Data from: Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize
High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using Zea mays our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%. Furthermore, by capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines. Using local haplotypes reduces the marker dimensionality of the genotype matrix while increasing the informativeness of the data. Phased GBS in maize also revealed the existence of reproducibly inaccurate (apparent accuracy) genotypes that were due to divergent copy number variants (CNVs) unobservable in the underlying single nucleotide polymorphism (SNP) data.
Resources in this dataset:
Resource Title: Supplementary Data.
File Name: Web Page, url: https://academic.oup.com/g3journal/article/7/7/2161/6053605#supplementary-data
Funding
USDA-NIFA: 2011-67003-30342
National Institutes of Health: 2R01 CA132897
National Institutes of Health: P20 GM103446
History
Data contact name
Wisser, Randall J.Data contact email
rjw@udel.eduPublisher
G3: Genes, Genomes, GeneticsIntended use
By capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines.Temporal Extent Start Date
2017-07-01Theme
- Not specified
Geographic Coverage
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- biota
- farming
National Agricultural Library Thesaurus terms
genotyping by sequencing; genetic variation; corn; high-throughput nucleotide sequencing; genomic libraries; heterozygosity; loci; inbred lines; linkage disequilibrium; Zea mays; pedigree; filters; haplotypes; single nucleotide polymorphism; pipelinesOMB Bureau Code
- 005:18 - Agricultural Research Service
OMB Program Code
- 005:040 - National Research
Pending citation
- No
Public Access Level
- Public