Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants. Swarts, K., Li, H., Romero Navarro, J. A., An, D., Romay, M. C., Hearne, S., Acharya, C., Glaubitz, J. C., Mitchell, S., Elshire, R. J., Buckler, E. S., & Bradbury, P. J. The Plant Genome, 7(3):plantgenome2014.05.0023, 2014. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3835/plantgenome2014.05.0023![Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{swarts_novel_2014,
title = {Novel {Methods} to {Optimize} {Genotypic} {Imputation} for {Low}-{Coverage}, {Next}-{Generation} {Sequence} {Data} in {Crop} {Plants}},
volume = {7},
copyright = {© 2014 The Authors.},
issn = {1940-3372},
url = {https://onlinelibrary.wiley.com/doi/abs/10.3835/plantgenome2014.05.0023},
doi = {10.3835/plantgenome2014.05.0023},
abstract = {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.},
language = {en},
number = {3},
urldate = {2024-03-22},
journal = {The Plant Genome},
author = {Swarts, Kelly and Li, Huihui and Romero Navarro, J. Alberto and An, Dong and Romay, Maria Cinta and Hearne, Sarah and Acharya, Charlotte and Glaubitz, Jeffrey C. and Mitchell, Sharon and Elshire, Robert J. and Buckler, Edward S. and Bradbury, Peter J.},
year = {2014},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3835/plantgenome2014.05.0023},
pages = {plantgenome2014.05.0023},
}
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