Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato

ilustraciones, gráficas, tablas

Autores:: Parra Galindo, Maria Angelica

Tipo de recurso:

Fecha de publicación:: 2019

Institución:: Universidad Nacional de Colombia

Repositorio:: Universidad Nacional de Colombia

Idioma:: eng

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network_acronym_str	UNACIONAL2
network_name_str	Universidad Nacional de Colombia
repository_id_str
dc.title.eng.fl_str_mv	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
dc.title.translated.spa.fl_str_mv	Análisis de rutas biológicas y estudio de asociación amplia del genoma identificaron factores genéticos del cromosoma 10 asociados con la variación de antocianinas en papa
title	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
spellingShingle	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato 630 - Agricultura y tecnologías relacionadas::631 - Técnicas específicas, aparatos, equipos, materiales Genomas Antocianinas Papa genomes anthocyanins potatoes Biological pathway analysis Anthocyanin biosynthesis Phenylalanine ammonia-lyase Biosynthetic cluster Análisis de rutas biológicas Biosíntesis de antocianinas Fenilalanina amonio-liasa Cluster biosintético
title_short	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
title_full	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
title_fullStr	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
title_full_unstemmed	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
title_sort	Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato
dc.creator.fl_str_mv	Parra Galindo, Maria Angelica
dc.contributor.advisor.spa.fl_str_mv	Soto Sedano, Johana Carolina Mosquera Vásquez, Teresa De Jesús
dc.contributor.author.spa.fl_str_mv	Parra Galindo, Maria Angelica
dc.contributor.corporatename.spa.fl_str_mv	Universidad Nacional de Colombia
dc.contributor.researchgroup.spa.fl_str_mv	Genética de Rasgos de Interés Agronómico
dc.subject.ddc.spa.fl_str_mv	630 - Agricultura y tecnologías relacionadas::631 - Técnicas específicas, aparatos, equipos, materiales
topic	630 - Agricultura y tecnologías relacionadas::631 - Técnicas específicas, aparatos, equipos, materiales Genomas Antocianinas Papa genomes anthocyanins potatoes Biological pathway analysis Anthocyanin biosynthesis Phenylalanine ammonia-lyase Biosynthetic cluster Análisis de rutas biológicas Biosíntesis de antocianinas Fenilalanina amonio-liasa Cluster biosintético
dc.subject.agrovoc.spa.fl_str_mv	Genomas Antocianinas Papa
dc.subject.agrovoc.eng.fl_str_mv	genomes anthocyanins potatoes
dc.subject.proposal.eng.fl_str_mv	Biological pathway analysis Anthocyanin biosynthesis Phenylalanine ammonia-lyase Biosynthetic cluster
dc.subject.proposal.spa.fl_str_mv	Análisis de rutas biológicas Biosíntesis de antocianinas Fenilalanina amonio-liasa Cluster biosintético
description	ilustraciones, gráficas, tablas
publishDate	2019
dc.date.issued.spa.fl_str_mv	2019-12-16
dc.date.accessioned.spa.fl_str_mv	2020-04-06T16:54:54Z
dc.date.available.spa.fl_str_mv	2020-04-06T16:54:54Z
dc.type.spa.fl_str_mv	Trabajo de grado - Maestría
dc.type.driver.spa.fl_str_mv	info:eu-repo/semantics/masterThesis
dc.type.version.spa.fl_str_mv	info:eu-repo/semantics/acceptedVersion
dc.type.content.spa.fl_str_mv	Text
dc.type.redcol.spa.fl_str_mv	http://purl.org/redcol/resource_type/TM
status_str	acceptedVersion
dc.identifier.uri.none.fl_str_mv	https://repositorio.unal.edu.co/handle/unal/77404
dc.identifier.instname.spa.fl_str_mv	Universidad Nacional de Colombia
dc.identifier.reponame.spa.fl_str_mv	Repositorio Institucional Universidad Nacional de Colombia
dc.identifier.repourl.none.fl_str_mv	https://repositorio.unal.edu.co/
url	https://repositorio.unal.edu.co/handle/unal/77404 https://repositorio.unal.edu.co/
identifier_str_mv	Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia
dc.language.iso.spa.fl_str_mv	eng
language	eng
dc.relation.spa.fl_str_mv	https://www.mdpi.com/2073-4395/9/7/366
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dc.relation.references.spa.fl_str_mv	Ripley, Brian D. 2001. “The R Project in Statistical Computing.” MSOR Connections. The Newsletter of the LTSN Maths, Stats & OR Network 1 (1). Citeseer: 23–25.
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dc.format.extent.spa.fl_str_mv	xvi, 130 páginas
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dc.publisher.spa.fl_str_mv	Universidad Nacional de Colombia
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dc.publisher.faculty.spa.fl_str_mv	Facultad de Ciencias Agrarias
dc.publisher.place.spa.fl_str_mv	Bogotá, Colombia
dc.publisher.branch.spa.fl_str_mv	Universidad Nacional de Colombia - Sede Bogotá
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spelling	Atribución-NoComercial-SinDerivadas 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Soto Sedano, Johana Carolina8aea8bfb-1caf-4d26-a769-c512341e0522Mosquera Vásquez, Teresa De Jesús70c61109-5b5c-44a4-a617-9a527eae04caParra Galindo, Maria Angelica0f3bcecc-61bf-4eeb-9116-db1a7f30b255Universidad Nacional de ColombiaGenética de Rasgos de Interés Agronómico2020-04-06T16:54:54Z2020-04-06T16:54:54Z2019-12-16https://repositorio.unal.edu.co/handle/unal/77404Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, gráficas, tablasPotato is considered a basic crop worldwide and is the third source of antioxidants in the human diet, due to its per capita consumption. Some of the most relevant antioxidant compounds in potatoes within dietary polyphenols are anthocyanin pigments. The anthocyanin compounds’ synthesis implies a chain of potentially superimposed regulatory signals. Since their synthesis cannot be seen exclusively from the transcription of the genes included in the synthesis of the enzymes involved in the biosynthetic pathway but it is important to consider different allelic variants not associated in the pathway and / or transcription factors that may be playing an important role in the regulation of the synthesis of the enzymes and, therefore, in the production and accumulation of these bioactive compounds in different plant tissues. To approach the understanding of the genetic architecture that controls complex traits such as nutritional quality, specifically the dietary polyphenols compounds. In different species and also in potato, the genome wide association mapping strategy (GWAS) has been implemented, in order to identify genes and sequences that control different traits of agronomic interest, especially quantitative traits to apply in genetic breeding programs. Thus, since regulation and accumulation of bioactive compounds in plants is governed by multiple genes organized within complex biological networks, the genome-wide association study approach presents a limitation does not offer direct evidence about the biological process that link the variant associated with the trait. In this way, the integration of the biological pathway approach is considered in the study of the genetic association of anthocyanin compounds in potatoes. The objective of this research was the integration of allelic variants / genes obtained by a study of wide genome association and allelic variants of genes putatively related in the biosynthetic pathway of anthocyanin compounds. The approach integrating the genetic participation of each associated genomic regions, allowing a biological interpretation of each association. An association panel of 109 Phureja Group diploid potato genotypes was used. which phenotyping for the five-anthocyanin content by means of High Performance Liquid Chromatography (HPLC) and genotyping under the genotyping by sequencing (GBS) methodology with a matrix of 87,657 single nucleotide polymorphic markers. Promising biosinthetic pathway models were established that integrated the gene participation of each associated gene. Promising biosynthetic pathway models were established that integrated the gene involvement of each associated gene. As a result, a region of interest on chromosome 10 was identified, identifying genes associated with the anthocyanin biosynthetic pathway in a 4Mpb region on the final arm of chromosome 10; a marker linked to the phenylalanine ammonia lyase gene, which encodes the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with the five anthocyanin compounds evaluated, explaining the greater phenotypic variation of the trait. The L-methionine biosynthetic pathway was identified as being important for the late anthocyanin pathway. This investigation confirmed genomic regions whose allelic variability is associated with the analyzed compounds and which had previously been detected. It also allowed the identification of other new genomic regions in a “biological pathways” approach complementing existing knowledge. The results contribute to the understanding of anthocyanin regulation in potatoes and can be used in future studies for integration into potato improvement programs.La papa es considerada un cultivo básico a nivel mundial y constituye la tercera fuente de antioxidantes en la dieta humana, debido a su consumo per cápita. Algunos de los compuestos antioxidantes más relevantes en papa dentro de los polifenoles dietarios son los pigmentos antociánicos. La síntesis de los compuestos antociánicos implica una matriz de señales reguladoras potencialmente superpuestas, por lo que, no se puede ver su síntesis exclusivamente a partir de la transcripción de los genes incluidos en la síntesis de las enzimas involucradas en la ruta biosintética, sino que, es importante considerar diferentes variantes alélicas no asociadas en las rutas y/o factores de transcripción que pueden estar desempeñando un papel importante en la regulación y acumulación de estos compuestos en diferentes tejidos vegetales. Para entender la arquitectura genética que gobierna rasgos complejos relacionados con la composición nutricional de los alimentos, como es la composición de antocianinas en diferentes especies y en papa; se han implementado estrategias como los estudios de mapeo de asociación amplia del genoma (GWAS), en programas de mejoramiento genético, con el fin de identificar loci de caracteres cuantitativos asociados al rasgo, para luego aplicar en programas de mejoramiento genético. En el caso de polifenoles dietarios, debido a que su síntesis y acumulación en plantas está regulada por múltiples genes que se organizan dentro de redes biológicas complejas, la metodología de GWAS presenta una limitante y es que no ofrece evidencia directa acerca del proceso biológico que liga la variante asociada con el rasgo. Esta investigación plantea la integración de la aproximación de rutas biológicas “biological pathway” en un estudio de asociación genética de compuestos de antocianinas en papa. El objetivo de esta investigación fue la integración de variantes alélicas/genes obtenidos por un estudio de asociación amplia del genoma y variantes alélicas de genes putativamente relacionados en la ruta biosintética de los compuestos antociánicos, integrando la participación génica de cada una de las regiones genómicas asociadas, permitiendo una interpretación biológica de cada asociación. Para lo cual, se empleó un panel de asociación de 109 genotipos de papa diploide Grupo Phureja, fenotipado para el rasgo del contenido de cinco antocianindinas por medio de cromatografía liquida de alta precisión (HPLC) y, genotipado bajo la metodología de “genotyping by sequencing” con una matriz de 87,657 marcadores polimórficos de un solo nucleótido. Se establecieron modelos de rutas biosintéticas promisorias que integraron la participación génica de cada gen asociado. Como resultado se identificó una región de interés en el cromosoma 10, identificando genes asociados a la ruta biosintética de las antocianinas en una región de 4Mpb en el brazo final del cromosoma 10; un marcador ligado al gen de fenilalanina amoniaco-liasa, que codifica la primera enzima en la ruta biosintética de fenilpropanoides, se asoció a los cinco compuestos antociánicos evaluados explicando la mayor variación fenotípica del rasgo. Se identificó que la ruta biosintética de la L-metionina es importante para la ruta tardía de las antocianinas. Esta investigación confirmó regiones genómicas cuya variabilidad alélica está asociada con los compuestos analizados y que ya previamente habían sido detectadas. También permitió la identificación de otras nuevas regiones genómicas en un enfoque de “rutas biológicas” complementando el conocimiento existente. 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Citeseer: 23–25.630 - Agricultura y tecnologías relacionadas::631 - Técnicas específicas, aparatos, equipos, materialesGenomasAntocianinasPapagenomesanthocyaninspotatoesBiological pathway analysisAnthocyanin biosynthesisPhenylalanine ammonia-lyaseBiosynthetic clusterAnálisis de rutas biológicasBiosíntesis de antocianinasFenilalanina amonio-liasaCluster biosintéticoBiological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potatoAnálisis de rutas biológicas y estudio de asociación amplia del genoma identificaron factores genéticos del cromosoma 10 asociados con la variación de antocianinas en papaTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMEstudiantesInvestigadoresPúblico generalORIGINAL1030637000.2019.pdf1030637000.2019.pdfTesis de Maestría en Ciencias 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Biological pathway analysis and genome wide association study identified genetic factors on chromosome 10 associated with anthocyanin variation in potato

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