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Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau

To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in...

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Autores principales: Kong, Doudou, Xu, Jinqing, Wang, Lei, Wang, Handong, You, En, Li, Xiaolan, Chen, Tongrui, Shen, Yuhu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847792/
https://www.ncbi.nlm.nih.gov/pubmed/35185989
http://dx.doi.org/10.3389/fpls.2022.822607
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author Kong, Doudou
Xu, Jinqing
Wang, Lei
Wang, Handong
You, En
Li, Xiaolan
Chen, Tongrui
Shen, Yuhu
author_facet Kong, Doudou
Xu, Jinqing
Wang, Lei
Wang, Handong
You, En
Li, Xiaolan
Chen, Tongrui
Shen, Yuhu
author_sort Kong, Doudou
collection PubMed
description To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size.
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spelling pubmed-88477922022-02-17 Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau Kong, Doudou Xu, Jinqing Wang, Lei Wang, Handong You, En Li, Xiaolan Chen, Tongrui Shen, Yuhu Front Plant Sci Plant Science To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size. Frontiers Media S.A. 2022-02-02 /pmc/articles/PMC8847792/ /pubmed/35185989 http://dx.doi.org/10.3389/fpls.2022.822607 Text en Copyright © 2022 Kong, Xu, Wang, Wang, You, Li, Chen and Shen. https://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) and the copyright owner(s) 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.
spellingShingle Plant Science
Kong, Doudou
Xu, Jinqing
Wang, Lei
Wang, Handong
You, En
Li, Xiaolan
Chen, Tongrui
Shen, Yuhu
Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title_full Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title_fullStr Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title_full_unstemmed Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title_short Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai–Tibetan Plateau
title_sort combined rna-seq and phenotype analysis reveals a potential molecular mechanism of the difference in grain size of naked barley from the qinghai–tibetan plateau
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847792/
https://www.ncbi.nlm.nih.gov/pubmed/35185989
http://dx.doi.org/10.3389/fpls.2022.822607
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