Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq

Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq

Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the...

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Main Authors: Zhang, Jinlong, Wang, Jiaxue, Jiang, Wei, Liu, Juge, Yang, Songnan, Gai, Junyi, Li, Yan
Format: Online
Language:English
Published: Frontiers Media S.A. 2016
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161042/
id pubmed-5161042
recordtype oai_dc
spelling pubmed-51610422016-12-23 Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq Zhang, Jinlong Wang, Jiaxue Jiang, Wei Liu, Juge Yang, Songnan Gai, Junyi Li, Yan Plant Science Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed “phenylpropanoid biosynthesis” and “phenylalanine metabolism” pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity. Frontiers Media S.A. 2016-12-09 /pmc/articles/PMC5161042/ /pubmed/28018382 http://dx.doi.org/10.3389/fpls.2016.01842 Text en Copyright © 2016 Zhang, Wang, Jiang, Liu, Yang, Gai and Li. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Zhang, Jinlong
Wang, Jiaxue
Jiang, Wei
Liu, Juge
Yang, Songnan
Gai, Junyi
Li, Yan
spellingShingle Zhang, Jinlong
Wang, Jiaxue
Jiang, Wei
Liu, Juge
Yang, Songnan
Gai, Junyi
Li, Yan
Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
author_facet Zhang, Jinlong
Wang, Jiaxue
Jiang, Wei
Liu, Juge
Yang, Songnan
Gai, Junyi
Li, Yan
author_sort Zhang, Jinlong
title Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
title_short Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
title_full Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
title_fullStr Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
title_full_unstemmed Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
title_sort identification and analysis of nahco3 stress responsive genes in wild soybean (glycine soja) roots by rna-seq
description Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed “phenylpropanoid biosynthesis” and “phenylalanine metabolism” pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity.
publisher Frontiers Media S.A.
publishDate 2016
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161042/
_version_ 1613786768530735104

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