{"title":"Comparative analysis of transcriptome and metabolome explores the underlying mechanism of pod color variation in pea (Pisum sativum L.)","authors":"","doi":"10.1007/s13562-024-00872-6","DOIUrl":null,"url":null,"abstract":"<h3>Abstract</h3> <p>The pea (<em>Pisum sativum</em> L.) is one of widely cultivated crops over the world, but the mechanism of pod coloration is still unclear. Understanding the underlying mechanism regulating pea pod coloration can broaden pea breeding. In this study, the comparative analysis of transcriptome and metabolome was performed to examine the changes in metabolites accumulation and gene expression at two pod developmental stages in two pea accessions with green pods (GP) and yellow pods (YP). At the two omics levels, a total of 4504 differential metabolites (DEMs) were detected in four samples, and 2709 and 3725 differential expression genes (DEGs) were detected at two pod developmental stages between GP and YP, respectively. The verification results of RT-qPCR showed that the relative expression of ten genes randomly detected showed statistically high correlations between RT-qPCR and RNA-seq. The functional analysis of DEMs and DEGs found that the flavonoid metabolism pathway was the most direct metabolic pathway for the variation of pod coloration between two pea accessions. The 34 DEMs and 21 DEGs related to flavonoid metabolism pathway exhibited different expression pattern between GP and YP samples. Additionally, the combined analysis of transcriptome and metabolome in flavonoid biosynthesis pathway revealed that a direct correlation between the decreased expression level of genes and reduction accumulation of metabolites in the delphinidin biosynthesis pathway. The obtained results of this study provided a foundation to reveal the candidate genes controlling the pod color variation, and provide new germplasm resources for genetic improvement in pea.</p>","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s13562-024-00872-6","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
Abstract
The pea (Pisum sativum L.) is one of widely cultivated crops over the world, but the mechanism of pod coloration is still unclear. Understanding the underlying mechanism regulating pea pod coloration can broaden pea breeding. In this study, the comparative analysis of transcriptome and metabolome was performed to examine the changes in metabolites accumulation and gene expression at two pod developmental stages in two pea accessions with green pods (GP) and yellow pods (YP). At the two omics levels, a total of 4504 differential metabolites (DEMs) were detected in four samples, and 2709 and 3725 differential expression genes (DEGs) were detected at two pod developmental stages between GP and YP, respectively. The verification results of RT-qPCR showed that the relative expression of ten genes randomly detected showed statistically high correlations between RT-qPCR and RNA-seq. The functional analysis of DEMs and DEGs found that the flavonoid metabolism pathway was the most direct metabolic pathway for the variation of pod coloration between two pea accessions. The 34 DEMs and 21 DEGs related to flavonoid metabolism pathway exhibited different expression pattern between GP and YP samples. Additionally, the combined analysis of transcriptome and metabolome in flavonoid biosynthesis pathway revealed that a direct correlation between the decreased expression level of genes and reduction accumulation of metabolites in the delphinidin biosynthesis pathway. The obtained results of this study provided a foundation to reveal the candidate genes controlling the pod color variation, and provide new germplasm resources for genetic improvement in pea.
期刊介绍：
Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance.
Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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