RustFungiGenomicsV1, Main, Exploration, bibRecord, 000020

In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach.

Identifieur interne : 000020 ( Main/Exploration ); précédent : 000019; suivant : 000021

In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach.

Auteurs : Geleta Dugassa Barka [Brésil, Éthiopie] ; Eveline Teixeira Caixeta [Brésil] ; Sávio Siqueira Ferreira [Brésil] ; Laércio Zambolim [Brésil]

Source :

PloS one [ 1932-6203 ] ; 2020.

RBID : pubmed:32639982

Descripteurs français

KwdFr :
- Alignement de séquences (MeSH), Banque de gènes (MeSH), Basidiomycota (physiologie), Cadres ouverts de lecture (génétique), Café (classification), Café (génétique), Facteurs de virulence (génétique), Facteurs de virulence (métabolisme), Génome végétal (MeSH), Lycopersicon esculentum (classification), Lycopersicon esculentum (génétique), Maladies des plantes (microbiologie), Phylogenèse (MeSH), Polymorphisme génétique (MeSH), Protéines végétales (composition chimique), Protéines végétales (génétique), Protéines végétales (métabolisme), Résistance à la maladie (génétique), Sites de fixation (MeSH), Séquence d'acides aminés (MeSH), Vitis (classification), Vitis (génétique).
MESH :
- composition chimique : Café, Lycopersicon esculentum, Protéines végétales, Vitis.
- génétique : Cadres ouverts de lecture, Café, Facteurs de virulence, Lycopersicon esculentum, Protéines végétales, Résistance à la maladie, Vitis.
- microbiologie : Maladies des plantes.
- métabolisme : Facteurs de virulence, Protéines végétales.
- physiologie : Basidiomycota.
- Alignement de séquences, Banque de gènes, Génome végétal, Phylogenèse, Polymorphisme génétique, Sites de fixation, Séquence d'acides aminés.

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Basidiomycota (physiology), Binding Sites (MeSH), Coffee (classification), Coffee (genetics), Disease Resistance (genetics), Gene Library (MeSH), Genome, Plant (MeSH), Lycopersicon esculentum (classification), Lycopersicon esculentum (genetics), Open Reading Frames (genetics), Phylogeny (MeSH), Plant Diseases (microbiology), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Polymorphism, Genetic (MeSH), Sequence Alignment (MeSH), Virulence Factors (genetics), Virulence Factors (metabolism), Vitis (classification), Vitis (genetics).
MESH :
- chemical , chemistry : Plant Proteins.
- chemical , classification : Coffee.
- chemical , genetics : Coffee, Plant Proteins, Virulence Factors.
- classification : Lycopersicon esculentum, Vitis.
- genetics : Disease Resistance, Lycopersicon esculentum, Open Reading Frames, Vitis.
- chemical , metabolism : Plant Proteins, Virulence Factors.
- microbiology : Plant Diseases.
- physiology : Basidiomycota.
- Amino Acid Sequence, Binding Sites, Gene Library, Genome, Plant, Phylogeny, Polymorphism, Genetic, Sequence Alignment.

Abstract

Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.

DOI: 10.1371/journal.pone.0222747
PubMed: 32639982
PubMed Central: PMC7343155

Affiliations:

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

to stream Main, to step Corpus: 000014
to stream Main, to step Curation: 000014

Le document en format XML

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<term>Binding Sites (MeSH)</term>
<term>Coffee (classification)</term>
<term>Coffee (genetics)</term>
<term>Disease Resistance (genetics)</term>
<term>Gene Library (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Lycopersicon esculentum (classification)</term>
<term>Lycopersicon esculentum (genetics)</term>
<term>Open Reading Frames (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Diseases (microbiology)</term>
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<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Polymorphism, Genetic (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Virulence Factors (genetics)</term>
<term>Virulence Factors (metabolism)</term>
<term>Vitis (classification)</term>
<term>Vitis (genetics)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term>
<term>Banque de gènes (MeSH)</term>
<term>Basidiomycota (physiologie)</term>
<term>Cadres ouverts de lecture (génétique)</term>
<term>Café (classification)</term>
<term>Café (génétique)</term>
<term>Facteurs de virulence (génétique)</term>
<term>Facteurs de virulence (métabolisme)</term>
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<term>Lycopersicon esculentum (génétique)</term>
<term>Maladies des plantes (microbiologie)</term>
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<term>Lycopersicon esculentum</term>
<term>Open Reading Frames</term>
<term>Vitis</term>
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<term>Facteurs de virulence</term>
<term>Lycopersicon esculentum</term>
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<term>Génome végétal</term>
<term>Phylogenèse</term>
<term>Polymorphisme génétique</term>
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<front><div type="abstract" xml:lang="en">Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.</div>
</front>
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<Abstract><AbstractText>Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Barka</LastName>
<ForeName>Geleta Dugassa</ForeName>
<Initials>GD</Initials>
<Identifier Source="ORCID">0000-0002-1521-9705</Identifier>
<AffiliationInfo><Affiliation>Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Applied Biology Department, Adama Science and Technology University (ASTU), Adama, Oromia, Ethiopia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Caixeta</LastName>
<ForeName>Eveline Teixeira</ForeName>
<Initials>ET</Initials>
<Identifier Source="ORCID">0000-0001-8850-6273</Identifier>
<AffiliationInfo><Affiliation>Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Embrapa Café, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ferreira</LastName>
<ForeName>Sávio Siqueira</ForeName>
<Initials>SS</Initials>
<Identifier Source="ORCID">0000-0001-9926-9066</Identifier>
<AffiliationInfo><Affiliation>Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zambolim</LastName>
<ForeName>Laércio</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Laboratório de Biotecnologia do Cafeeiro (BIOCAFÉ), BIOAGRO, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil.</Affiliation>
</AffiliationInfo>
</Author>
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<Language>eng</Language>
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<ArticleDate DateType="Electronic"><Year>2020</Year>
<Month>07</Month>
<Day>08</Day>
</ArticleDate>
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<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
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<CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>PLoS One. 2020 Sep 3;15(9):e0238967</RefSource>
<PMID Version="1">32881959</PMID>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName>
<QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003069" MajorTopicYN="N">Coffee</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D060467" MajorTopicYN="N">Disease Resistance</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName>
</MeshHeading>
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In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach.

In silico guided structural and functional analysis of genes with potential involvement in resistance to coffee leaf rust: A functional marker based approach.

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