Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants
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 introduc...
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2014-11-01
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Series: | The Plant Genome |
Online Access: | https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.05.0023 |
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doaj-a6110aa89d6e445f9e21371ffad1caf42020-11-25T02:54:40ZengWileyThe Plant Genome1940-33722014-11-017310.3835/plantgenome2014.05.0023plantgenome2014.05.0023Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop PlantsKelly SwartsHuihui LiJ. Alberto Romero NavarroDong AnMaria Cinta RomaySarah HearneCharlotte AcharyaJeffrey C. GlaubitzSharon MitchellRobert J. ElshireEdward S. BucklerPeter J. BradburyNext-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 ( 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.https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.05.0023 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kelly Swarts Huihui Li J. Alberto Romero Navarro Dong An Maria Cinta Romay Sarah Hearne Charlotte Acharya Jeffrey C. Glaubitz Sharon Mitchell Robert J. Elshire Edward S. Buckler Peter J. Bradbury |
spellingShingle |
Kelly Swarts Huihui Li J. Alberto Romero Navarro Dong An Maria Cinta Romay Sarah Hearne Charlotte Acharya Jeffrey C. Glaubitz Sharon Mitchell Robert J. Elshire Edward S. Buckler Peter J. Bradbury Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants The Plant Genome |
author_facet |
Kelly Swarts Huihui Li J. Alberto Romero Navarro Dong An Maria Cinta Romay Sarah Hearne Charlotte Acharya Jeffrey C. Glaubitz Sharon Mitchell Robert J. Elshire Edward S. Buckler Peter J. Bradbury |
author_sort |
Kelly Swarts |
title |
Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants |
title_short |
Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants |
title_full |
Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants |
title_fullStr |
Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants |
title_full_unstemmed |
Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants |
title_sort |
novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants |
publisher |
Wiley |
series |
The Plant Genome |
issn |
1940-3372 |
publishDate |
2014-11-01 |
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 ( 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. |
url |
https://dl.sciencesocieties.org/publications/tpg/articles/7/3/plantgenome2014.05.0023 |
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