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Authors = Stéphane Deschamps

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30 pages, 1368 KiB  
Review
Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement
by Yuzhao Hu, Linkan Dash, Gregory May, Nagesh Sardesai and Stéphane Deschamps
Plants 2024, 13(24), 3476; https://doi.org/10.3390/plants13243476 - 11 Dec 2024
Viewed by 2632
Abstract
Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial [...] Read more.
Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial role in the coordinated response of an organism to its environment. Single-cell transcriptomics enables the dissection of this heterogeneity, offering insights into the cell-specific transcriptomic responses of plants to various environmental stimuli. Spatial transcriptomics technologies complement single-cell approaches by preserving the spatial context of gene expression profiles, allowing for the in situ localization of transcripts. Together, single-cell and spatial transcriptomics facilitate the discovery of novel genes and gene regulatory networks that can be targeted for genetic manipulation and breeding strategies aimed at enhancing crop yield, quality, and resilience. This review highlights significant findings from recent studies, discusses the expanding roles of these technologies, and explores future opportunities for their application in crop improvement. Full article
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24 pages, 358 KiB  
Review
Genotyping-by-Sequencing in Plants
by Stéphane Deschamps, Victor Llaca and Gregory D. May
Biology 2012, 1(3), 460-483; https://doi.org/10.3390/biology1030460 - 25 Sep 2012
Cited by 252 | Viewed by 31878
Abstract
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is [...] Read more.
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application. Full article
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)
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