Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering

Autores
Palombo, Nahuel Ezequiel; Carrizo Garcia, Carolina
Año de publicación
2021
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
The hot chile Capsicum pubescens is mainly cultivated in Central-South America's mid-highlands, from Mexico to northwest Argentina. Despite being a crop of economic and cultural importance, little is known about its evolution and the genetic diversity and structure it harbors. Thus, RAD-sequencing technology was applied to generate genomic single nucleotide polymorphism (SNP) data from 67 samples of locoto chile cultigens from different Latin American countries, to characterize the diversity and genomic structure of the species throughout its range of distribution/cultivation. After applying various information content and quality filters, 1462 SNPs (out of 183569) were retained and used for population inferences. Three geographically structured main groups were distinguished, associated with a North-South distribution pattern: G1) cultigens from Central America to Mexico, G2) from Ecuador, Peru, to central-western Bolivia, G3) from central-southern Bolivia to Argentina. The AMOVA showed a moderate degree of divergence between the inferred clusters, while the pairwise FST values were consistent in showing a correlation between genetic and geographic distance. A high level of admixture/shared ancestry was also detected, mainly in G2 that presented higher genetic diversity. Indeed, G2 includes individuals from La Paz (Bolivia) surroundings with a broad morphological variation, including the smallest and fleshiest fruits, which suggests that new and extensive expeditions in central-western Bolivian highlands are needed to gain a better understanding of C. pubescens origin and diversification. Overall, this study provides new genome-wide supported insights into the diversity and differentiation of the locoto chile and will be useful for conservation and management strategies.
Fil: Palombo, Nahuel Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
Fil: Carrizo Garcia, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana
Valdivia
Chile
Asociación Latinoamericana de Genética
Materia
Capsicum pubescens
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/159545
Acceder
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spelling Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clusteringPalombo, Nahuel EzequielCarrizo Garcia, CarolinaCapsicum pubescenshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The hot chile Capsicum pubescens is mainly cultivated in Central-South America's mid-highlands, from Mexico to northwest Argentina. Despite being a crop of economic and cultural importance, little is known about its evolution and the genetic diversity and structure it harbors. Thus, RAD-sequencing technology was applied to generate genomic single nucleotide polymorphism (SNP) data from 67 samples of locoto chile cultigens from different Latin American countries, to characterize the diversity and genomic structure of the species throughout its range of distribution/cultivation. After applying various information content and quality filters, 1462 SNPs (out of 183569) were retained and used for population inferences. Three geographically structured main groups were distinguished, associated with a North-South distribution pattern: G1) cultigens from Central America to Mexico, G2) from Ecuador, Peru, to central-western Bolivia, G3) from central-southern Bolivia to Argentina. The AMOVA showed a moderate degree of divergence between the inferred clusters, while the pairwise FST values were consistent in showing a correlation between genetic and geographic distance. A high level of admixture/shared ancestry was also detected, mainly in G2 that presented higher genetic diversity. Indeed, G2 includes individuals from La Paz (Bolivia) surroundings with a broad morphological variation, including the smallest and fleshiest fruits, which suggests that new and extensive expeditions in central-western Bolivian highlands are needed to gain a better understanding of C. pubescens origin and diversification. Overall, this study provides new genome-wide supported insights into the diversity and differentiation of the locoto chile and will be useful for conservation and management strategies.Fil: Palombo, Nahuel Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Carrizo Garcia, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaXVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética HumanaValdiviaChileAsociación Latinoamericana de GenéticaSociedad Argentina de Genética2021info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/159545Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering; XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Valdivia; Chile; 2021; 134-1341852-6322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://sag.org.ar/jbag/project/vol-xxxii-suppl-1/Internacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:54:49Zoai:ri.conicet.gov.ar:11336/159545instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:54:49.325CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
title Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
spellingShingle Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
Palombo, Nahuel Ezequiel
Capsicum pubescens
title_short Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
title_full Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
title_fullStr Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
title_full_unstemmed Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
title_sort Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering
dc.creator.none.fl_str_mv Palombo, Nahuel Ezequiel
Carrizo Garcia, Carolina
author Palombo, Nahuel Ezequiel
author_facet Palombo, Nahuel Ezequiel
Carrizo Garcia, Carolina
author_role author
author2 Carrizo Garcia, Carolina
author2_role author
dc.subject.none.fl_str_mv Capsicum pubescens
topic Capsicum pubescens
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The hot chile Capsicum pubescens is mainly cultivated in Central-South America's mid-highlands, from Mexico to northwest Argentina. Despite being a crop of economic and cultural importance, little is known about its evolution and the genetic diversity and structure it harbors. Thus, RAD-sequencing technology was applied to generate genomic single nucleotide polymorphism (SNP) data from 67 samples of locoto chile cultigens from different Latin American countries, to characterize the diversity and genomic structure of the species throughout its range of distribution/cultivation. After applying various information content and quality filters, 1462 SNPs (out of 183569) were retained and used for population inferences. Three geographically structured main groups were distinguished, associated with a North-South distribution pattern: G1) cultigens from Central America to Mexico, G2) from Ecuador, Peru, to central-western Bolivia, G3) from central-southern Bolivia to Argentina. The AMOVA showed a moderate degree of divergence between the inferred clusters, while the pairwise FST values were consistent in showing a correlation between genetic and geographic distance. A high level of admixture/shared ancestry was also detected, mainly in G2 that presented higher genetic diversity. Indeed, G2 includes individuals from La Paz (Bolivia) surroundings with a broad morphological variation, including the smallest and fleshiest fruits, which suggests that new and extensive expeditions in central-western Bolivian highlands are needed to gain a better understanding of C. pubescens origin and diversification. Overall, this study provides new genome-wide supported insights into the diversity and differentiation of the locoto chile and will be useful for conservation and management strategies.
Fil: Palombo, Nahuel Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
Fil: Carrizo Garcia, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana
Valdivia
Chile
Asociación Latinoamericana de Genética
description The hot chile Capsicum pubescens is mainly cultivated in Central-South America's mid-highlands, from Mexico to northwest Argentina. Despite being a crop of economic and cultural importance, little is known about its evolution and the genetic diversity and structure it harbors. Thus, RAD-sequencing technology was applied to generate genomic single nucleotide polymorphism (SNP) data from 67 samples of locoto chile cultigens from different Latin American countries, to characterize the diversity and genomic structure of the species throughout its range of distribution/cultivation. After applying various information content and quality filters, 1462 SNPs (out of 183569) were retained and used for population inferences. Three geographically structured main groups were distinguished, associated with a North-South distribution pattern: G1) cultigens from Central America to Mexico, G2) from Ecuador, Peru, to central-western Bolivia, G3) from central-southern Bolivia to Argentina. The AMOVA showed a moderate degree of divergence between the inferred clusters, while the pairwise FST values were consistent in showing a correlation between genetic and geographic distance. A high level of admixture/shared ancestry was also detected, mainly in G2 that presented higher genetic diversity. Indeed, G2 includes individuals from La Paz (Bolivia) surroundings with a broad morphological variation, including the smallest and fleshiest fruits, which suggests that new and extensive expeditions in central-western Bolivian highlands are needed to gain a better understanding of C. pubescens origin and diversification. Overall, this study provides new genome-wide supported insights into the diversity and differentiation of the locoto chile and will be useful for conservation and management strategies.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Congreso
Journal
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/159545
Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering; XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Valdivia; Chile; 2021; 134-134
1852-6322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/159545
identifier_str_mv Population genomic analysis of locoto chile (Capsicum pubescens): New insights on its diversity and geographic clustering; XVIII Congreso Latinoamericano de Genética; LIV Reunión Anual de la Sociedad de Genética de Chile; XLIX Congreso Argentino de Genética; VIII Congreso de la Sociedad Uruguaya de Genética; I Congreso Paraguayo de Genética y V Congreso Latinoamericano de Genética Humana; Valdivia; Chile; 2021; 134-134
1852-6322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://sag.org.ar/jbag/project/vol-xxxii-suppl-1/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Sociedad Argentina de Genética
publisher.none.fl_str_mv Sociedad Argentina de Genética
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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