Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

SF Zanini, PE Bayer, R Wells, RJ Snowdon… - The plant …, 2022 - Wiley Online Library
regulatory elements for crop improvement Mounting evidence supports the importance of
regulatory region variation for crop improvement. … variation in putative regulatory elements and …

Lessons from domestication: targeting cis-regulatory elements for crop improvement

G Swinnen, A Goossens, L Pauwels - Trends in plant science, 2016 - cell.com
… For over ten millennia, the domestication of our crops relied only on human selection (…
crop species was followed by the acquisition of improvement traits that are variable among crop

[HTML][HTML] Engineering quantitative trait variation for crop improvement by genome editing

D Rodríguez-Leal, ZH Lemmon, J Man, ME Bartlett… - Cell, 2017 - cell.com
… animal evolution and domestication, cis-regulatory variants are far from saturated and thus
… -regulatory alleles has also precluded a deeper understanding of how regulatory changes …

Exploiting induced and natural epigenetic variation for crop improvement

NM Springer, RJ Schmitz - Nature reviews genetics, 2017 - nature.com
… for creating novel epiallelic variants by alteration of DNA methylation or other chromatin
modifications. These tools can be used for crop improvement through epigenome engineering. …

Epigenetics and crop improvement

NM Springer - Trends in genetics, 2013 - cell.com
crop improvement strategies including the selection for favorable epigenetic states, creation
of novel epialleles, and regulation … the epigenetic variant conferred an improved phenotype. …

[HTML][HTML] CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

S Saeed, B Usman, SH Shim, SU Khan, S Nizamuddin… - Plant Science, 2022 - Elsevier
… CRE variants for the regulation of complex quantitative traits. … the domestication of natural
CRE variants to regulate complex … CREs for transcriptional regulation for crop improvement. …

Challenges of translating gene regulatory information into agronomic improvements

N Springer, N de León, E Grotewold - Trends in plant science, 2019 - cell.com
… mapping analyses to predict regulatory interactions that impact crop improvement. It is …
differences in how regulatory variants were uncovered. An improved understanding of the …

Natural and induced epigenetic variation for crop improvement

M Lieberman-Lazarovich, E Kaiserli, E Bucher… - Current Opinion in Plant …, 2022 - Elsevier
… categorizes the germplasm into five morphological variants. Although variation in DNA …
our knowledge there's currently no regulation on epigenetically modified crops in the world, …

Major impacts of widespread structural variation on gene expression and crop improvement in tomato

M Alonge, X Wang, M Benoit, S Soyk, L Pereira… - Cell, 2020 - cell.com
… Structural variants (SVs) underlie important crop improvement and domestication traits. …
Compared to SNPs, SVs can cause large-scale perturbations of cis-regulatory regions and are …

Genetic approaches to crop improvement: responding to environmental and population changes

S Takeda, M Matsuoka - Nature Reviews Genetics, 2008 - nature.com
variants of interest and putting these to practical use in crop … key regulatory mechanism that
influences two aspects of crop … same regulatory mechanism operates in other crop species, …