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- Title
A capture-based assay for detection and characterization of transposon polymorphisms in maize.
- Authors
Minqi Li; Noshay, Jaclyn M.; Xiaoxiao Dong; Springer, Nathan M.; Qing Li
- 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.
- Subjects
GENE expression; PHENOTYPES; TRANSPOSONS; CORN breeding; GENETIC polymorphisms; CORN
- Publication
G3: Genes | Genomes | Genetics, 2021, Vol 11, Issue 7, p1
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1093/g3journal/jkab138