SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis

Autores
Cappa, Eduardo Pablo; Klapste, Jaroslav; Garcia, Martin Nahuel; Villalba, Pamela Victoria; Marcucci Poltri, Susana Noemi
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión aceptada
Descripción
Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihoodbased estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.
Inst. de Biotecnología
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Klapste, Jaroslav. University of British Columbia. Department of Forest and Conservation Sciences; Canadá. Czech University of Life Sciences. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República Checa
Fil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Villalba, Pamela Victoria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fuente
Molecular breeding 36 : 97. (July 2016)
Materia
Genética
Fitomejoramiento
Eucalyptus grandis
Marcadores genéticos
Genetics
Plant Breeding
Genetic Markers
Marcadores Moleculares
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/985
Acceder
id INTADig_704e9ef9db22678f5b78071df650f568
oai_identifier_str oai:localhost:20.500.12123/985
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandisCappa, Eduardo PabloKlapste, JaroslavGarcia, Martin NahuelVillalba, Pamela VictoriaMarcucci Poltri, Susana NoemiGenéticaFitomejoramientoEucalyptus grandisMarcadores genéticosGeneticsPlant BreedingGenetic MarkersMarcadores MolecularesSimple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihoodbased estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.Inst. de BiotecnologíaFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Klapste, Jaroslav. University of British Columbia. Department of Forest and Conservation Sciences; Canadá. Czech University of Life Sciences. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República ChecaFil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Villalba, Pamela Victoria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina2017-08-16T16:47:11Z2017-08-16T16:47:11Z2016info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/985https://link.springer.com/article/10.1007%2Fs11032-016-0522-71572-9788 (Online)1380-3743 (Print)https://doi.org/10.1007/s11032-016-0522-7Molecular breeding 36 : 97. (July 2016)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-10-16T09:28:59Zoai:localhost:20.500.12123/985instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:28:59.407INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
title SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
spellingShingle SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
Cappa, Eduardo Pablo
Genética
Fitomejoramiento
Eucalyptus grandis
Marcadores genéticos
Genetics
Plant Breeding
Genetic Markers
Marcadores Moleculares
title_short SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
title_full SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
title_fullStr SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
title_full_unstemmed SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
title_sort SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
dc.creator.none.fl_str_mv Cappa, Eduardo Pablo
Klapste, Jaroslav
Garcia, Martin Nahuel
Villalba, Pamela Victoria
Marcucci Poltri, Susana Noemi
author Cappa, Eduardo Pablo
author_facet Cappa, Eduardo Pablo
Klapste, Jaroslav
Garcia, Martin Nahuel
Villalba, Pamela Victoria
Marcucci Poltri, Susana Noemi
author_role author
author2 Klapste, Jaroslav
Garcia, Martin Nahuel
Villalba, Pamela Victoria
Marcucci Poltri, Susana Noemi
author2_role author
author
author
author
dc.subject.none.fl_str_mv Genética
Fitomejoramiento
Eucalyptus grandis
Marcadores genéticos
Genetics
Plant Breeding
Genetic Markers
Marcadores Moleculares
topic Genética
Fitomejoramiento
Eucalyptus grandis
Marcadores genéticos
Genetics
Plant Breeding
Genetic Markers
Marcadores Moleculares
dc.description.none.fl_txt_mv Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihoodbased estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.
Inst. de Biotecnología
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Klapste, Jaroslav. University of British Columbia. Department of Forest and Conservation Sciences; Canadá. Czech University of Life Sciences. Faculty of Forestry and Wood Sciences. Department of Genetics and Physiology of Forest Trees; República Checa
Fil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Villalba, Pamela Victoria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
description Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihoodbased estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017-08-16T16:47:11Z
2017-08-16T16:47:11Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/985
https://link.springer.com/article/10.1007%2Fs11032-016-0522-7
1572-9788 (Online)
1380-3743 (Print)
https://doi.org/10.1007/s11032-016-0522-7
url http://hdl.handle.net/20.500.12123/985
https://link.springer.com/article/10.1007%2Fs11032-016-0522-7
https://doi.org/10.1007/s11032-016-0522-7
identifier_str_mv 1572-9788 (Online)
1380-3743 (Print)
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Molecular breeding 36 : 97. (July 2016)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
_version_ 1846143494473646080
score 12.712165

Publicaciones similares