Serveur d'exploration Phytophthora

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Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study.

Identifieur interne : 000475 ( Main/Exploration ); précédent : 000474; suivant : 000476

Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study.

Auteurs : Muhammad Irfan Siddique [Corée du Sud] ; Hea-Young Lee [Corée du Sud] ; Na-Young Ro [Corée du Sud] ; Koeun Han [Corée du Sud] ; Jelli Venkatesh [Corée du Sud] ; Abate Mekonnen Solomon [Corée du Sud] ; Abhinandan Surgonda Patil [Corée du Sud] ; Amornrat Changkwian [Corée du Sud] ; Jin-Kyung Kwon [Corée du Sud] ; Byoung-Cheorl Kang [Corée du Sud]

Source :

RBID : pubmed:31292472

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English descriptors

Abstract

Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.

DOI: 10.1038/s41598-019-46342-1
PubMed: 31292472
PubMed Central: PMC6620314


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<term>Capsicum (genetics)</term>
<term>Chromosome Mapping (methods)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Disease Resistance (genetics)</term>
<term>Genes, Plant (genetics)</term>
<term>Genetic Markers (genetics)</term>
<term>Genome-Wide Association Study (methods)</term>
<term>Genotype (MeSH)</term>
<term>Phytophthora (MeSH)</term>
<term>Plant Diseases (genetics)</term>
<term>Quantitative Trait Loci (genetics)</term>
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<term>Capsicum (génétique)</term>
<term>Cartographie chromosomique (méthodes)</term>
<term>Chromosomes de plante (génétique)</term>
<term>Gènes de plante (génétique)</term>
<term>Génotype (MeSH)</term>
<term>Locus de caractère quantitatif (génétique)</term>
<term>Maladies des plantes (génétique)</term>
<term>Marqueurs génétiques (génétique)</term>
<term>Phytophthora (MeSH)</term>
<term>Résistance à la maladie (génétique)</term>
<term>Étude d'association pangénomique (méthodes)</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Capsicum</term>
<term>Chromosomes, Plant</term>
<term>Disease Resistance</term>
<term>Genes, Plant</term>
<term>Plant Diseases</term>
<term>Quantitative Trait Loci</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Capsicum</term>
<term>Chromosomes de plante</term>
<term>Gènes de plante</term>
<term>Locus de caractère quantitatif</term>
<term>Maladies des plantes</term>
<term>Marqueurs génétiques</term>
<term>Résistance à la maladie</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en">
<term>Chromosome Mapping</term>
<term>Genome-Wide Association Study</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr">
<term>Cartographie chromosomique</term>
<term>Étude d'association pangénomique</term>
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<keywords scheme="MESH" xml:lang="en">
<term>Genotype</term>
<term>Phytophthora</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
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<div type="abstract" xml:lang="en">Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.</div>
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<AbstractText>Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.</AbstractText>
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