Cargando…

Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)

BACKGROUND: High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was c...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhang, Hongmei, Xu, Wenjing, Chen, Huatao, Chen, Jingbin, Liu, Xiaoqing, Chen, Xin, Yang, Shouping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447766/
https://www.ncbi.nlm.nih.gov/pubmed/34530724
http://dx.doi.org/10.1186/s12863-021-00989-w
_version_ 1784569086969118720
author Zhang, Hongmei
Xu, Wenjing
Chen, Huatao
Chen, Jingbin
Liu, Xiaoqing
Chen, Xin
Yang, Shouping
author_facet Zhang, Hongmei
Xu, Wenjing
Chen, Huatao
Chen, Jingbin
Liu, Xiaoqing
Chen, Xin
Yang, Shouping
author_sort Zhang, Hongmei
collection PubMed
description BACKGROUND: High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. RESULTS: Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in “Glycolysis/Gluconeogenesis” (ko00010), “Cutin, suberine and wax biosynthesis” (ko00073), and “phenylpropanoid biosynthesis” (ko00940) in Sujiang 1419, although “cysteine/methionine metabolism” (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties. CONCLUSIONS: These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-021-00989-w.
format Online
Article
Text
id pubmed-8447766
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-84477662021-09-20 Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis) Zhang, Hongmei Xu, Wenjing Chen, Huatao Chen, Jingbin Liu, Xiaoqing Chen, Xin Yang, Shouping BMC Genom Data Research BACKGROUND: High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. RESULTS: Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in “Glycolysis/Gluconeogenesis” (ko00010), “Cutin, suberine and wax biosynthesis” (ko00073), and “phenylpropanoid biosynthesis” (ko00940) in Sujiang 1419, although “cysteine/methionine metabolism” (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties. CONCLUSIONS: These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-021-00989-w. BioMed Central 2021-09-16 /pmc/articles/PMC8447766/ /pubmed/34530724 http://dx.doi.org/10.1186/s12863-021-00989-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Zhang, Hongmei
Xu, Wenjing
Chen, Huatao
Chen, Jingbin
Liu, Xiaoqing
Chen, Xin
Yang, Shouping
Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title_full Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title_fullStr Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title_full_unstemmed Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title_short Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis)
title_sort transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (vigna unguiculata ssp. sesquipedialis)
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447766/
https://www.ncbi.nlm.nih.gov/pubmed/34530724
http://dx.doi.org/10.1186/s12863-021-00989-w
work_keys_str_mv AT zhanghongmei transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT xuwenjing transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT chenhuatao transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT chenjingbin transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT liuxiaoqing transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT chenxin transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis
AT yangshouping transcriptomicanalysisofsalttoleranceassociatedgenesanddiversityanalysisusingindelmarkersinyardlongbeanvignaunguiculatasspsesquipedialis