Alice Pieri, Romina Beleggia, Tania Gioia, Hao Tong, Valerio Di Vittori, Giulia Frascarelli, Elena Bitocchi, Laura Nanni, Elisa Bellucci, Fabio Fiorani, Nicola Pecchioni, Stefania Marzario, Concetta De Quattro, Antonina Rita Limongi, Pasquale De Vita, Marzia Rossato, Ulrich Schurr, Jacques L David, Zoran Nikoloski, Roberto Papa
{"title":"转录组对氮可用性的响应揭示了四倍体小麦驯化过程中的适应可塑性特征。","authors":"Alice Pieri, Romina Beleggia, Tania Gioia, Hao Tong, Valerio Di Vittori, Giulia Frascarelli, Elena Bitocchi, Laura Nanni, Elisa Bellucci, Fabio Fiorani, Nicola Pecchioni, Stefania Marzario, Concetta De Quattro, Antonina Rita Limongi, Pasquale De Vita, Marzia Rossato, Ulrich Schurr, Jacques L David, Zoran Nikoloski, Roberto Papa","doi":"10.1093/plcell/koae202","DOIUrl":null,"url":null,"abstract":"<p><p>The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":null,"pages":null},"PeriodicalIF":10.0000,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371143/pdf/","citationCount":"0","resultStr":"{\"title\":\"Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.\",\"authors\":\"Alice Pieri, Romina Beleggia, Tania Gioia, Hao Tong, Valerio Di Vittori, Giulia Frascarelli, Elena Bitocchi, Laura Nanni, Elisa Bellucci, Fabio Fiorani, Nicola Pecchioni, Stefania Marzario, Concetta De Quattro, Antonina Rita Limongi, Pasquale De Vita, Marzia Rossato, Ulrich Schurr, Jacques L David, Zoran Nikoloski, Roberto Papa\",\"doi\":\"10.1093/plcell/koae202\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. 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Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.
The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.
期刊介绍:
Title: Plant Cell
Publisher:
Published monthly by the American Society of Plant Biologists (ASPB)
Produced by Sheridan Journal Services, Waterbury, VT
History and Impact:
Established in 1989
Within three years of publication, ranked first in impact among journals in plant sciences
Maintains high standard of excellence
Scope:
Publishes novel research of special significance in plant biology
Focus areas include cellular biology, molecular biology, biochemistry, genetics, development, and evolution
Primary criteria: articles provide new insight of broad interest to plant biologists and are suitable for a wide audience
Tenets:
Publish the most exciting, cutting-edge research in plant cellular and molecular biology
Provide rapid turnaround time for reviewing and publishing research papers
Ensure highest quality reproduction of data
Feature interactive format for commentaries, opinion pieces, and exchange of information in review articles, meeting reports, and insightful overviews.