Development of Targeting Induced Local Lesions IN Genomes (TILLING) Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis

Summary

Described is a protocol for developing a Targeting Induced Local Lesions IN Genomes (TILLING) population in small grain crops with use of ethyl methanesulfonate (EMS) as a mutagen. Also provided is a protocol for mutation detection using the Cel-1 assay.

Abstract

Targeting Induced Local Lesions IN Genomes (TILLING) is a powerful reverse genetics tool that includes chemical mutagenesis and detection of sequence variation in target genes. TILLING is a highly valuable functional genomics tool for gene validation, especially in small grains in which transformation-based approaches hold serious limitations. Developing a robust mutagenized population is key to determining the efficiency of a TILLING-based gene validation study. A TILLING population with a low overall mutation frequency indicates that an impractically large population must be screened to find desired mutations, whereas a high mutagen concentration leads to high mortality in the population, leading to an insufficient number of mutagenized individuals. Once an effective population is developed, there are multiple ways to detect mutations in a gene of interest, and the choice of platform depends upon the experimental scale and availability of resources. The Cel-1 assay and agarose gel-based approach for mutant identification is convenient, reproducible, and a less resource-intensive platform. It is advantageous in that it is simple, requiring no computational knowledge, and it is especially suitable for validation of a small number of genes with basic lab equipment. In the present article, described are the methods for development of a good TILLING population, including preparation of the dosage curve, mutagenesis and maintenance of the mutant population, and screening of the mutant population using the PCR-based Cel-1 assay.

Introduction

Point mutations in genomes can serve many useful purposes for researchers. Depending on their nature and location, these mutations can be used to assign functions to genes or even distinct domains of proteins of interest. On the other hand, as a source of novel genetic variation, useful mutations can be selected for desired traits using phenotyping screens and further used in crop improvement. TILLING is a powerful reverse genetics tool that includes chemical mutagenesis and detection of sequence variation in the target gene. First developed in Arabidopsis¹ and Drosophilia melanogaster², TILLING populat....

Protocol

1. Preparation of dosage curve for effective mutagenesis

1. Soak 100 seeds with the genotype of interest in six 250 mL glass flasks (100 in each flask) containing 50 mL of distilled water. Shake at 100 rpm for 8 h at room temperature (RT) for imbibition by the seeds.
2. In a fume hood, prepare 50 mL of 0.4%, 0.6%, 0.8%, 1.0%, and 1.2% (w/v) ethyl methanesulfonate (EMS) solution by dissolving 0.167, 0.249, 0.331, 0.415, and 0.498 mL of EMS in distilled water, respectively.
   NOTE: EMS is liquid at RT .......

Discussion

TILLING is a highly valuable reverse genetics tool for gene validation, especially for small grains where transformation-based approaches have serious bottlenecks¹¹. Developing a mutagenized population with a high mutation frequency is one of the critical steps in conducting functional genomics studies. The most important step in developing a robust TILLING population is to determine the optimal concentration of EMS. The 40%-60% survival rate in the M₁ has been found to be a good indica.......

Materials

Name	Company	Catalog Number	Comments
96 well 1.1 ml microtubes in microracks	National Scientific	TN0946-08R	For collecting leaf tissues
Agarose I biotechnology grade	VWR	0710-500G
Biosprint 96 DNA Plant Kit	Qiagen	941558	Kit for DNA extraction
Cel-1 endonuclease	Extracted as described by Till et al 2006		Single strand specific endonuclease
Centrifuge 5430 R	Eppendorf
Ethyl methanesulfonate	Sigma Aldrich	M-0880-25G	EMS, Chemical mutagen
Freeze Dry/Shell freeze system	Labconco		For lyophilization of leaf tissue
Kingfisher Flex purification system	Thermo fisher scientific	5400610	High throughput DNA extraction robot
My Taq DNA Polymerase	Bioline	BIO-21107
Nuclease free water	Sigma aldrich	W4502-1L
NuGenius gel imaging system	Syngene
Orbit Environ-shaker	Lab-line
SPECTROstar Nano	BMG LABTECH		Nano drop for DNA quantification
T100 Thermal cycler	BIO-RAD	1861096