Journal Article

FZJ-2023-01161

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

Gui, S. ; Martinez-Rivas, F. J. ; Wen, W. ; Meng, M. ; Yan, J. ; Usadel, B. (Corresponding author)FZJ* ; Fernie, A. R. (Corresponding author)

2023
Wiley-Blackwell Oxford [u.a.]

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Please use a persistent id in citations: http://hdl.handle.net/2128/33878  doi:10.1111/tpj.16070

Abstract: Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.

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Contributing Institute(s):

1. Bioinformatik (IBG-4)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)

Appears in the scientific report 2023

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Database coverage:
; ; ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; DEAL Wiley ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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