Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

Delong Wang,Zujun Yin,Junjuan Wang,Lixue Guo,Quanjia Chen,Xiugui Chen,Shuai Wang,Xuke Lu,Wuwei Ye

doi:10.1186/s12864-020-07260-z

Delong Wang, Zujun Yin + Show 7 more

Open Access

https://doi.org/10.1186/s12864-020-07260-z

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Abstract

BackgroundCotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG).ResultsAntioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton.ConclusionCollectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.

Highlights

Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality
We identified a wealth of novel transcripts based on the Pacific Biosciences (PacBio) long reads sequencing approach, which is accordance with previous report of Wang et al [55]
We studied the molecular response of an upland cotton genotype under temporal salt stress based on long reads transcriptome analysis

Summary

Introduction

Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. Plant salt stress response mechanism is mainly stimulated by osmotic stress and Na+ [3]. Plant’s physiological responses to salt stress involve a number of pathways, including hormone signaling transduction pathway, salt over sensitive pathway (SOS) and hormone biosynthesis pathways [5,6,7,8,9]. Phytohormones such as abscisic acid (ABA), ethylene (ET) and jasmonates (JA) play major roles against abiotic stresses. Molecular mechanisms of plant stress tolerance are much more complex than physiological and biochemical processes. Much efforts have been devoted to reveal the molecular mechanisms of plant salt tolerance, with the ultimate goal of improving salt tolerance of crop plants [16]

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