PoplarV1, Main, Exploration, bibRecord, 000A43

Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data.

Identifieur interne : 000A43 ( Main/Exploration ); précédent : 000A42; suivant : 000A44

Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data.

Auteurs : Pei Sun [République populaire de Chine] ; Huixia Jia [République populaire de Chine] ; Yahong Zhang [République populaire de Chine] ; Jianbo Li [République populaire de Chine] ; Mengzhu Lu [République populaire de Chine] ; Jianjun Hu [République populaire de Chine]

Source :

International journal of molecular sciences [ 1422-0067 ] ; 2019.

RBID : pubmed:31817197

Descripteurs français

KwdFr :
- ARN des plantes (composition chimique), ARN des plantes (métabolisme), Analyse de regroupements (MeSH), Analyse de séquence d'ARN (MeSH), Analyse en composantes principales (MeSH), Génotype (MeSH), Liaison génétique (MeSH), Locus de caractère quantitatif (MeSH), Phénotype (MeSH), Populus (génétique), Pousses de plante (génétique), Racines de plante (génétique), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH).
MESH :
- composition chimique : ARN des plantes.
- génétique : Populus, Pousses de plante, Racines de plante.
- métabolisme : ARN des plantes.
- Analyse de regroupements, Analyse de séquence d'ARN, Analyse en composantes principales, Génotype, Liaison génétique, Locus de caractère quantitatif, Phénotype, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique.

English descriptors

KwdEn :
- Cluster Analysis (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genetic Linkage (MeSH), Genotype (MeSH), Phenotype (MeSH), Plant Roots (genetics), Plant Shoots (genetics), Populus (genetics), Principal Component Analysis (MeSH), Quantitative Trait Loci (MeSH), RNA, Plant (chemistry), RNA, Plant (metabolism), Sequence Analysis, RNA (MeSH).
MESH :
- chemical , chemistry : RNA, Plant.
- genetics : Plant Roots, Plant Shoots, Populus.
- chemical , metabolism : RNA, Plant.
- Cluster Analysis, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genetic Linkage, Genotype, Phenotype, Principal Component Analysis, Quantitative Trait Loci, Sequence Analysis, RNA.

Abstract

Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F₁ genotypes originating from Populus deltoides 'Danhong' × Populus simonii 'Tongliao1' and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1-6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1-19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that PtAAAP19 (Potri.004G111400) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with 'Danhong', 153 bp deletion in the coding sequence of PtAAAP19 in 'Tongliao1' gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.

DOI: 10.3390/ijms20246114
PubMed: 31817197
PubMed Central: PMC6941115

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<term>Gene Regulatory Networks (MeSH)</term>
<term>Genetic Linkage (MeSH)</term>
<term>Genotype (MeSH)</term>
<term>Phenotype (MeSH)</term>
<term>Plant Roots (genetics)</term>
<term>Plant Shoots (genetics)</term>
<term>Populus (genetics)</term>
<term>Principal Component Analysis (MeSH)</term>
<term>Quantitative Trait Loci (MeSH)</term>
<term>RNA, Plant (chemistry)</term>
<term>RNA, Plant (metabolism)</term>
<term>Sequence Analysis, RNA (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (composition chimique)</term>
<term>ARN des plantes (métabolisme)</term>
<term>Analyse de regroupements (MeSH)</term>
<term>Analyse de séquence d'ARN (MeSH)</term>
<term>Analyse en composantes principales (MeSH)</term>
<term>Génotype (MeSH)</term>
<term>Liaison génétique (MeSH)</term>
<term>Locus de caractère quantitatif (MeSH)</term>
<term>Phénotype (MeSH)</term>
<term>Populus (génétique)</term>
<term>Pousses de plante (génétique)</term>
<term>Racines de plante (génétique)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Réseaux de régulation génique (MeSH)</term>
</keywords>
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</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ARN des plantes</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Roots</term>
<term>Plant Shoots</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term>
<term>Pousses de plante</term>
<term>Racines de plante</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Plant</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN des plantes</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term>
<term>Gene Expression Regulation, Plant</term>
<term>Gene Regulatory Networks</term>
<term>Genetic Linkage</term>
<term>Genotype</term>
<term>Phenotype</term>
<term>Principal Component Analysis</term>
<term>Quantitative Trait Loci</term>
<term>Sequence Analysis, RNA</term>
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<term>Analyse de séquence d'ARN</term>
<term>Analyse en composantes principales</term>
<term>Génotype</term>
<term>Liaison génétique</term>
<term>Locus de caractère quantitatif</term>
<term>Phénotype</term>
<term>Régulation de l'expression des gènes végétaux</term>
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<front><div type="abstract" xml:lang="en">Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F<sub>1</sub>
 genotypes originating from <i>Populus deltoides</i>
 'Danhong' × <i>Populus simonii</i>
 'Tongliao1' and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1-6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1-19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that <i>PtAAAP19</i>
 (<i>Potri.004G111400</i>
) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with 'Danhong', 153 bp deletion in the coding sequence of <i>PtAAAP19</i>
 in 'Tongliao1' gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31817197</PMID>
<DateCompleted><Year>2020</Year>
<Month>04</Month>
<Day>20</Day>
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<DateRevised><Year>2020</Year>
<Month>04</Month>
<Day>20</Day>
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<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>20</Volume>
<Issue>24</Issue>
<PubDate><Year>2019</Year>
<Month>Dec</Month>
<Day>04</Day>
</PubDate>
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<Title>International journal of molecular sciences</Title>
<ISOAbbreviation>Int J Mol Sci</ISOAbbreviation>
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<ArticleTitle>Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in <i>Populus</i>
 Using QTL Mapping and RNA-Seq Data.</ArticleTitle>
<ELocationID EIdType="pii" ValidYN="Y">E6114</ELocationID>
<ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms20246114</ELocationID>
<Abstract><AbstractText>Understanding the genetic architecture of adventitious root and related shoot traits will facilitate the cultivation of superior genotypes. In this study, we measured 12 adventitious root and related shoot traits of 434 F<sub>1</sub>
 genotypes originating from <i>Populus deltoides</i>
 'Danhong' × <i>Populus simonii</i>
 'Tongliao1' and conducted an integrative analysis of quantitative trait locus (QTL) mapping and RNA-Seq data to dissect their genetic architecture and regulatory genes. Extensive segregation, high repeatability, and significant correlation relationship were detected for the investigated traits. A total of 150 QTLs were associated with adventitious root traits, explaining 3.1-6.1% of phenotypic variation (PVE); while 83 QTLs were associated with shoot traits, explaining 3.1-19.8% of PVE. Twenty-five QTL clusters and 40 QTL hotspots were identified for the investigated traits. Ten QTL clusters were overlapped in both adventitious root traits and related shoot traits. Transcriptome analysis identified 10,172 differentially expressed genes (DEGs) among two parents, three fine rooting and three poor-rooting genotypes, 143 of which were physically located within the QTL intervals. K-means cluster and weighted gene co-expression network analysis showed that <i>PtAAAP19</i>
 (<i>Potri.004G111400</i>
) encoding amino acid transport protein was tightly associated with adventitious roots and highly expressed in fine-rooting genotypes. Compare with 'Danhong', 153 bp deletion in the coding sequence of <i>PtAAAP19</i>
 in 'Tongliao1' gave rise to lack one transmembrane domain, which might cause the variation of adventitious roots. Taken together, this study deciphered the genetic basis of adventitious root and related shoot traits and provided potential function genes for genetic improvement of poplar breeding.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><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 State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</Affiliation>
</AffiliationInfo>
</Author>
<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 State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Yahong</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, 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 102300, 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 State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, 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 State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>(CAFYBB2017ZY008, CAFYBB2018ZY001-9)</GrantID>
<Agency>National Nonprofit Institute Research Grant of CAF</Agency>
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Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data.

Deciphering Genetic Architecture of Adventitious Root and Related Shoot Traits in Populus Using QTL Mapping and RNA-Seq Data.

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