Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies
Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata.
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dig-cirad-fr-5627332024-02-16T19:01:41Z http://agritrop.cirad.fr/562733/ http://agritrop.cirad.fr/562733/ Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies. Garcia-Lor Andrés, Luro François, Navarro Luis, Ollitrault Patrick. 2012. Molecular Genetics and Genomics, 287 (1) : 77-94.https://doi.org/10.1007/s00438-011-0658-4 <https://doi.org/10.1007/s00438-011-0658-4> Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies Garcia-Lor, Andrés Luro, François Navarro, Luis Ollitrault, Patrick eng 2012 Molecular Genetics and Genomics F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/562733/1/document_562733.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1007/s00438-011-0658-4 10.1007/s00438-011-0658-4 info:eu-repo/semantics/altIdentifier/doi/10.1007/s00438-011-0658-4 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1007/s00438-011-0658-4 |
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Biblioteca del CIRAD Francia |
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F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 |
spellingShingle |
F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 Garcia-Lor, Andrés Luro, François Navarro, Luis Ollitrault, Patrick Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
description |
Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Citrus Citrus medica Citrus reticulata Citrus maxima hybridation marqueur génétique variation génétique phylogénie microsatellite taxon taxonomie pool de gènes germoplasme hybride génotype polymorphisme génétique http://aims.fao.org/aos/agrovoc/c_1637 http://aims.fao.org/aos/agrovoc/c_1644 http://aims.fao.org/aos/agrovoc/c_1646 http://aims.fao.org/aos/agrovoc/c_1642 http://aims.fao.org/aos/agrovoc/c_3706 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_36574 http://aims.fao.org/aos/agrovoc/c_7624 http://aims.fao.org/aos/agrovoc/c_7631 http://aims.fao.org/aos/agrovoc/c_3212 http://aims.fao.org/aos/agrovoc/c_3249 http://aims.fao.org/aos/agrovoc/c_3707 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 |
author |
Garcia-Lor, Andrés Luro, François Navarro, Luis Ollitrault, Patrick |
author_facet |
Garcia-Lor, Andrés Luro, François Navarro, Luis Ollitrault, Patrick |
author_sort |
Garcia-Lor, Andrés |
title |
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
title_short |
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
title_full |
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
title_fullStr |
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
title_full_unstemmed |
Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity : A perspective for genetic association studies |
title_sort |
comparative use of indel and ssr markers in deciphering the interspecific structure of cultivated citrus genetic diversity : a perspective for genetic association studies |
url |
http://agritrop.cirad.fr/562733/ http://agritrop.cirad.fr/562733/1/document_562733.pdf |
work_keys_str_mv |
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