Name: development of targeting induced local lesions in genomes (tilling) populations in small grain crops by ethyl methanesulfonate mutagenesis
Uploaded: 2019-07-16T13:00:00
Description: Watch this Scientific Journal Video about Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis at JoVE.com

This work was supported by the USDA National Institute of Food and Agriculture, Hatch project 1016879 and Maryland Agricultural Experiment Station via MAES Grant No. 2956952.

1. Preparation of dosage curve for effective mutagenesis
<ol>
	<li>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.</li>
	<li>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 ...

<ol>
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V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Uncovering+hidden+variation+in+polyploid+wheat.">Uncovering hidden variation in polyploid wheat.</a> Proceedings of the National Academy of Sciences. , 201619268 (2017).</li><li>Dong, C., Dalton-Morgan, J., Vincent, K., Sharp, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Modified+TILLING+Method+for+Wheat+Breeding.">A Modified TILLING Method for Wheat Breeding.</a> The Plant Genome. 2 (1), 39-47 (2009).</li><li>Till, B. J., Zerr, T., Comai, L., Henikoff, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+protocol+for+TILLING+and+Ecotilling+in+plants+and+animals.">A protocol for TILLING and Ecotilling in plants and animals.</a> Nature Protocols. 1 (5), 2465-2477 (2006).</li><li>Wu, J. -. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical-+and+Irradiation-induced+Mutants+of+Indica+Rice+IR64+for+Forward+and+Reverse+Genetics.">Chemical- and Irradiation-induced Mutants of Indica Rice IR64 for Forward and Reverse Genetics.</a> Plant Molecular Biology. 59 (1), 85-97 (2005).</li><li>Feldman, M., Levy, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome+Evolution+Due+to+Allopolyploidization+in+Wheat.">Genome Evolution Due to Allopolyploidization in Wheat.</a> Genetics. 192 (3), 763-774 (2012).</li><li>Comai, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+advantages+and+disadvantages+of+being+polyploid.">The advantages and disadvantages of being polyploid.</a> Nature Reviews Genetics. 6 (11), 836-846 (2005).</li><li>Guo, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+High-Efficient+Mutation+Resource+with+Phenotypic+Variation+in+Hexaploid+Winter+Wheat+and+Identification+of+Novel+Alleles+in+the+TaAGP.L-B1+Gene.">Development of a High-Efficient Mutation Resource with Phenotypic Variation in Hexaploid Winter Wheat and Identification of Novel Alleles in the TaAGP.L-B1 Gene.</a> Frontiers in Plant Science. 8, (2017).</li><li>Rakszegi, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+of+agronomic+and+morphological+traits+in+a+mutant+population+of+bread+wheat+studied+in+the+Healthgrain+program.">Diversity of agronomic and morphological traits in a mutant population of bread wheat studied in the Healthgrain program.</a> Euphytica. 174 (3), 409-421 (2010).</li><li>Tsai, H., Ngo, K., Lieberman, M., Missirian, V., Comai, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tilling+by+Sequencing.">Tilling by Sequencing.</a> Plant Functional Genomics: Methods and Protocols. , 359-380 (2015).</li></ol>

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...

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 populations have been developed and utilized in many small grain crops such as hexaploid bread wheat (Triticum aestivum)3, barley (Hordeum vulgare)4, tetraploid durum wheat (T. dicoccoides durum)5, diploid wheat (T. monococcum)6 and the &#34;D&#34; genome progenitor of wheat Aegilops tauschii7. These resources have been used to validate the roles of genes in regulating abiotic and biotic stress tolerance8, regulating flowering time9, and developing nutritionally superior crop varieties5.
TILLING, along with the use of alkylating mutagenic agents such as ethyl methanesulfonate (EMS), sodium azide, N-methyl-N-nitrosourea (MNU), and methyl methanesulfonate (MMS), has advantages over other reverse genetics tools for several reasons. First, mutagenesis can be conducted on practically any species or variety of plant10 and is independent of the transformation bottleneck, which is particularly challenging in the case of small grains11. Second, in addition to generating knockout mutations that can be obtained by other gene validation approaches, a range of missense and splicing mutations can be induced, which can discern functions of individual domains of the proteins of interest12. Moreover, TILLING generates an immortal collection of mutations throughout the genome; thus, a single population can be used for functional validation of multiple genes. In contrast, other reverse genetics tools generate resources specific to only the gene under study13. Useful mutations identified through TILLING can be deployed for breeding purposes and are not subject to regulation, unlike gene editing, whose non-transgenic classification is still uncertain in many countries. This becomes especially relevant to small grains that are internationally traded14.
TILLING is a simple and efficient gene validation strategy and requires mutagenized populations to be developed for investigating genes of interest. Developing an effective 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 for desired mutations, whereas a high mutagen concentration leads to high mortality in the population and an insufficient number of mutagenized individuals. Once a good population is developed, there are multiple ways to detect mutations in the genes of interest, and the choice of platform depends on the experimental scale and availability of resources. Whole genome sequencing and exome sequencing has been used to characterize all mutations in TILLING populations in plants with small genomes15,16. Exome sequencing of two TILLING populations has been performed in bread and durum wheat and is available to the public for identifying desirable mutations and ordering mutant lines of interest17. It is a great public resource in terms of availability of desirable mutations; however, in gene validation studies, the wild-type line should possess the candidate gene of interest. Unfortunately, it is still cost-prohibitive to sequence the exome of the entire TILLING population for reverse genetics-based validation of a few candidate genes in another background. Amplicon sequencing and Cel-1-based assays have been used in detecting mutations in targeted populations in wheat, and Cel-1 assays are simpler, requiring no computational knowledge, and are especially suitable for validation of a small number of genes with basic lab equipment6,18.
In the present article, described are methods for the 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. This protocol has already been implemented successfully in developing and utilizing mutagenized populations of Triticum aestivum, Triticum monoccocum6, barley, Aegilops tauchii7, and several others. Included are explicit details of these methods along with useful tips that will help researchers develop TILLING populations, using EMS as a mutagen in any small grain plant of choice.

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

development of targeting induced local lesions in genomes (tilling) populations in small grain crops by ethyl methanesulfonate mutagenesis

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.

Figure 2 shows the dosage curve of hexaploid bread wheat cultivar Jagger, diploid wheat Triticum monococcum6, and a genome donor of wheat Aegilops tauschii7. The EMS doses for desired 50% survival rates were about 0.25%, 0.6% and 0.7% for T. monococcum, Ae. tauschii, and T. aestivum, respectively. The higher EMS tolerance of hexaploid wheat is due to its genome buffer...

Watch this Scientific Journal Video about Development of Targeting Induced Local Lesions IN Genomes TILLING Populations in Small Grain Crops by Ethyl Methanesulfonate Mutagenesis at JoVE.com

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

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.

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

Targeting Induced Local Lesions IN Genomes (TILLING) is a powerful reverse genetics tool that includes chemical mutagenesis and detection of sequence ...

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