Graph Pangenomes Track Genetic Variants for Crop Improvement

Hameed, Amir; Poznanski, Pawel; Nadolska‐Orczyk, Anna; Orczyk, Wacław

doi:10.3390/ijms232113420

Cited by 1 publication

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References 52 publications

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“…Recently, several African orphan crops have had their genome sequenced (reviewed in Ghazal et al., 2021), which provides opportunities to perform pangenomic analyses to further understand the domestication history and support genome‐assisted breeding of these African orphan crops. With the development of more whole genome comparative algorithms (Kille et al., 2022), graph‐genome‐based mapping (Siren et al., 2021), and downstream analysis tools (Liao et al., 2022), we could soon be able to get accurate multi‐alignment results of whole genomes, identify more complex sequence variations such as transposable elements (TEs) and nested SVs, and use pan‐reference genomes to update traditional bioinformatics pipelines for different omics (for the further application of graph pangenomes in crop improvement, please also refer to Hameed et al., 2022, Wang et al., 2022b, Zanini et al., 2022). By then, pangenomic analysis could help us better understand the evolution of different plants, the origin of new genes, and the molecular basis of complex phenotype variations.…”

Section: Plant Pangenomesmentioning

confidence: 99%

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

et al. 2023

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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.

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