TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize

In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site id...

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Bibliographic Details
Published in:Journal of genetics and genomics 2021-11, Vol.48 (11), p.961-971
Main Authors: Lyu, Mingjie, Liu, Huafeng, Waititu, Joram Kiriga, Sun, Ying, Wang, Huan, Fu, Junjie, Chen, Yanhui, Liu, Jun, Ku, Lixia, Cheng, Xiliu
Format: Article
Language:English
Subjects:
Chromosome Mapping
DNA Transposable Elements
Ds transposon
Functional genomics
Gene Library
Genetic Association Studies
Genome, Plant
Genome-Wide Association Study
Genomics - methods
High-Throughput Nucleotide Sequencing
Insertion identification
Maize
Mutagenesis, Insertional
Mutant library
Next-generation sequencing
Phenotype
Plants, Genetically Modified
Polymorphism, Genetic
Zea mays
Zea mays - genetics
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Summary:In plants, transposable element (TE)-triggered mutants are important resources for functional genomic studies. However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious. This study developed a novel, rapid, and high-throughput TE insertion site identification workflow based on next-generation sequencing and named it Transposable Element Amplicon Sequencing (TEAseq). Using TEAseq, we systemically profiled the Dissociation (Ds) insertion sites in 1606 independent Ds insertional mutants in advanced backcross generation using K17 as background. The Ac-containing individuals were excluded for getting rid of the potential somatic insertions. We characterized 35,696 germinal Ds insertions tagging 10,323 genes, representing approximately 23.3% of the total genes in the maize genome. The insertion sites were presented in chromosomal hotspots around the ancestral Ds loci, and insertions occurred preferentially in gene body regions. Furthermore, we mapped a loss-of-function AGL2 gene using bulked segregant RNA-sequencing assay and proved that AGL2 is essential for seed development. We additionally established an open-access database named MEILAM for easy access to Ds insertional mutations. Overall, our results have provided an efficient workflow for TE insertion identification and rich sequence-indexed mutant resources for maize functional genomic studies.
ISSN:1673-8527
DOI:10.1016/j.jgg.2021.07.010