A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

Ulrike Frank; Susanne Kublik; Dörte Mayer; Marion Engel; Michael Schloter; Jörg Durner; Frank Gaupels

doi:10.1186/s12870-019-2162-7

A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

BMC Plant Biol. 2019 Dec 4;19(1):539. doi: 10.1186/s12870-019-2162-7.

Authors

Ulrike Frank¹, Susanne Kublik², Dörte Mayer¹, Marion Engel³, Michael Schloter², Jörg Durner^{1

4}, Frank Gaupels⁵

Affiliations

¹ Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
² Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
³ Scientific Computing Research Unit, Helmholtz Zentrum München, Neuherberg, Germany.
⁴ Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany.
⁵ Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany. frank.gaupels@gmx.de.

Abstract

Background: Nitrogen dioxide (NO₂) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death.

Results: Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO₂ fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO₂ whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO₂. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO₂-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation.

Conclusions: The presented NO₂ dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.

Keywords: Adapter ligation-mediated PCR; Arabidopsis thaliana; High-throughput phenotyping; Mutant screen; Next generation sequencing; T-DNA insertion; Target enrichment.

MeSH terms

Arabidopsis / genetics*
DNA, Bacterial / genetics*
Genome, Plant*
High-Throughput Nucleotide Sequencing / methods*
Mutation*
Phenotype

Substances

DNA, Bacterial
T-DNA