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  • Review Article
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The art and design of genetic screens: maize

Nature Reviews Genetics volume 9, pages 192–203 (2008)Cite this article

Key Points

  • Genetic screens in maize (Zea mays) are used to great effect to uncover genes for important developmental, agronomic and evolutionary traits. These screens have informed our understanding of maize as well as other cereal crops.

  • Both chemical mutagenesis (mainly ethyl methanesulphonate (EMS)) and transposons provide useful material for forward screens; the diversity of maize inbred lines are also exploited to associate unique alleles with phenotypes.

  • The physical separation of the male and female flowers facilitates crosses in maize. Another practical advantage is the availability of many traits, such as kernel colour, that can be easily scored and quantified.

  • The many chromosome translocation stocks that exist for maize can be used to map recessive mutations, carry out dosage analysis of dominant mutations and identify gametophytic mutations.

  • Although genome sizes vary considerably in grass species, gene order is often conserved. This property facilitates the cloning of maize genes using the genome sequences that are available for other cereals such as sorghum and rice.

  • EMS mutagenesis is carried out in the pollen, which has a vegetative cell and two sperm cells.

  • Three main families of endogenous transposable elements have been used for gene tagging in maize. These are the Activator (Ac) and its nonautonomous derivative Dissociation (Ds), Suppressor–mutator (Spm), and Mutator (Mu) transposon families, the last being the most popular choice owing to its higher mutation rate.

  • The propensity for linked transpositions makes the Ac/Ds transposon family useful for regional mutagenesis.

  • The high copy number makes Mutator elements useful for forward and reverse genetics.

  • Reverse genetic resources rely on endogenous transposons and TILLING (targeting induced local lesions in genomes).

  • The rich natural allelic variation of maize is being exploited to identify genes for important traits. Association analysis takes advantage of a large number of maize inbreds that have been evaluated phenotypically for many traits. A collection of 5,000 recombinant inbred lines that uses one common parent crossed to 25 diverse inbreds has the potential to fine map genetic variation to a single gene.

  • Once the maize genome sequence is made available in 2008, it will make it easier for researchers to use genetic screens in maize.

Abstract

Maize (Zea mays) is an excellent model for basic research. Genetic screens have informed our understanding of developmental processes, meiosis, epigenetics and biochemical pathways — not only in maize but also in other cereal crops. We discuss the forward and reverse genetic screens that are possible in this organism, and emphasize the available tools. Screens exploit the well-studied behaviour of transposon systems, and the distinctive chromosomes allow an integration of cytogenetics into mutagenesis screens and analyses. The imminent completion of the maize genome sequence provides the essential resource to move seamlessly from gene to phenotype and back.

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Figure 1: Anatomy and life cycle of maize.
Figure 2: Ethyl methanesulphonate mutagenesis screens.
Figure 3: Generation and selection of transposed Activator elements.
Figure 4: Intermated recombinant inbred lines.

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Acknowledgements

We thank M. G. Neuffer for his inspiration. We thank E. Vollbrecht for comments and for allowing us to reference his unpublished work. H. C. and S. H. are supported by the US Department of Agriculture, the Agricultural Research Service and the National Science Foundation.

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  1. Plant Gene Expression Center, 800 Buchanan Street, Albany, 94710, California, USA

    Héctor Candela & Sarah Hake

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  1. Héctor Candela
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FURTHER INFORMATION

The Hake laboratory homepage

Functional Genomics of Maize Endosperm

Maize Genetic Mapping Project

Maize Genetics and Diversity

Maize Genetics and Genomics Database (MaizeGDB)

Maize Genetics Cooperation Stock Center (MGCSC)

Maize Inflorescence Architecture Project — EMS Phenotype Database

Maize Targeted Mutagenesis (MTM)

Maize TILLING Project

Mu killer

Mu Transposon Information Resource

Nature Reviews Genetics series on 'The art and design of genetic screens'

Panzea – Molecular and Functional Diversity of the Maize Genome

Photosynthetic Mutant Library

PlantGDB Ac/Ds resources

Plant Genome Database (PlantGDB)

Projects at PlantGDB

Regional Mutagenesis Utilizing Activator (Ac) in Maize

RescueMu collection of insertional mutants at MaizeGDB

Rice genome sequence at TIGR

Sorghum genome sequence at Phytozome

The Maize Genome Sequencing Project

UniformMu Maize Project

Glossary

Teosinte

The name given to several wild subspecies of maize, including the ones from which cultivated varieties were domesticated.

Tassel

The inflorescence that carries the male flowers. It is located at the top of the plant and develops from the shoot apical meristem after all vegetative leaves are produced.

Ear

The inflorescence that carries the female flowers. Ears are modified branches located in the axil of vegetative leaves.

Pericarp

The maternally derived outer layer of the kernel.

Retrotransposons

Transposable elements that transpose via an rna intermediate.

Anthers

The organs of a flower in which pollen grains are produced.

Chromosome knobs

Cytogenetically defined heterochromatic regions that are visible in a stained pachytene chromosome.

Hyperploid

The property of having more genetic material (either a chromosome or segment of chromosome) than the diploid. By contrast, a hypoploid has less genetic material than the diploid.

Accessions

Each of the strains in a collection of germplasm.

Silks

The styles of the maize female flowers. Pollen germinates on silks and grows through them to reach the ovule.

Non-complementation screen

A mutant search that is used to identify additional recessive mutations of a given gene. In maize, ears from a known loss-of-function mutant are pollinated with mutagenized pollen, and the F1 is screened for mutant phenotypes. Apart from rare exceptions (known as non-allelic non-complementation), these are only expected to occur when both the new and the known mutations affect the same gene (that is, they do not complement).

Segregation distortion

Deviation from the expected Mendelian ratios.

Suppressor screen

A screen aimed at identifying mutations that alleviate the phenotype of an existing mutation, often resulting in a 'normal' appearance.

Gene tagging

Obtaining a transposon insertion into a gene.

Acentric

Fragment of a chromosome missing the centromere.

Meristem

A group of totipotent cells at the growing tip of a shoot or root. Leaves initiate from the shoot meristem.

Allelic series

A collection of alleles of a gene, often differing in the level of gene activity.

Thermal asymmetric interlaced PCR

(TAIL-PCR). A technique based on the polymerase chain reaction that allows the amplification of genomic sequences adjacent to an insertion. It is based on the combined use of nested primers that are specific to a known inserted sequence together with other shorter, degenerate primers.

Introgressed

Introgression is the replacement of the genome of one strain with that of another, usually by repeated backcrossing, with the purpose of making them isogenic. Introgressed lines allow researchers to discern the phenotypic effects of a mutation from the effects of other unlinked loci.

Plasmid rescue

A technique that allows the recovery of the genomic sequence that is adjacent to an insertion. Genomic DNA from an individual carrying the insertion is digested with a restriction endonuclease, and the resulting restriction fragments are circularized (self-ligated) and transformed into competent bacteria. Recovery of the flanking sequences is made possible by the presence of a plasmid replication origin and a selectable marker in the inserted sequence.

Land races

Varieties of maize that, in contrast to the inbred lines, have traditionally been propagated by open pollination.

Recombinant inbred line

(RIL). A homozygous plant line obtained after crossing two distinct parental accessions and subsequent inbreeding over several generations.

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Candela, H., Hake, S. The art and design of genetic screens: maize. Nat Rev Genet 9, 192–203 (2008). https://doi.org/10.1038/nrg2291

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