Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants

doi:10.3835/plantgenome2014.05.0023

	Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants
	Swarts, Kelly 1; Li, Huihui 2,3; Navarro, J. Alberto Romero 1,4; An, Dong 5; Romay, Maria Cinta 6; Hearne, Sarah 7; Acharya, Charlotte 6; Glaubitz, Jeffrey C.6; Mitchell, Sharon 6; Elshire, Robert J.8
刊名	PLANT GENOME
	2014
卷号	7 期号:3 页码:-
ISSN号	1940-3372
DOI	10.3835/plantgenome2014.05.0023
通讯作者	Swarts, Kelly
英文摘要	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.
学科主题	Plant Sciences ; Genetics & Heredity
语种	英语
出版者	CROP SCIENCE SOC AMER
WOS记录号	WOS:000345157300009
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4812]
专题	作物科学研究所_分子生物学系
作者单位	1.Cornell Univ, Dept Plant Breeding & Genet, Ithaca, NY 14853 USA 2.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100081, Peoples R China 3.Chinese Acad Agr Sci, CIMMYT China Off, Beijing 100081, Peoples R China 4.Cornell Univ, CIMMYT, Ithaca, NY 14853 USA 5.China Agr Univ, Coll Informat & Elect Engn, Beijing 100083, Peoples R China 6.Cornell Univ, Inst Genom Divers, Ithaca, NY 14853 USA 7.CIMMYT, Texcoco 56237, Edo De Mexico, Mexico 8.AgResearch Ltd, Grasslands Res Ctr, Palmerston North 4442, New Zealand 9.Cornell Univ, USDA ARS, Inst Genom Divers, Ithaca, NY 14853 USA 10.Cornell Univ, Dept Plant Breeding & Genet, Ithaca, NY 14853 USA
推荐引用方式 GB/T 7714	Swarts, Kelly,Li, Huihui,Navarro, J. Alberto Romero,et al. Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants[J]. PLANT GENOME,2014,7(3):-.
APA	Swarts, Kelly.,Li, Huihui.,Navarro, J. Alberto Romero.,An, Dong.,Romay, Maria Cinta.,...&Bradbury, Peter J..(2014).Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants.PLANT GENOME,7(3),-.
MLA	Swarts, Kelly,et al."Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants".PLANT GENOME 7.3(2014):-.