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Title: A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis

Abstract

C4 photosynthesis is used by only three percent of all flowering plants, but explains a quarter of global primary production, including some of the worlds’ most important cereals and bioenergy grasses. Recent advances in our understanding of C4 development can be attributed to the application of comparative transcriptomics approaches that has been fueled by high throughput sequencing. Global surveys of gene expression conducted between different developmental stages or on phylogenetically closely related C3 and C4 species are providing new insights into C4 function, development and evolution. Importantly, through co-expression analysis and comparative genomics, these studies help define novel candidate genes that transcend traditional genetic screens. In this review, we briefly summarize the major findings from recent transcriptomic studies, compare and contrast these studies to summarize emerging consensus, and suggest new approaches to exploit the data. Lastly, we suggest using Setaria viridis as a model system to relieve a major bottleneck in genetic studies of C4 photosynthesis, and discuss the challenges and new opportunities for future comparative transcriptomic studies.

Authors:
ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1247069
Alternate Identifier(s):
OSTI ID: 1437230
Grant/Contract Number:  
SC0008769
Resource Type:
Published Article
Journal Name:
Current Opinion in Plant Biology
Additional Journal Information:
Journal Name: Current Opinion in Plant Biology Journal Volume: 31 Journal Issue: C; Journal ID: ISSN 1369-5266
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Huang, Pu, and Brutnell, Thomas P. A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis. United Kingdom: N. p., 2016. Web. doi:10.1016/j.pbi.2016.03.014.
Huang, Pu, & Brutnell, Thomas P. A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis. United Kingdom. doi:10.1016/j.pbi.2016.03.014.
Huang, Pu, and Brutnell, Thomas P. Wed . "A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis". United Kingdom. doi:10.1016/j.pbi.2016.03.014.
@article{osti_1247069,
title = {A synthesis of transcriptomic surveys to dissect the genetic basis of C4 photosynthesis},
author = {Huang, Pu and Brutnell, Thomas P.},
abstractNote = {C4 photosynthesis is used by only three percent of all flowering plants, but explains a quarter of global primary production, including some of the worlds’ most important cereals and bioenergy grasses. Recent advances in our understanding of C4 development can be attributed to the application of comparative transcriptomics approaches that has been fueled by high throughput sequencing. Global surveys of gene expression conducted between different developmental stages or on phylogenetically closely related C3 and C4 species are providing new insights into C4 function, development and evolution. Importantly, through co-expression analysis and comparative genomics, these studies help define novel candidate genes that transcend traditional genetic screens. In this review, we briefly summarize the major findings from recent transcriptomic studies, compare and contrast these studies to summarize emerging consensus, and suggest new approaches to exploit the data. Lastly, we suggest using Setaria viridis as a model system to relieve a major bottleneck in genetic studies of C4 photosynthesis, and discuss the challenges and new opportunities for future comparative transcriptomic studies.},
doi = {10.1016/j.pbi.2016.03.014},
journal = {Current Opinion in Plant Biology},
number = C,
volume = 31,
place = {United Kingdom},
year = {2016},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1016/j.pbi.2016.03.014

Citation Metrics:
Cited by: 9 works
Citation information provided by
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Works referencing / citing this record:

Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
journal, January 2017

  • Denton, Alisandra K.; Maß, Janina; Külahoglu, Canan
  • Journal of Experimental Botany, Vol. 68, Issue 2
  • DOI: 10.1093/jxb/erw463

Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data
journal, January 2017

  • Denton, Alisandra K.; Maß, Janina; Külahoglu, Canan
  • Journal of Experimental Botany, Vol. 68, Issue 2
  • DOI: 10.1093/jxb/erw463