Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment
Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the fiel...
| Autores: | , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2020 |
| País: | México |
| Institución: | Centro Internacional de Mejoramiento de Maíz y Trigo |
| Repositorio: | Repositorio Institucional de Publicaciones Multimedia del CIMMYT |
| OAI Identifier: | oai:repository.cimmyt.org:10883/21082 |
| Acceso en línea: | https://hdl.handle.net/10883/21082 |
| Access Level: | acceso abierto |
| Palabra clave: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY GWAS Anther Extrusion Floral Traits Hybrid Wheat Genome-Wide Prediction ANTHERS WHEAT HYBRIDS GENOMES BREEDING |
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Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environmentAdhikari, A.Basnet, B.R.Crossa, J.Dreisigacker, S.Camarillo-Castillo, F.Bhati, P.Jarquin, D.Yann ManesIbrahim, A.M.H.AGRICULTURAL SCIENCES AND BIOTECHNOLOGYGWASAnther ExtrusionFloral TraitsHybrid WheatGenome-Wide PredictionANTHERSWHEATHYBRIDSGENOMESBREEDINGAnther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017–2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from −0.03 to 0.74 for AC and −0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle.Frontiers Media2020-12-19T01:20:14Z2020-12-19T01:20:14Z2020Published Versioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10883/2108210.3389/fgene.2020.586687111664-8021Frontiers in Genetics586687reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYTinstname:Centro Internacional de Mejoramiento de Maíz y Trigoinstacron:CIMMYTEnglishhttp://hdl.handle.net/11529/10548495https://figshare.com/collections/Genome-Wide_Association_Mapping_and_Genomic_Prediction_of_Anther_Extrusion_in_CIMMYT_Hybrid_Wheat_Breeding_Program_via_Modeling_Pedigree_Genomic_Relationship_and_Interaction_With_the_Environment/5233379SwitzerlandCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purposeOpen Accessinfo:eu-repo/semantics/openAccessoai:repository.cimmyt.org:10883/210822024-10-11T19:59:12Z |
| dc.title.none.fl_str_mv |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| title |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| spellingShingle |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment Adhikari, A. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY GWAS Anther Extrusion Floral Traits Hybrid Wheat Genome-Wide Prediction ANTHERS WHEAT HYBRIDS GENOMES BREEDING |
| title_short |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| title_full |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| title_fullStr |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| title_full_unstemmed |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| title_sort |
Genome-wide association mapping and genomic prediction of anther extrusion in CIMMYT hybrid wheat breeding program via modeling pedigree, genomic relationship, and interaction with the environment |
| dc.creator.none.fl_str_mv |
Adhikari, A. Basnet, B.R. Crossa, J. Dreisigacker, S. Camarillo-Castillo, F. Bhati, P. Jarquin, D. Yann Manes Ibrahim, A.M.H. |
| author |
Adhikari, A. |
| author_facet |
Adhikari, A. Basnet, B.R. Crossa, J. Dreisigacker, S. Camarillo-Castillo, F. Bhati, P. Jarquin, D. Yann Manes Ibrahim, A.M.H. |
| author_role |
author |
| author2 |
Basnet, B.R. Crossa, J. Dreisigacker, S. Camarillo-Castillo, F. Bhati, P. Jarquin, D. Yann Manes Ibrahim, A.M.H. |
| author2_role |
author author author author author author author author |
| dc.subject.none.fl_str_mv |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY GWAS Anther Extrusion Floral Traits Hybrid Wheat Genome-Wide Prediction ANTHERS WHEAT HYBRIDS GENOMES BREEDING |
| topic |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY GWAS Anther Extrusion Floral Traits Hybrid Wheat Genome-Wide Prediction ANTHERS WHEAT HYBRIDS GENOMES BREEDING |
| description |
Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field experiments in 2017–2019 and genotyped with the 20K Infinitum is elect SNP array. GWAS produced five marker trait associations with small effects. For GP, the main effects of lines (L), environment (E), genomic (G) and pedigree relationships (A), and their interaction effects with environments were used to develop seven statistical models of incremental complexity. The base model used only L and E, whereas the most complex model included L, E, G, A, and G × E and A × E. These models were evaluated in three cross-validation scenarios (CV0, CV1, and CV2). In cross-validation CV0, data from two environments were used to predict an untested environment; in random cross-validation CV1, the test set was never evaluated in any environment; and in CV2, the genotypes in the test set were evaluated in only a subset of environments. The prediction accuracies ranged from −0.03 to 0.74 for AC and −0.01 to 0.54 for VS across different models and CV schemes. For both traits, the highest prediction accuracies with low variance were observed in CV2, and inclusion of the interaction effects increased prediction accuracy for AC only. In CV0, the prediction accuracy was 0.73 and 0.45 for AC and VS, respectively, indicating the high reliability of across environment prediction. Genomic prediction appears to be a very reliable tool for AE in hybrid wheat breeding. Moreover, high prediction accuracy in CV0 demonstrates the possibility of implementing genomic selection across breeding cycles in related germplasm, aiding the rapid breeding cycle. |
| publishDate |
2020 |
| dc.date.none.fl_str_mv |
2020-12-19T01:20:14Z 2020-12-19T01:20:14Z 2020 |
| dc.type.none.fl_str_mv |
Published Version info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10883/21082 10.3389/fgene.2020.586687 |
| url |
https://hdl.handle.net/10883/21082 |
| identifier_str_mv |
10.3389/fgene.2020.586687 |
| dc.language.none.fl_str_mv |
English |
| language_invalid_str_mv |
English |
| dc.relation.none.fl_str_mv |
http://hdl.handle.net/11529/10548495 https://figshare.com/collections/Genome-Wide_Association_Mapping_and_Genomic_Prediction_of_Anther_Extrusion_in_CIMMYT_Hybrid_Wheat_Breeding_Program_via_Modeling_Pedigree_Genomic_Relationship_and_Interaction_With_the_Environment/5233379 |
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Open Access info:eu-repo/semantics/openAccess |
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Open Access |
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openAccess |
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application/pdf |
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Switzerland |
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Frontiers Media |
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Frontiers Media |
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11 1664-8021 Frontiers in Genetics 586687 reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYT instname:Centro Internacional de Mejoramiento de Maíz y Trigo instacron:CIMMYT |
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Centro Internacional de Mejoramiento de Maíz y Trigo |
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Repositorio Institucional de Publicaciones Multimedia del CIMMYT |
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