A capture-based assay for detection and characterization of transposon polymorphisms in maize
Open Access
- 27 April 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 11 (7)
- https://doi.org/10.1093/g3journal/jkab138
Abstract
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 a 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.Keywords
Funding Information
- National Natural Science Foundation of China (31871635)
- Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (2016RC012)
This publication has 40 references indexed in Scilit:
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsGenome Biology, 2013
- Mendelian and Non-Mendelian Regulation of Gene Expression in MaizePLoS Genetics, 2013
- McClintock’s challenge in the 21st centuryProceedings of the National Academy of Sciences of the United States of America, 2012
- Somatic retrotransposition alters the genetic landscape of the human brainNature, 2011
- Identification of a functional transposon insertion in the maize domestication gene tb1Nature Genetics, 2011
- The B73 Maize Genome: Complexity, Diversity, and DynamicsScience, 2009
- Transposable elements and the evolution of regulatory networksNature Reviews Genetics, 2008
- Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maizeProceedings of the National Academy of Sciences of the United States of America, 2007
- Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysisNature Protocols, 2007
- Transposable elements and the epigenetic regulation of the genomeNature Reviews Genetics, 2007