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

Authors: KIM, SAET-BYUL - North Carolina State University; KARRE, SHAILESH - North Carolina State University; WU, QINGYU - Cold Spring Harbor Laboratory; PARK, MINKYU - University Of Florida; MEYERS, EMILY - North Carolina State University; CLAEYS, HANNES - Cold Spring Harbor Laboratory; WISSER, RANDALL - University Of Delaware; JACKSON, DAVID - Cold Spring Harbor Laboratory; Balint-Kurti, Peter

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2020
Publication Date: 7/1/2020
Citation: Kim, S., Karre, S., Wu, Q., Park, M., Meyers, E., Claeys, H., Wisser, R., Jackson, D., Balint Kurti, P.J. 2020. Multiple insertions of COIN, a novel maize Foldback transposable element, in the Conring gene cause a spontaneous progressive cell death phenotype. Plant Journal. https://doi.org/10.1111/tpj.14945.
DOI: https://doi.org/10.1111/tpj.14945

Interpretive Summary: We identified a concentric ring lesion phenotype in 10 independently derived lines. We found that insertions in the same gene were responsible for the phenotype in each case. Nine of the 10 insertions were by members of a novel transposable element gene family. We present data on the mutation phenotype, the mutated gene and the transposable element.

Technical 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 138bp transposable element (TE) sequences at precisely the same site in exon 4 in nine of the 10 conring alleles. The tenth conring allele had a distinct insertion of 226bp of in exon 3. Genetic evidence suggested that the 10 conring alleles were independently-derived, and arose during the seven to 10 generations used to derive 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 Conring 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.