Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.

Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify...

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Autores principales:	Mahmut Can Hiz, Balkan Canher, Harun Niron, Muge Turet
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4e3252df01ac42909017bd442a84bd74
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spelling	oai:doaj.org-article:4e3252df01ac42909017bd442a84bd742021-11-18T08:27:09ZTranscriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.1932-620310.1371/journal.pone.0092598https://doaj.org/article/4e3252df01ac42909017bd442a84bd742014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24651267/?tool=EBIhttps://doaj.org/toc/1932-6203Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.Mahmut Can HizBalkan CanherHarun NironMuge TuretPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e92598 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mahmut Can Hiz Balkan Canher Harun Niron Muge Turet Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
description	Salinity is one of the important abiotic stress factors that limit crop production. Common bean, Phaseolus vulgaris L., a major protein source in developing countries, is highly affected by soil salinity and the information on genes that play a role in salt tolerance is scarce. We aimed to identify differentially expressed genes (DEGs) and related pathways by comprehensive analysis of transcriptomes of both root and leaf tissues of the tolerant genotype grown under saline and control conditions in hydroponic system. We have generated a total of 158 million high-quality reads which were assembled into 83,774 all-unigenes with a mean length of 813 bp and N50 of 1,449 bp. Among the all-unigenes, 58,171 were assigned with Nr annotations after homology analyses. It was revealed that 6,422 and 4,555 all-unigenes were differentially expressed upon salt stress in leaf and root tissues respectively. Validation of the RNA-seq quantifications (RPKM values) was performed by qRT-PCR (Quantitative Reverse Transcription PCR) analyses. Enrichment analyses of DEGs based on GO and KEGG databases have shown that both leaf and root tissues regulate energy metabolism, transmembrane transport activity, and secondary metabolites to cope with salinity. A total of 2,678 putative common bean transcription factors were identified and classified under 59 transcription factor families; among them 441 were salt responsive. The data generated in this study will help in understanding the fundamentals of salt tolerance in common bean and will provide resources for functional genomic studies.
format	article
author	Mahmut Can Hiz Balkan Canher Harun Niron Muge Turet
author_facet	Mahmut Can Hiz Balkan Canher Harun Niron Muge Turet
author_sort	Mahmut Can Hiz
title	Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
title_short	Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
title_full	Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
title_fullStr	Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
title_full_unstemmed	Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.
title_sort	transcriptome analysis of salt tolerant common bean (phaseolus vulgaris l.) under saline conditions.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/4e3252df01ac42909017bd442a84bd74
work_keys_str_mv	AT mahmutcanhiz transcriptomeanalysisofsalttolerantcommonbeanphaseolusvulgarislundersalineconditions AT balkancanher transcriptomeanalysisofsalttolerantcommonbeanphaseolusvulgarislundersalineconditions AT harunniron transcriptomeanalysisofsalttolerantcommonbeanphaseolusvulgarislundersalineconditions AT mugeturet transcriptomeanalysisofsalttolerantcommonbeanphaseolusvulgarislundersalineconditions
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Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions.

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