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An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A(n)- and C(n)-sub-genomes, and that genes derived from Brassica r...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203523/ https://www.ncbi.nlm.nih.gov/pubmed/37229128 http://dx.doi.org/10.3389/fpls.2023.1187552 |
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author | Li, Pengfeng Du, Runjie Li, Zhaopeng Chen, Zhuo Li, Jiana Du, Hai |
author_facet | Li, Pengfeng Du, Runjie Li, Zhaopeng Chen, Zhuo Li, Jiana Du, Hai |
author_sort | Li, Pengfeng |
collection | PubMed |
description | Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A(n)- and C(n)-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus. |
format | Online Article Text |
id | pubmed-10203523 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-102035232023-05-24 An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus Li, Pengfeng Du, Runjie Li, Zhaopeng Chen, Zhuo Li, Jiana Du, Hai Front Plant Sci Plant Science Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A(n)- and C(n)-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus. Frontiers Media S.A. 2023-05-09 /pmc/articles/PMC10203523/ /pubmed/37229128 http://dx.doi.org/10.3389/fpls.2023.1187552 Text en Copyright © 2023 Li, Du, Li, Chen, Li and Du 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 Li, Pengfeng Du, Runjie Li, Zhaopeng Chen, Zhuo Li, Jiana Du, Hai An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus |
title | An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
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title_full | An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
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title_fullStr | An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
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title_full_unstemmed | An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
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title_short | An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus
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title_sort | integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in brassica napus |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203523/ https://www.ncbi.nlm.nih.gov/pubmed/37229128 http://dx.doi.org/10.3389/fpls.2023.1187552 |
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