Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 501414
Title Orphan Crops Browser : a bridge between model and orphan crops
Author(s) Kamei, Claire Lessa Alvim; Severing, E.I.; Dechesne, Annemarie; Furrer, Heleen; Dolstra, Oene; Trindade, L.M.
Source Molecular Breeding 36 (2016)1. - ISSN 1380-3743 - p. 1 - 18.
DOI https://doi.org/10.1007/s11032-015-0430-2
Department(s) Laboratory of Plant Breeding
WUR PB Biobased Economy
WUR Plant Breeding
PBR Biobased Economy
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) Bioinformatics tool - Breeding targets - De novo transcriptome - Orphan crops - Orthologous genes
Abstract

Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information. Our goal was to develop a tool that enables molecular breeders, without extensive bioinformatics knowledge, to efficiently study de novo transcriptome data from any orphan crop (http://www.bioinformatics.nl/denovobrowser/db/species/index). The Orphan Crops Browser has been designed to facilitate the following tasks (1) search and identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data from a set of related species and (2) design specific and degenerate primers for expression studies in the orphan crop of interest. To demonstrate the usability and reliability of the browser, it was used to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis. Expression studies in miscanthus stem internode tissue differing in maturation were subsequently carried out, to follow the expression of these genes during lignification. Our results showed a negative correlation between lignin content and gene expression. The present data are in agreement with recent findings in maize and other crops, and it is further discussed in this paper.

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