Multi‐omics atlas of combinatorial abiotic stress responses in wheat

Letitia Da Ros; Venkatesh Bollina; Raju Soolanayakanahally; Shankar Pahari; Raed Elferjani; Manoj Kulkarni; Neha Vaid; Eddy Risseuw; Dustin Cram; Asher Pasha; Eddi Esteban; David Konkin; Nicholas Provart; Eiji Nambara; Sateesh Kagale

doi:10.1111/tpj.16332

journal article Open Access Jun 28, 2023

Multi‐omics atlas of combinatorial abiotic stress responses in wheat

Letitia Da Ros Venkatesh Bollina Raju Soolanayakanahally

Shankar Pahari Raed Elferjani Manoj Kulkarni Neha Vaid Eddy Risseuw Dustin Cram Asher Pasha Eddi Esteban David Konkin Nicholas Provart

Eiji Nambara

Sateesh Kagale

The Plant Journal Vol. 116 No. 4 pp. 1118-1135 · Wiley

View at Publisher Save 10.1111/tpj.16332

Abstract

SUMMARYField‐grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is required to meet future crop production needs. Here, we employed a systems biology approach in wheat (Triticum aestivum L.) to investigate physio‐metabolic adjustments and transcriptome reprogramming involved in acclimations to heat, drought, salinity and all combinations therein. A significant shift in magnitude and complexity of plant response was evident across stress scenarios based on the agronomic losses, increased proline concentrations and 8.7‐fold increase in unique differentially expressed transcripts (DETs) observed under the triple stress condition. Transcriptome data from all stress treatments were assembled into an online, open access eFP browser for visualizing gene expression during abiotic stress. Weighted gene co‐expression network analysis revealed 152 hub genes of which 32% contained the ethylene‐responsive element binding factor‐associated amphiphilic repression (EAR) transcriptional repression motif. Cross‐referencing against the 31 DETs common to all stress treatments isolated TaWRKY33 as a leading candidate for greater plant tolerance to combinatorial stresses. Integration of our findings with available literature on gene functional characterization allowed us to further suggest flexible gene combinations for future adaptive gene stacking in wheat. Our approach demonstrates the strength of robust multi‐omics‐based data resources for gene discovery in complex environmental conditions. Accessibility of such datasets will promote cross‐validation of candidate genes across studies and aid in accelerating causal gene validation for crop resiliency.

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References

87

[1]

10.3389/fpls.2018.00734

[2]

Acevedo E. (2002)

[3]

10.1038/s41598‐019‐40659‐7

[4]

10.3389/fchem.2017.00121

[5]

10.1016/j.biotechadv.2009.11.005

[6]

10.1038/nclimate2470

[7]

10.1105/tpc.18.00612

[8]

10.2135/cropsci2018.05.0292

[9]

10.1007/s11032‐013‐9847‐7

[10]

10.2135/cropsci2006.05.0286

[11]

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel

Bioinformatics 10.1093/bioinformatics/btu170

[12]

10.1016/j.gene.2011.06.026

[13]

10.1038/s41514‐017‐0013‐z

[14]

10.1007/s42729‐022‐01032‐2

[15]

10.1104/pp.122.3.823

[16]

10.4141/cjps08227

[17]

10.1186/1471‐2229‐10‐47

[18]

10.1104/pp.112.211854

[19]

10.3389/fpls.2018.01224

[20]

10.1080/07352689.2011.615687

[21]

10.1111/jac.12222

[22]

Carbon Isotope Discrimination and Photosynthesis

G D Farquhar, J R Ehleringer, K T Hubick

Annual Review of Plant Physiology and Plant Molecu... 10.1146/annurev.pp.40.060189.002443

[23]

ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web

Geoffrey Fucile, David Di Biase, Hardeep Nahal et al.

PLoS ONE 10.1371/journal.pone.0015237

[24]

10.1093/pcp/pcq036

[25]

10.1111/j.1365‐3040.2007.01726.x

[26]

10.4161/psb.21949

[27]

10.1186/s12870‐016‐0806‐4

[28]

Hoagland D.R. "The water culture method for growing plants without soil" California Agriculture Experimental Station (1950)

[29]

10.1002/bimj.200810425

[30]

10.1104/pp.104.3.881

[31]

10.1126/science.aar7191

[32]

10.1007/s00425‐013‐1880‐6

[33]

10.1104/pp.109.151704

[34]

10.4161/psb.5.6.11576

[35]

10.1016/j.tplants.2006.01.004

[36]

10.4161/psb.26374

[37]

10.1023/a:1002868519779

[38]

10.1016/j.jbiotec.2018.05.008

[39]

10.1007/s11033‐020‐05906‐5

[40]

10.3389/fpls.2017.01151

[41]

10.1186/1471‐2105‐9‐559

[42]

Lenth R. "Emmeans: estimated marginal means. R package version 1.4. 4" The American Statistician (2020)

[43]

10.1186/1471‐2105‐12‐323

[44]

10.1093/jxb/erw193

[45]

10.1186/s12864‐020‐06985‐1

[46]

10.3389/fpls.2018.00521

[47]

10.1186/s12870‐020‐2288‐7

[48]

10.1111/ppl.12483

[49]

10.1134/s0026893313040109

[50]

10.1111/pce.13595

Showing 50 of 87 references

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Citations

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References

Details

Published: Jun 28, 2023
Vol/Issue: 116(4)
Pages: 1118-1135
License: View

Authors

L

Letitia Da Ros

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada; Summerland Research and Development Centre Agriculture and Agri‐Food Canada Summerland British Columbia Canada

V

Venkatesh Bollina

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

R

Raju Soolanayakanahally

Saskatoon Research and Development Centre Agriculture and Agri‐Food Canada Saskatoon Saskatchewan Canada

S

Shankar Pahari

Saskatoon Research and Development Centre Agriculture and Agri‐Food Canada Saskatoon Saskatchewan Canada

R

Raed Elferjani

Saskatoon Research and Development Centre Agriculture and Agri‐Food Canada Saskatoon Saskatchewan Canada

M

Manoj Kulkarni

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

N

Neha Vaid

Department of Biological Sciences University of Calgary Calgary Alberta Canada

E

Eddy Risseuw

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

D

Dustin Cram

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

A

Asher Pasha

Department of Cell and Systems Biology University of Toronto Toronto Ontario Canada

E

Eddi Esteban

Department of Cell and Systems Biology University of Toronto Toronto Ontario Canada

D

David Konkin

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

N

Nicholas Provart

Department of Cell and Systems Biology University of Toronto Toronto Ontario Canada

E

Eiji Nambara

Department of Cell and Systems Biology University of Toronto Toronto Ontario Canada

S

Sateesh Kagale

Aquatic and Crop Resource Development National Research Council Canada Saskatoon Saskatchewan Canada

Funding

Natural Sciences and Engineering Research Council of Canada

Cite This Article

Letitia Da Ros, Venkatesh Bollina, Raju Soolanayakanahally, et al. (2023). Multi‐omics atlas of combinatorial abiotic stress responses in wheat. The Plant Journal, 116(4), 1118-1135. https://doi.org/10.1111/tpj.16332

Multi‐omics atlas of combinatorial abiotic stress responses in wheat

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