High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time

Author(s)Jamann, Tiffany M
Author(s)Sood, Shilpa
Author(s)Wisser, Randall J
Author(s)Holland, James B
Ordered AuthorTiffany M. Jamannen_US
Ordered AuthorShilpa Sooden_US
Ordered AuthorRandall J. Wisseren_US
Ordered AuthorJames B. Hollanden_US
UD AuthorWisser, RJen_US
Date Accessioned2017-03-09T22:49:52Z
Date Available2017-03-09T22:49:52Z
Copyright DatePublic Domainen_US
Publication Date2017-01-03
DescriptionPublisher's PDFen_US
AbstractDespite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize ‘B73’ reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials.en_US
DepartmentDepartment of Plant and Soil Sciencesen_US
CitationJamann TM, Sood S, Wisser RJ, Holland JB (2017) High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time. PLoS ONE 12(1): e0168910. doi:10.1371/journal.pone.0168910en_US
DOI10.1371/journal.pone.0168910en_US
ISSN1932-6203en_US
URLhttp://udspace.udel.edu/handle/19716/21135
LanguageEnglishen_US
PublisherPublic Library of Scienceen_US
dc.rightsCC0 1.0 Universalen_US
dc.sourcePLoS ONEen_US
dc.source.urihttp://journals.plos.org/plosone/en_US
TitleHigh-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Timeen_US
TypeArticleen_US
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