Novel methods to optimize genotypic imputation for low-coverage, next- generation sequence data in crops 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 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.

Bibliographic Details

Main Authors:	Swarts, K., Huihui Li, Romero Navarro, J. A., Dong An, Romay, M.C., Hearne, S., Acharya, C., Glaubitz, J.C., Mitchell, S.E., Elshire, R.J., Buckler, E.S., Bradbury, P.J.
Format:	Article biblioteca
Language:	English
Published:	CSSA 2014
Subjects:	AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, GENOTYPES, DNA SEQUENCE, GENETIC MARKERS,
Online Access:	https://hdl.handle.net/10883/21453
Tags:	Add Tag No Tags, Be the first to tag this record!