SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of eucalyptus grandis
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 Dive...
| Autores principales: | , , , , |
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| Formato: | info:eu-repo/semantics/article |
| Lenguaje: | Inglés |
| Publicado: |
2017
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| Materias: | |
| Acceso en línea: | 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 |
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| author | Cappa, Eduardo Pablo Klapste, Jaroslav Garcia, Martin Nahuel Villalba, Pamela Victoria Marcucci Poltri, Susana Noemi |
| author_browse | Cappa, Eduardo Pablo Garcia, Martin Nahuel Klapste, Jaroslav Marcucci Poltri, Susana Noemi Villalba, Pamela Victoria |
| author_facet | Cappa, Eduardo Pablo Klapste, Jaroslav Garcia, Martin Nahuel Villalba, Pamela Victoria Marcucci Poltri, Susana Noemi |
| author_sort | Cappa, Eduardo Pablo |
| collection | INTA Digital |
| 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. |
| format | info:eu-repo/semantics/article |
| id | INTA985 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA9852018-02-26T12:51:13Z 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 Klapste, Jaroslav Garcia, Martin Nahuel Villalba, Pamela Victoria Marcucci Poltri, Susana Noemi Genética Fitomejoramiento Eucalyptus grandis Marcadores genéticos Genetics Plant Breeding Genetic Markers Marcadores Moleculares 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 2017-08-16T16:47:11Z 2017-08-16T16:47:11Z 2016 info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion info:ar-repo/semantics/artículo 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 eng info:eu-repo/semantics/restrictedAccess application/pdf Molecular breeding 36 : 97. (July 2016) |
| spellingShingle | Genética Fitomejoramiento Eucalyptus grandis Marcadores genéticos Genetics Plant Breeding Genetic Markers Marcadores Moleculares Cappa, Eduardo Pablo Klapste, Jaroslav Garcia, Martin Nahuel Villalba, Pamela Victoria Marcucci Poltri, Susana Noemi 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 |
| 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_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_sort | ssrs snps and darts comparison on estimation of relatedness and genetic parameters precision from a small half sib sample population of eucalyptus grandis |
| topic | Genética Fitomejoramiento Eucalyptus grandis Marcadores genéticos Genetics Plant Breeding Genetic Markers Marcadores Moleculares |
| 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 |
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