Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

Swinnen, Gwen; Goossens, Alain; Pauwels, Laurens

doi:10.1016/j.tplants.2016.01.014

Cited by 172 publications

(108 citation statements)

References 96 publications

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“…The molecular genetic characterization of the candidate genes, in the model systems rice and Arabidopsis , highlighted transcription factors as major players in shaping the plant morphology and architecture23.…”

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confidence: 99%

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

Francis

Dhaka

Bakshi

et al. 2016

Sci Rep

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Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.

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confidence: 99%

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

Francis

Dhaka

Bakshi

et al. 2016

Sci Rep

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“…While they used transgenics, the 364 modifications used -increased amounts of PsbS, violaxanthin de-epoxidase and 365 zeaxanthin epoxidase -could have occurred naturally. In fact, altering gene expression 366 patterns has been a major route to improving the usefulness of plants for agriculture 367 (Swinnen et al, 2016), either through natural variation in the gene pool of natural 368 ancestors, or through mutations occurring during domestication. Naturally occurring 369 variation in a trait can be used to analyse the genetic architecture of the trait, and this 370 can be used to increase the efficiency of improving the trait by breeding.…”

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confidence: 99%

Fluctuating Light Takes Crop Photosynthesis on a Rollercoaster Ride

2017

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“…Disruption of TF binding sites (TFBS) has been associated with phenotypic diversity, including agriculturally important adaptive traits 1 and various disease states such as cancer 2 . Characterizing the genome-wide binding profiles of individual TFs is essential for identifying the mechanisms underlying these changes.…”

Section: Introductionmentioning

confidence: 99%

Mapping genome-wide transcription-factor binding sites using DAP-seq

Bartlett¹,

O’Malley²,

Huang³

et al. 2017

Nat Protoc

441

285

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In order to enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF) binding site discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than ChIP-seq. DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell-and tissue-specific chemical modifications that are known to impact TF binding (such as DNA methylation) and providing increased specificity compared to in silico motif prediction methods such as protein binding microarrays (PBM) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro expressed TF, and TF-DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be

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Lessons from Domestication: Targeting Cis -Regulatory Elements for Crop Improvement

Cited by 172 publications

References 96 publications

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

Fluctuating Light Takes Crop Photosynthesis on a Rollercoaster Ride

Mapping genome-wide transcription-factor binding sites using DAP-seq

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