Taekyeom Kim , Heeyoun Hwang , Geul Bang , Jungmin Ha , Yong-Jin Park , Jae Yoon Kim
{"title":"通过基于多组学的替代剪接预测了解野生大豆(Glycine soja)耐旱性的分子机制","authors":"Taekyeom Kim , Heeyoun Hwang , Geul Bang , Jungmin Ha , Yong-Jin Park , Jae Yoon Kim","doi":"10.1016/j.envexpbot.2024.105872","DOIUrl":null,"url":null,"abstract":"<div><p>The absence of adequate moisture resulting from drought poses a significant threat to both the viability and productivity of soybean cultivation. Genetic variation in common soybeans has been noticeably reduced through continuous breeding, and wild relatives with wider genetic diversity are one of the best tools in the search for new tolerance genes. In this study, we selected 139 genes co-expressed at transcript and protein levels in response to drought in <em>Glycine soja</em> through a multi-omics analysis. Drought stress induced co-expression of transcripts and proteins involved in dopamine synthesis within tyrosine metabolism. Polyphenol oxidase, involved in the dopamine synthesis process, was uniquely identified in both DEGs and DEPs, with its protein abundance increased. Co-expression of 9-lipoxygenase during linoleic acid metabolism was confirmed, along with consistent protein accumulation. The co-expression profiling of transcripts and proteins suggests that they may influence their regulatory feedback loops or unknown regulatory mechanisms. Additionally, we predicted the regulation of alternative splicing (AS) in response to drought. AS was predicted for 139 co-expressed genes, and four drought-tolerance-related gene candidate groups were selected. The expression levels of four genes, <em>FT1</em>, <em>CCR1L</em>, <em>RPL18</em>, and <em>uncharacterized LOC114422617</em>, varied depending on their transcript isoforms under drought stress. The occurrence of AS under drought stress may play a role in eliminating susceptibility genes or inducing tolerance genes to adapt to drought stress. Overall, this study reveals a novel mechanism of drought adaptation in wild soybean by predicting the regulation of metabolic pathways and AS events at the transcriptome and proteome levels and presents potential targets for soybean breeding.</p></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":null,"pages":null},"PeriodicalIF":4.5000,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0098847224002302/pdfft?md5=01e7d9472df16571a5bc813c8d11d4c4&pid=1-s2.0-S0098847224002302-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions\",\"authors\":\"Taekyeom Kim , Heeyoun Hwang , Geul Bang , Jungmin Ha , Yong-Jin Park , Jae Yoon Kim\",\"doi\":\"10.1016/j.envexpbot.2024.105872\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>The absence of adequate moisture resulting from drought poses a significant threat to both the viability and productivity of soybean cultivation. Genetic variation in common soybeans has been noticeably reduced through continuous breeding, and wild relatives with wider genetic diversity are one of the best tools in the search for new tolerance genes. In this study, we selected 139 genes co-expressed at transcript and protein levels in response to drought in <em>Glycine soja</em> through a multi-omics analysis. Drought stress induced co-expression of transcripts and proteins involved in dopamine synthesis within tyrosine metabolism. Polyphenol oxidase, involved in the dopamine synthesis process, was uniquely identified in both DEGs and DEPs, with its protein abundance increased. Co-expression of 9-lipoxygenase during linoleic acid metabolism was confirmed, along with consistent protein accumulation. The co-expression profiling of transcripts and proteins suggests that they may influence their regulatory feedback loops or unknown regulatory mechanisms. Additionally, we predicted the regulation of alternative splicing (AS) in response to drought. AS was predicted for 139 co-expressed genes, and four drought-tolerance-related gene candidate groups were selected. The expression levels of four genes, <em>FT1</em>, <em>CCR1L</em>, <em>RPL18</em>, and <em>uncharacterized LOC114422617</em>, varied depending on their transcript isoforms under drought stress. The occurrence of AS under drought stress may play a role in eliminating susceptibility genes or inducing tolerance genes to adapt to drought stress. Overall, this study reveals a novel mechanism of drought adaptation in wild soybean by predicting the regulation of metabolic pathways and AS events at the transcriptome and proteome levels and presents potential targets for soybean breeding.</p></div>\",\"PeriodicalId\":11758,\"journal\":{\"name\":\"Environmental and Experimental Botany\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.5000,\"publicationDate\":\"2024-06-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0098847224002302/pdfft?md5=01e7d9472df16571a5bc813c8d11d4c4&pid=1-s2.0-S0098847224002302-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Environmental and Experimental Botany\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0098847224002302\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"ENVIRONMENTAL SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Environmental and Experimental Botany","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0098847224002302","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions
The absence of adequate moisture resulting from drought poses a significant threat to both the viability and productivity of soybean cultivation. Genetic variation in common soybeans has been noticeably reduced through continuous breeding, and wild relatives with wider genetic diversity are one of the best tools in the search for new tolerance genes. In this study, we selected 139 genes co-expressed at transcript and protein levels in response to drought in Glycine soja through a multi-omics analysis. Drought stress induced co-expression of transcripts and proteins involved in dopamine synthesis within tyrosine metabolism. Polyphenol oxidase, involved in the dopamine synthesis process, was uniquely identified in both DEGs and DEPs, with its protein abundance increased. Co-expression of 9-lipoxygenase during linoleic acid metabolism was confirmed, along with consistent protein accumulation. The co-expression profiling of transcripts and proteins suggests that they may influence their regulatory feedback loops or unknown regulatory mechanisms. Additionally, we predicted the regulation of alternative splicing (AS) in response to drought. AS was predicted for 139 co-expressed genes, and four drought-tolerance-related gene candidate groups were selected. The expression levels of four genes, FT1, CCR1L, RPL18, and uncharacterized LOC114422617, varied depending on their transcript isoforms under drought stress. The occurrence of AS under drought stress may play a role in eliminating susceptibility genes or inducing tolerance genes to adapt to drought stress. Overall, this study reveals a novel mechanism of drought adaptation in wild soybean by predicting the regulation of metabolic pathways and AS events at the transcriptome and proteome levels and presents potential targets for soybean breeding.
期刊介绍:
Environmental and Experimental Botany (EEB) publishes research papers on the physical, chemical, biological, molecular mechanisms and processes involved in the responses of plants to their environment.
In addition to research papers, the journal includes review articles. Submission is in agreement with the Editors-in-Chief.
The Journal also publishes special issues which are built by invited guest editors and are related to the main themes of EEB.
The areas covered by the Journal include:
(1) Responses of plants to heavy metals and pollutants
(2) Plant/water interactions (salinity, drought, flooding)
(3) Responses of plants to radiations ranging from UV-B to infrared
(4) Plant/atmosphere relations (ozone, CO2 , temperature)
(5) Global change impacts on plant ecophysiology
(6) Biotic interactions involving environmental factors.