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Depicting the richest source of pathogen linked miscellaneous gene expression in orphan crops by Nanopore.

Project description

Why one pepper crop is resistant to disease

Piper colubrinum, which is used to cure foot rot, is a wild relative of the cultivated species of black pepper, Piper nigrum. While P. colubrinum is resistant to disease, P. nigrum (a valuable spice crop) is not. There is a lack of validated genome sequence data for either species. Also, the exact reason behind the resistance of P. colubrinum is not yet understood. The EU-funded OCNANO project will use the MinION, a portable real-time device for DNA and RNA sequencing, to find answers. Specifically, it will annotate the transcriptomes of both Piper species. It will also use an array-based capture to identify pathogen gene expression during infection. The project will also compare analysis of both P. nigrum and P. colubrinum gene expression during infection.

Objective

Modern agriculture is dominated by crops noticeable for intense food supply leaving behind a class of neglected or orphan crops. Relatively poorly studied orphan crops have the potential to diversify the human diet, increase agricultural food productivity levels and enable more sustainable and resilient agro- and horti-food systems. Here, we focus on two such crops-Piper nigrum (black pepper) the most important spice traded internationally and Piper colubrinum, a wild relative of black pepper introduced from Brazil, which is the only known source of resistance to diseases such as foot rot or quick wilt caused by an Oomycete Phytophthora capsici. Negligible genome sequence data exists for either species. Although agricultural practices for making P. nigrum resistant to this Oomycete by interspecific hybridization with P.colubrinum are well known, no effective strategies have been generated yet. The exact reason behind the resistance of P.colubrinum is not yet understood, thus leaving open a fertile area of investigation.With this background, OCNANO aims to reveal the basis of pathogen resistance that distinguish resistant from susceptible species of Piper. We will employ Oxford nanopore MinION technology to address this issue with three specific objectives:(1) Annotate the transcriptomes of P.nigrum and P. colubrinum; (2) Identify pathogen gene expression during infection using a capture array; (3) Comparative analysis of P. nigrum and P. colubrinum gene expression during infection. Innovative strategies like nanopore in combination with other sequencing approaches can transform annotation and enable the richest understanding of gene expression during pathogen attack. Research progressing towards the rescue of such orphan crops from their environmental stresses, by applying leading edge technologies, can further enhance crop productivity, food security, knowledge based economy and society and contribute to the achievement of several UN Sustainable Development Goals.

Coordinator

UNIVERSITY OF DUNDEE
Net EU contribution
€ 224 933,76
Address
Nethergate
DD1 4HN Dundee
United Kingdom

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Region
Scotland Eastern Scotland Angus and Dundee City
Activity type
Higher or Secondary Education Establishments
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Total cost
€ 224 933,76