Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

Abstract

SUMMARY 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 (http://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.

Editorial: The past, present and future of The Plant Journal Resource Articles

“…The articles also differ with regard to the number of genotypes sequenced with many articles providing high-quality sequence of only a single genotype, while others such as that of (Aflitos et al, 2014) reported the sequencing of up to 1000. In keeping with the expansion of the breadth of sequencing (Gui et al, 2022), the pan-genome of bread wheat is reported in a recent resource article (Montenegro et al, 2017;Zhu et al, 2021).…”

Plant biochemical genetics in the multiomics era

“…1 ). In parallel, the advent and adoption of techniques that can simultaneously determine the levels of hundreds of metabolites ( Fiehn et al , 2000 ; Alseekh and Fernie, 2018 ) alongside the opportunities afforded by next-generation sequencing ( Purugganan and Jackson, 2021 ; Gui et al , 2023 ) have opened up the possibility of evaluating much broader genetic variance, such as that available in advanced breeding populations ( Alseekh et al , 2021 ; Sharwood et al , 2022 ; Bulut et al , 2023 ) and panels of natural variants ( Fang and Luo, 2019 ). Although such populations have been reviewed extensively elsewhere ( Fernie and Klee, 2011 ; Wijnen and Keurentjes, 2014 ), we will briefly describe their development here since they are highly relevant to the following sections.…”

DataPLAN: a web-based data management plan generator for the plant sciences

“…Technologies such as nanopore sequencing [45][46][47] and high-throughput phenotyping [48,49] have increased the rate of data collection. The analysis of such data will provide a deeper understanding of plants leading to the generation of new knowledge and new paths to exploitation.…”