Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars

Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying...

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Autores principales:	Muhammad Zeeshan, Cheng-Wei Qiu, Shama Naz, Fangbin Cao, Feibo Wu
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	miRNAs high-throughput sequencing roots wheat salt stress Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/7095c1e501a24ef8a9fb29f9b0495f8e
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spelling	oai:doaj.org-article:7095c1e501a24ef8a9fb29f9b0495f8e2021-11-25T17:57:47ZGenome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars10.3390/ijms2222125561422-00671661-6596https://doaj.org/article/7095c1e501a24ef8a9fb29f9b0495f8e2021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12556https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying molecular mechanisms by which miRNAs confer salt tolerance in wheat are unclear. We conducted a genome-wide discovery study using Illumina high throughput sequencing and comprehensive in silico analysis to obtain insight into the underlying mechanisms by which small RNAs confer tolerance to salinity in roots of two contrasting wheat cvv., namely Suntop (salt-tolerant) and Sunmate (salt-sensitive). A total of 191 microRNAs were identified in both cultivars, consisting of 110 known miRNAs and 81 novel miRNAs; 181 miRNAs were shared between the two cultivars. The known miRNAs belonged to 35 families consisted of 23 conserved and 12 unique families. Salinity stress induced 43 and 75 miRNAs in Suntop and Sunmate, respectively. Among them, 14 and 29 known and novel miRNAs were expressed in Suntop and 37 and 38 in Sunmate. In silico analysis revealed 861 putative target mRNAs for the 75 known miRNAs and 52 putative target mRNAs for the 15 candidate novel miRNAs. Furthermore, seven miRNAs including tae-miR156, tae-miR160, tae-miR171a-b, tae-miR319, tae-miR159a-b, tae-miR9657 and novel-mir59 that regulate auxin responsive-factor, SPL, SCL6, PCF5, R2R3 MYB, and CBL-CIPK, respectively, were predicted to contribute to salt tolerance in Suntop. This information helps further our understanding of how the molecular mechanisms of salt tolerance are mediated by miRNAs and may facilitate the genetic improvement of wheat cultivars.Muhammad ZeeshanCheng-Wei QiuShama NazFangbin CaoFeibo WuMDPI AGarticlemiRNAshigh-throughput sequencingrootswheatsalt stressBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12556, p 12556 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	miRNAs high-throughput sequencing roots wheat salt stress Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	miRNAs high-throughput sequencing roots wheat salt stress Biology (General) QH301-705.5 Chemistry QD1-999 Muhammad Zeeshan Cheng-Wei Qiu Shama Naz Fangbin Cao Feibo Wu Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
description	Salinity is a serious environmental issue. It has a substantial effect on crop yield, as many crop species are sensitive to salinity due to climate change, and it impact is continuing to increase. Plant microRNAs (miRNAs) contribute to salinity stress response in bread wheat. However, the underlying molecular mechanisms by which miRNAs confer salt tolerance in wheat are unclear. We conducted a genome-wide discovery study using Illumina high throughput sequencing and comprehensive in silico analysis to obtain insight into the underlying mechanisms by which small RNAs confer tolerance to salinity in roots of two contrasting wheat cvv., namely Suntop (salt-tolerant) and Sunmate (salt-sensitive). A total of 191 microRNAs were identified in both cultivars, consisting of 110 known miRNAs and 81 novel miRNAs; 181 miRNAs were shared between the two cultivars. The known miRNAs belonged to 35 families consisted of 23 conserved and 12 unique families. Salinity stress induced 43 and 75 miRNAs in Suntop and Sunmate, respectively. Among them, 14 and 29 known and novel miRNAs were expressed in Suntop and 37 and 38 in Sunmate. In silico analysis revealed 861 putative target mRNAs for the 75 known miRNAs and 52 putative target mRNAs for the 15 candidate novel miRNAs. Furthermore, seven miRNAs including tae-miR156, tae-miR160, tae-miR171a-b, tae-miR319, tae-miR159a-b, tae-miR9657 and novel-mir59 that regulate auxin responsive-factor, SPL, SCL6, PCF5, R2R3 MYB, and CBL-CIPK, respectively, were predicted to contribute to salt tolerance in Suntop. This information helps further our understanding of how the molecular mechanisms of salt tolerance are mediated by miRNAs and may facilitate the genetic improvement of wheat cultivars.
format	article
author	Muhammad Zeeshan Cheng-Wei Qiu Shama Naz Fangbin Cao Feibo Wu
author_facet	Muhammad Zeeshan Cheng-Wei Qiu Shama Naz Fangbin Cao Feibo Wu
author_sort	Muhammad Zeeshan
title	Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
title_short	Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
title_full	Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
title_fullStr	Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
title_full_unstemmed	Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars
title_sort	genome-wide discovery of mirnas with differential expression patterns in responses to salinity in the two contrasting wheat cultivars
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/7095c1e501a24ef8a9fb29f9b0495f8e
work_keys_str_mv	AT muhammadzeeshan genomewidediscoveryofmirnaswithdifferentialexpressionpatternsinresponsestosalinityinthetwocontrastingwheatcultivars AT chengweiqiu genomewidediscoveryofmirnaswithdifferentialexpressionpatternsinresponsestosalinityinthetwocontrastingwheatcultivars AT shamanaz genomewidediscoveryofmirnaswithdifferentialexpressionpatternsinresponsestosalinityinthetwocontrastingwheatcultivars AT fangbincao genomewidediscoveryofmirnaswithdifferentialexpressionpatternsinresponsestosalinityinthetwocontrastingwheatcultivars AT feibowu genomewidediscoveryofmirnaswithdifferentialexpressionpatternsinresponsestosalinityinthetwocontrastingwheatcultivars
_version_	1718411809224916992

Genome-Wide Discovery of miRNAs with Differential Expression Patterns in Responses to Salinity in the Two Contrasting Wheat Cultivars

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