Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit cr...

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Authors: Talavera, Alicia, Soorni, Aboozar, Bombarely, Aureliano, Matas, Antonio J, Hormaza, Jose I
Format: article
Status:Versión aceptada para publicación
Publication Date:2023
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/372034
Online Access:http://hdl.handle.net/10261/372034
https://api.elsevier.com/content/abstract/scopus_id/85077336536
Access Level:Open access
Keyword:avocado
Genome-Wide SNP
Persea americana Mill
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spelling Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)Talavera, AliciaSoorni, AboozarBombarely, AurelianoMatas, Antonio JHormaza, Jose IavocadoGenome-Wide SNPPersea americana MillModern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado 'Hass' draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.Tis work was supported by Ministerio de Economía y Competitividad- European Regional Development Fund. (AGL2016-77267-R). AT was supported by an FPI fellowship from Ministerio de Economía y Competitividad (BES-2014-068832)Peer reviewedSpringer NatureEuropean CommissionMinisterio de Economía y Competitividad (España)0000-0002-1285-78910000-0001-5917-66900000-0001-6257-89140000-0003-4348-39300000-0001-5449-7444Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/372034https://api.elsevier.com/content/abstract/scopus_id/85077336536reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO//AGL2016-77267-Rinfo:eu-repo/grantAgreement/MINECO//BES-2014-068832Scientific reportshttps://doi.org/10.1038/s41598-019-56526-4Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3720342026-05-22T06:33:51Z
dc.title.none.fl_str_mv Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
title Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
spellingShingle Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
Talavera, Alicia
avocado
Genome-Wide SNP
Persea americana Mill
title_short Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
title_full Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
title_fullStr Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
title_full_unstemmed Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
title_sort Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)
dc.creator.none.fl_str_mv Talavera, Alicia
Soorni, Aboozar
Bombarely, Aureliano
Matas, Antonio J
Hormaza, Jose I
author Talavera, Alicia
author_facet Talavera, Alicia
Soorni, Aboozar
Bombarely, Aureliano
Matas, Antonio J
Hormaza, Jose I
author_role author
author2 Soorni, Aboozar
Bombarely, Aureliano
Matas, Antonio J
Hormaza, Jose I
author2_role author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Ministerio de Economía y Competitividad (España)
0000-0002-1285-7891
0000-0001-5917-6690
0000-0001-6257-8914
0000-0003-4348-3930
0000-0001-5449-7444
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv avocado
Genome-Wide SNP
Persea americana Mill
topic avocado
Genome-Wide SNP
Persea americana Mill
description Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado 'Hass' draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.
publishDate 2023
dc.date.none.fl_str_mv 2023
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/372034
https://api.elsevier.com/content/abstract/scopus_id/85077336536
url http://hdl.handle.net/10261/372034
https://api.elsevier.com/content/abstract/scopus_id/85077336536
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO//AGL2016-77267-R
info:eu-repo/grantAgreement/MINECO//BES-2014-068832
Scientific reports
https://doi.org/10.1038/s41598-019-56526-4
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
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repository.name.fl_str_mv
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