Journal
GENETICS
Volume 193, Issue 4, Pages 1073-1081Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.112.147710
Keywords
-
Categories
Funding
- Department of Energy (DOE) Great Lakes Bioenergy Research Center (BER) (DOE BER Office of Science) [DE-FC02-07ER64494]
- DuPont-Pioneer Hi-Bred International
- Hatch funds from the National Institute of Food and Agriculture, United States Department of Agriculture Project [WIS01330]
Ask authors/readers for more resources
Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, similar to 8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the context of empirically defined read depth to achieve desired marker density for genetic mapping studies.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available