Forward genetics and reverse genetics There are basically two ways to link the sequence and function of a specific gene: forward and reverse genetics Forward genetics: from phenotype to gene sequence Reverse genetics : from gene sequence to phenotype Mutation Phenotype Gene Gene Mutation Phenotype

Forward genetics and reverse genetics Select a biological process Generate a random and highly redundant mutant population Screen a large number of mutagenized M2 plants Map and clone the mutation Select a gene or genes Generate a collection of mutants or tools Catalogue the mutants in the collection Select mutants in the gene or genes of interest Jose M. Alonso et al., 2006

Generation of genetic diversity Jose M. Alonso et al., 2006

Tandem gene multiplications pose a challenge for functional analysis In sequenced plant genomes, 15% or more of the identified genes are members of tandem-arrayed gene Families. Assigning function to unknown plant genes is to study phenotypic changes associated with knockout mutations. Mutating only one gene in a duplicated pair often produces no measurable phenotype, this poses a particular challenge for functional analysis. It is often necessary to knock out more than one member of a plant gene family to obtain a mutant phenotype. Here describe alternate strategies that can be used to identify knockouts of two or more tandem-arrayed plant genes for functional analysis.

Table 1. Advantages and disadvantages of approaches for generating mutations in tandem-arrayed genes

Selection for deletions spanning multiple genes Lox P : locus of X-over P1 Cre : Cyclization Recombination Figure 1. Deletion of tandem-arrayed genes.

Silencing gene families by RNA interference RNA interference allows down-regulation of gene expression in transgenic plants, including the genes of interest are located in tandem arrays. RNA interference was used to silence all members of the gene family. Silencing efficiency depends on the type of construct that is used, the site of integration, and the particular target genes. Gene silencing is generally not 100% effective, mutant phenotypes that require the complete knockout of a gene family might not be detected using the described silencing approaches.

Selection for meiotic recombination between adjacent genes Figure 2. Selection for recombination between T-DNA or transposon insertions

Sequential mutagenesis to create a double mutant Figure 3. Localized transposon mutagenesis. Ds elements tend to transpose to nearby genetic locations, allowing screens for insertions in adjacent genes. Imperfect DNA repair can leave the gene at the original insertion site inactivated .

Prospects for site-directed mutagenesis in higher plants zinc finger DNA binding domains FokⅠ DNA nuclease Figure 4. Site-directed mutagenesis with a zinc finger nuclease (ZFN). Double-strand cleavage by a ZFN leads to target gene knockout by imperfect repair or homologous recombination

High-throughput TILLING Trenton Colbert et al., 2001

Total 50,000 lines Xin Li et al., 2001