Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Battenfield SD

PROVIDER: S-EPMC6264898 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Battenfield Sarah D SD Sheridan Jaime L JL Silva Luciano D C E LDCE Miclaus Kelci J KJ Dreisigacker Susanne S Wolfinger Russell D RD Peña Roberto J RJ Singh Ravi P RP Jackson Eric W EW Fritz Allan K AK Guzmán Carlos C Poland Jesse A JA

PloS one 20181129 11

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 qua ...[more]

PMID: 30496187

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Dataset Information

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

Publications

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

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