Multiple insertions of COIN, a novel maize Foldback transposable element, in the Conring gene cause a spontaneous progressive cell death phenotype

Kim, S. B., Karre, S., Wu, Q., Park, M., Meyers, E., Claeys, H., Wisser, R., Jackson, D., Balint-Kurti, P. (August 2020) Multiple insertions of COIN, a novel maize Foldback transposable element, in the Conring gene cause a spontaneous progressive cell death phenotype. Plant J. ISSN 0960-7412

URL: https://pubmed.ncbi.nlm.nih.gov/32748440/
DOI: 10.1111/tpj.14945

Abstract

Similar progressive leaf lesion phenotypes, named conring for "concentric ring", were identified in 10 independently-derived maize lines. Complementation and mapping experiments indicated that the phenotype had the same genetic basis in each line - a single recessive gene located in a 1.1 Mb region on chromosome 2. Among the 15 predicted genes in this interval, Zm00001d003866 (subsequently renamed Conring or Cnr) had insertions of four related 138 bp transposable element (TE) sequences at precisely the same site in exon 4 in nine of the 10 cnr alleles. The tenth cnr allele had a distinct insertion of 226 bp of in exon 3. Genetic evidence suggested that the 10 cnr alleles were independently-derived, and arose during the derivation of each line. The four TEs, named COINa (for COnring INsertion) through COINd, have not been previously characterized and consist entirely of imperfect 69 bp terminal inverted repeats (TIRs) characteristic of the Foldback class of TEs. They belong to three clades of a family of maize TEs comprising hundreds of sequences in the genome of the B73 maize line. COIN elements preferentially insert at TNA sequences with a preference for C and G nucleotides in the immediately flanking 5' and 3' regions, respectively. They produce a three base target site duplication and do not have homology to other characterized TEs. We propose that Cnr is an unstable gene that is insertionally mutated at high frequency, most commonly due to COIN element insertions at a specific site in the gene.

Item Type: Paper
Additional Information: 1365-313x Kim, Saet-Byul Karre, Shailesh Wu, Qingyu Orcid: 0000-0003-3064-2445 Park, Minkyu Meyers, Emily Claeys, Hannes Wisser, Randall Jackson, David Balint-Kurti, Peter Orcid: 0000-0002-3916-194x Journal Article England Plant J. 2020 Aug 4. doi: 10.1111/tpj.14945.
Uncontrolled Keywords: Zea mays Lesion Maize Transposable element
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
CSHL Authors:
Communities: CSHL labs > Jackson lab
Depositing User: Matthew Dunn
Date: 4 August 2020
Date Deposited: 02 Oct 2020 19:18
Last Modified: 02 Oct 2020 19:18
Related URLs:
URI: https://repository.cshl.edu/id/eprint/39689

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