Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy

Shengjun Li, Shangang Jia, Lili Hou, Hanh Nguyen, Shirley Sato, David Holding, Edgar B Cahoon, Chi Zhang, Tom Clemente, Bin Yu

Research output: Contribution to journalArticle

Abstract

Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes. Here, we report a nanopore-based method to map the insertion position of a Ds transposable element originating in maize in the soybean genome. In this method, an oligo probe is used to capture the DNA fragments containing the Ds element from pooled DNA samples of transgenic soybean plants. The Ds element-enriched DNAs are then sequenced using the MinION-based platform of Nanopore. This method allowed us to rapidly map the Ds insertion positions in 51 transgenic soybean lines through a single sequencing run. This strategy is high throughput, convenient, reliable, and cost-efficient. The transgenic allele mapping protocol can be easily translated to other eukaryotes with complex genomes.

Original languageEnglish (US)
Pages (from-to)3825-3833
Number of pages9
JournalJournal of experimental botany
Volume70
Issue number15
DOIs
StatePublished - Aug 7 2019

Fingerprint

Nanopores
Soybeans
Alleles
genetically modified organisms
Genome
soybeans
alleles
Transgenes
DNA
transgenes
genome
DNA Transposable Elements
Genetically Modified Plants
Eukaryota
Zea mays
organisms
transposons
Technology
eukaryotic cells
Costs and Cost Analysis

Keywords

  • Complex genome
  • cost efficient
  • high throughput
  • mapping insertion position
  • MinNON sequencing
  • transgene

ASJC Scopus subject areas

  • Physiology
  • Plant Science

Cite this

Li, S., Jia, S., Hou, L., Nguyen, H., Sato, S., Holding, D., ... Yu, B. (2019). Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy. Journal of experimental botany, 70(15), 3825-3833. https://doi.org/10.1093/jxb/erz202

Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy. / Li, Shengjun; Jia, Shangang; Hou, Lili; Nguyen, Hanh; Sato, Shirley; Holding, David; Cahoon, Edgar B; Zhang, Chi; Clemente, Tom; Yu, Bin.

In: Journal of experimental botany, Vol. 70, No. 15, 07.08.2019, p. 3825-3833.

Research output: Contribution to journalArticle

Li, S, Jia, S, Hou, L, Nguyen, H, Sato, S, Holding, D, Cahoon, EB, Zhang, C, Clemente, T & Yu, B 2019, 'Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy', Journal of experimental botany, vol. 70, no. 15, pp. 3825-3833. https://doi.org/10.1093/jxb/erz202
Li, Shengjun ; Jia, Shangang ; Hou, Lili ; Nguyen, Hanh ; Sato, Shirley ; Holding, David ; Cahoon, Edgar B ; Zhang, Chi ; Clemente, Tom ; Yu, Bin. / Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy. In: Journal of experimental botany. 2019 ; Vol. 70, No. 15. pp. 3825-3833.
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