Novel Methods to Optimize Genotypic Imputation for Low‐Coverage, Next‐Generation Sequence Data in Crop Plants
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- Kelly Swarts
- Dep. of Plant Breeding and Genetics 175 Biotechnology Bldg. Cornell Univ. Ithaca NY 14853
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- Huihui Li
- Institute of Crop Science and CIMMYT‐China Office, Chinese Academy of Agricultural Sciences No. 12 Zhongguancun South St. Beijing 100081 China
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- J. Alberto Romero Navarro
- Dep. of Plant Breeding and Genetics and CIMMYT 175 Biotechnology Bldg. Cornell Univ. Ithaca NY 14853
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- Dong An
- China Agricultural Univ., College of Information and Electrical Engineering No. 17 Tinghua East Rd. Beijing China 100083
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- Maria Cinta Romay
- Inst. for Genomic Diversity 175 Biotechnology Bldg., Cornell Univ. Ithaca NY 14853
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- Sarah Hearne
- CIMMYT Km. 45 Carretera Mexico‐Veracruz, El Batán, Texcoco Edo. de Mexico CP 56237 Mexico
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- Charlotte Acharya
- Inst. for Genomic Diversity 175 Biotechnology Bldg., Cornell Univ. Ithaca NY 14853
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- Jeffrey C. Glaubitz
- Inst. for Genomic Diversity 175 Biotechnology Bldg., Cornell Univ. Ithaca NY 14853
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- Sharon Mitchell
- Inst. for Genomic Diversity 175 Biotechnology Bldg., Cornell Univ. Ithaca NY 14853
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- Robert J. Elshire
- AgResearch Limited, Grasslands Research Centre Tennent Dr. Palmerston North New Zealand 4442
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- Edward S. Buckler
- USDA‐ARS, Institute for Genomic Diversity, and Dep. of Plant Breeding and Genetics 159 Biotechnology Bldg. Cornell Univ. Ithaca NY 14853
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- Peter J. Bradbury
- USDA‐ARS 409 Bradfield Hall, Cornell Univ. Ithaca NY 14853
説明
<jats:p>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 (<jats:italic>Zea mays</jats:italic> 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.</jats:p>
収録刊行物
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- The Plant Genome
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The Plant Genome 7 (3), 0-, 2014-11
Wiley