A capture-based assay for detection and characterization of transposon polymorphisms in maize

Minqi Li, Jaclyn M. Noshay, Xiaoxiao Dong, Nathan M. Springer, Qing Li

Research output: Contribution to journalArticlepeer-review


Transposons can create allelic diversity that affects gene expression and phenotypic diversity. The detection of transposon polymorphisms at a genome-wide scale across a large population is difficult. Here we developed a targeted sequencing approach to monitor transposon polymorphisms of interest. This approach can interrogate the presence or absence of transposons reliably across various genotypes. Using this approach, we genotyped a set of 965 transposon-related presence/absence polymorphisms in a diverse panel of 16 maize (Zea mays L.) inbred lines that are representative of the major maize breeding groups. About 70% of the selected regions can be effectively assayed in each genotype. The consistency between the capture-based assay and PCR-based assay are 98.6% based on analysis of 24 randomly selected transposon polymorphisms. By integrating the transposon polymorphisms data with gene expression data, ∼18% of the assayed transposon polymorphisms were found to be associated with variable gene expression levels. A detailed analysis of 18 polymorphisms in a larger association panel confirmed the effects of 10 polymorphisms, with one of them having stronger association with expression than nearby SNP markers. The effects of seven polymorphisms were tested using a luciferase-based expression assay, and one was confirmed. Together, this study demonstrates that the targeted sequencing assay is an effective way to explore transposon function in a high-throughput manner.

Original languageEnglish (US)
Article numberjkab138
JournalG3: Genes, Genomes, Genetics
Issue number7
Early online dateApr 26 2021
StatePublished - Jul 2021

Bibliographical note

Funding Information:
This work was supported by the National Natural Science Foundation of China (No: 31871635) and the Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (Program No.2016RC012).

Publisher Copyright:
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.


  • Gene expression
  • Maize
  • Targeted sequencing
  • Transposon

PubMed: MeSH publication types

  • Journal Article


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