Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants
文献类型： 外文期刊
第一作者： Swarts, Kelly
作者： Swarts, Kelly;Navarro, J. Alberto Romero;Li, Huihui;Li, Huihui;Navarro, J. Alberto Romero;An, Dong;Romay, Maria Cinta;Acharya, Charlotte;Glaubitz, Jeffrey C.;Mitchell, Sharon;Hearne, Sarah;Elshire, Robert J.;Buckler, Edward S.;Buckler, Edward S.;Bradbury, Peter J.
作者机构：
期刊名称：PLANT GENOME （ 影响因子：4.089； 五年影响因子：4.972 ）
ISSN： 1940-3372
年卷期： 2014 年 7 卷 3 期
页码：
收录情况： SCI
摘要： 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.
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