Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits
Identifieur interne : 000413 ( Main/Exploration ); précédent : 000412; suivant : 000414Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits
Auteurs : Amel Oueslati [Tunisie, France] ; Amel Salhi-Hannachi [Tunisie] ; François Luro [France] ; Hélène Vignes [France] ; Pierre Mournet [France] ; Patrick Ollitrault [France]Source :
- PLoS ONE [ 1932-6203 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Citrus.
- classification : Caryotypage, Citrus, Gènes de plante, Phylogenèse, Réaction de polymérisation en chaîne, Spécificité d'espèce.
English descriptors
- KwdEn :
- MESH :
- classification : Citrus.
- genetics : Citrus.
- Genes, Plant, Karyotyping, Phylogeny, Polymerase Chain Reaction, Species Specificity.
Abstract
The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as
Url:
DOI: 10.1371/journal.pone.0185618
PubMed: 28982157
PubMed Central: 5628881
Affiliations:
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Le document en format XML
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admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genotyping by sequencing reveals the interspecific <italic>C</italic>
. <italic>maxima / C</italic>
. <italic>reticulata</italic>
admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits</title>
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<term>Citrus (genetics)</term>
<term>Genes, Plant (MeSH)</term>
<term>Karyotyping (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Polymerase Chain Reaction (MeSH)</term>
<term>Species Specificity (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Caryotypage (MeSH)</term>
<term>Citrus (classification)</term>
<term>Citrus (génétique)</term>
<term>Gènes de plante (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Réaction de polymérisation en chaîne (MeSH)</term>
<term>Spécificité d'espèce (MeSH)</term>
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<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Citrus</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus</term>
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</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genes, Plant</term>
<term>Karyotyping</term>
<term>Phylogeny</term>
<term>Polymerase Chain Reaction</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Caryotypage</term>
<term>Citrus</term>
<term>Gènes de plante</term>
<term>Phylogenèse</term>
<term>Réaction de polymérisation en chaîne</term>
<term>Spécificité d'espèce</term>
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<front><div type="abstract" xml:lang="en"><p>The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as <italic>C</italic>
. <italic>reticulata</italic>
is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by <italic>C</italic>
. <italic>maxima</italic>
(the pummelos). <italic>C</italic>
. <italic>maxima</italic>
and <italic>C</italic>
. <italic>reticulata</italic>
are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the “small citrus” modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the <italic>C</italic>
. <italic>reticulata</italic>
and <italic>C</italic>
. <italic>maxima</italic>
gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of <italic>C</italic>
. <italic>reticulata/C</italic>
. <italic>maxima</italic>
differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the “phylogenomic karyotypes” of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of <italic>C</italic>
. <italic>maxima</italic>
in different parts of the genome. <italic>C</italic>
. <italic>reticulata/C</italic>
. <italic>maxima</italic>
admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.</p>
</div>
</front>
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<author><name sortKey="Ollitrault, F" uniqKey="Ollitrault F">F Ollitrault</name>
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<author><name sortKey="Garcia Lor, A" uniqKey="Garcia Lor A">A Garcia-Lor</name>
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<author><name sortKey="Vicente Contador, Zp" uniqKey="Vicente Contador Z">ZP Vicente Contador</name>
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<author><name sortKey="Guerra, M" uniqKey="Guerra M">M Guerra</name>
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<author><name sortKey="Mccollum, Gregory T" uniqKey="Mccollum G">Gregory T. McCollum</name>
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<author><name sortKey="Driggers, Randall" uniqKey="Driggers R">Randall Driggers</name>
</author>
<author><name sortKey="Lee, Richard" uniqKey="Lee R">Richard Lee</name>
</author>
<author><name sortKey="Shatters, Robert" uniqKey="Shatters R">Robert Shatters</name>
</author>
<author><name sortKey="Duan, Yongping" uniqKey="Duan Y">YongPing Duan</name>
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<author><name sortKey="Ritenour, Mark" uniqKey="Ritenour M">Mark Ritenour</name>
</author>
<author><name sortKey="Chaparro, Jose X" uniqKey="Chaparro J">Jose X. Chaparro</name>
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<tree><country name="Tunisie"><noRegion><name sortKey="Oueslati, Amel" sort="Oueslati, Amel" uniqKey="Oueslati A" first="Amel" last="Oueslati">Amel Oueslati</name>
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