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Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program

One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year...

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Autores principales: Battenfield, Sarah D., Sheridan, Jaime L., Silva, Luciano D. C. E., Miclaus, Kelci J., Dreisigacker, Susanne, Wolfinger, Russell D., Peña, Roberto J., Singh, Ravi P., Jackson, Eric W., Fritz, Allan. K., Guzmán, Carlos, Poland, Jesse A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264898/
https://www.ncbi.nlm.nih.gov/pubmed/30496187
http://dx.doi.org/10.1371/journal.pone.0204757
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author Battenfield, Sarah D.
Sheridan, Jaime L.
Silva, Luciano D. C. E.
Miclaus, Kelci J.
Dreisigacker, Susanne
Wolfinger, Russell D.
Peña, Roberto J.
Singh, Ravi P.
Jackson, Eric W.
Fritz, Allan. K.
Guzmán, Carlos
Poland, Jesse A.
author_facet Battenfield, Sarah D.
Sheridan, Jaime L.
Silva, Luciano D. C. E.
Miclaus, Kelci J.
Dreisigacker, Susanne
Wolfinger, Russell D.
Peña, Roberto J.
Singh, Ravi P.
Jackson, Eric W.
Fritz, Allan. K.
Guzmán, Carlos
Poland, Jesse A.
author_sort Battenfield, Sarah D.
collection PubMed
description One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multi-year unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in ‘breeding-assisted genomics’ across many crops to greatly increase our functional understanding of plant genomes.
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spelling pubmed-62648982018-12-19 Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program Battenfield, Sarah D. Sheridan, Jaime L. Silva, Luciano D. C. E. Miclaus, Kelci J. Dreisigacker, Susanne Wolfinger, Russell D. Peña, Roberto J. Singh, Ravi P. Jackson, Eric W. Fritz, Allan. K. Guzmán, Carlos Poland, Jesse A. PLoS One Research Article One of the biggest challenges for genetic studies on natural or unstructured populations is the unbalanced datasets where individuals are measured at different times and environments. This problem is also common in crop and animal breeding where many individuals are only evaluated for a single year and large but unbalanced datasets can be generated over multiple years. Many wheat breeding programs have focused on increasing bread wheat (Triticum aestivum L.) yield, but processing and end-use quality are critical components when considering its use in feeding the rising population of the next century. The challenges with end-use quality trait improvements are high cost and seed amounts for testing, the latter making selection in early breeding populations impossible. Here we describe a novel approach to identify marker-trait associations within a breeding program using a meta-genome wide association study (GWAS), which combines GWAS analysis from multi-year unbalanced breeding nurseries, in a manner reflecting meta-GWAS in humans. This method facilitated mapping of processing and end-use quality phenotypes from advanced breeding lines (n = 4,095) of the CIMMYT bread wheat breeding program from 2009 to 2014. Using the meta-GWAS we identified marker-trait associations, allele effects, candidate genes, and can select using markers generated in this process. Finally, the scope of this approach can be broadly applied in ‘breeding-assisted genomics’ across many crops to greatly increase our functional understanding of plant genomes. Public Library of Science 2018-11-29 /pmc/articles/PMC6264898/ /pubmed/30496187 http://dx.doi.org/10.1371/journal.pone.0204757 Text en © 2018 Battenfield et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Battenfield, Sarah D.
Sheridan, Jaime L.
Silva, Luciano D. C. E.
Miclaus, Kelci J.
Dreisigacker, Susanne
Wolfinger, Russell D.
Peña, Roberto J.
Singh, Ravi P.
Jackson, Eric W.
Fritz, Allan. K.
Guzmán, Carlos
Poland, Jesse A.
Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title_full Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title_fullStr Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title_full_unstemmed Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title_short Breeding-assisted genomics: Applying meta-GWAS for milling and baking quality in CIMMYT wheat breeding program
title_sort breeding-assisted genomics: applying meta-gwas for milling and baking quality in cimmyt wheat breeding program
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264898/
https://www.ncbi.nlm.nih.gov/pubmed/30496187
http://dx.doi.org/10.1371/journal.pone.0204757
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