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Novel methods to optimize genotypic imputation for low-coverage, next- generation sequence data in crops plants

Creator: Swarts, K.
Creator: Huihui Li
Creator: Romero Navarro, J. A.
Creator: Dong An
Creator: Romay, C.
Creator: Hearne, S.
Creator: Acharya, C.
Creator: Glaubitz, J.C.
Creator: Mitchell, S.E.
Creator: Elshire, R.J.
Creator: Buckler, E.S.
Creator: Bradbury, P.J.
Year: 2014
Language: English
Publisher: CSSA
Publisher: Wiley
Copyright: CIMMYT 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 indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place of Publication: USA
Pages: 1-12
Issue: 3
Volume: 7
DOI: 10.3835/plantgenome2014.05.0023
Description: Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduce Full-Sib Family Haplotype Imputation (FSFHap), optimized for full-sib populations, and a generalized method, Fast Inbred Line Library ImputatioN (FILLIN), to rapidly and accurately impute missing genotypes in GBS-type data with ordered markers. FSFHap and FILLIN impute missing genotypes with high accuracy in GBS-genotyped maize (Zea mays L.) inbred lines and breeding populations, while Beagle v. 4 is still preferable for diverse heterozygous populations. FILLIN and FSFHap are implemented in TASSEL 5.0.
ISSN: 1940-3372
Journal: Plant Genome

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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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