Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica.
Identifieur interne : 000376 ( Main/Exploration ); précédent : 000375; suivant : 000377Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica.
Auteurs : Huixia Jia [République populaire de Chine] ; Guangjian Liu [République populaire de Chine] ; Jianbo Li [République populaire de Chine] ; Jin Zhang [États-Unis] ; Pei Sun [République populaire de Chine] ; Shutang Zhao [République populaire de Chine] ; Xun Zhou [République populaire de Chine] ; Mengzhu Lu [République populaire de Chine] ; Jianjun Hu [République populaire de Chine]Source :
- Journal of experimental botany [ 1460-2431 ] ; 2020.
Abstract
Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.
DOI: 10.1093/jxb/eraa172
PubMed: 32242238
PubMed Central: PMC7475257
Affiliations:
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Ltd, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Novogene Co. 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Ltd, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Novogene Co. Ltd, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Lu, Mengzhu" sort="Lu, Mengzhu" uniqKey="Lu M" first="Mengzhu" last="Lu">Mengzhu Lu</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Hu, Jianjun" sort="Hu, Jianjun" uniqKey="Hu J" first="Jianjun" last="Hu">Jianjun Hu</name><affiliation wicri:level="3"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Journal of experimental botany</title><idno type="eISSN">1460-2431</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32242238</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>11</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1460-2431</ISSN><JournalIssue CitedMedium="Internet"><Volume>71</Volume><Issue>14</Issue><PubDate><Year>2020</Year><Month>Jul</Month><Day>06</Day></PubDate></JournalIssue><Title>Journal of experimental botany</Title><ISOAbbreviation>J Exp Bot</ISOAbbreviation></Journal><ArticleTitle>Genome resequencing reveals demographic history and genetic architecture of seed salinity tolerance in Populus euphratica.</ArticleTitle><Pagination><MedlinePgn>4308-4320</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/jxb/eraa172</ELocationID><Abstract><AbstractText>Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jia</LastName><ForeName>Huixia</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Guangjian</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Beijing Novogene Co. Ltd, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jianbo</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Pei</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Shutang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Xun</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Beijing Novogene Co. Ltd, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Mengzhu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jianjun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Exp Bot</MedlineTA><NlmUniqueID>9882906</NlmUniqueID><ISSNLinking>0022-0957</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Demographic history</Keyword><Keyword MajorTopicYN="N">genome-wide association study</Keyword><Keyword MajorTopicYN="N">poplar (Populus euphratica)</Keyword><Keyword MajorTopicYN="N">population structure</Keyword><Keyword MajorTopicYN="N">salinity tolerance</Keyword><Keyword MajorTopicYN="N">transgene</Keyword><Keyword MajorTopicYN="N">whole-genome resequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>04</Month><Day>01</Day></PubMedPubDate><PubMedPubDate 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first="Mengzhu" last="Lu">Mengzhu Lu</name><name sortKey="Sun, Pei" sort="Sun, Pei" uniqKey="Sun P" first="Pei" last="Sun">Pei Sun</name><name sortKey="Zhao, Shutang" sort="Zhao, Shutang" uniqKey="Zhao S" first="Shutang" last="Zhao">Shutang Zhao</name><name sortKey="Zhou, Xun" sort="Zhou, Xun" uniqKey="Zhou X" first="Xun" last="Zhou">Xun Zhou</name></country><country name="États-Unis"><region name="Tennessee"><name sortKey="Zhang, Jin" sort="Zhang, Jin" uniqKey="Zhang J" first="Jin" last="Zhang">Jin Zhang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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