyrenophora tritici repentis). We also identified the bacterial genus Pseudomonas co-present with Puccinia and Zymoseptoria but not Pyrenophora infections. One limitation of the method is the over-representation of redundant wheat genome sequences from samples. This could be addressed by long-range amplicon-based sequencing approaches in future studies, which specifically target non-host organisms. Our work outlines a new approach for detection of a broad range of plant pathogens and associated microbes using a portable sequencer in a standard laboratory, providing the basis for future development of an on-site disease monitoring system.

biorxiv plant-biology 0-100-users 2018

 

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