An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant species

Abstract

Summary Transgenomics is the process of introducing genomic clones from a donor species into a recipient species and then screening the resultant transgenic lines for phenotypes of interest. This method might allow us to find genes involved in the evolution of phenotypic differences between species as well as genes that have the potential to contribute to reproductive isolation: potential speciation genes.More than 1,100 ~20 Kbp genomic clones from Leavenworthia alabamica were moved into Arabidopsis thaliana by transformation. After screening a single primary transformant for each line, clones associated with mutant phenotypes were tested for repeatability and cosegregation.We found 84 clones with possible phenotypic effects of which eight were repeatedly associated with the same phenotype. One clone, 11_11B, cosegregated with a short fruit phenotype. Further study showed that 11_11B affects seed development, with as much as one-third of the seeds aborted in some fruit.Transgenomics is a viable strategy for discovering genes of evolutionary interest. We identify methods to reduce false positives and false negatives in the future. 11_11B can be viewed as a potential speciation gene, illustrating the value of transgenomics for studying the molecular basis of reproductive isolation.

Evolutionary transgenomics: prospects and challenges

“… Correa et al (2012) piloted a clone-by-clone transgenomic screen using genomic clones with ∼20 kb inserts from the gladecress Leavenworthia alabamica Rollins introduced into A. thaliana . Leavenworthia alabamica , and A. thaliana differ in almost all visible morphologies and yet they are both members of Brassicaceae Lineage I ( Beilstein et al, 2008 , 2010 ; Franzke et al, 2011 ).…”

“…However, in only eight cases was the initial “abnormal” phenotype repeated in additional independent T1s. Correa et al (2012) focused on one clone that was shown to cause stunted fruit and increased seed abortion in a transdominant manner. Sequencing of the clone insert suggests that this effect is most likely explained by a gene region that shows homology to the A. thaliana SLOW-WALKER2 ( SWA2 ) gene.…”

“…The single gene identified by Correa et al (2012) is likely to reflect DSD rather than phenotypic divergence. The question this raises is whether this result indicates that the method has limited utility for scientists whose goal is to identify genes that explain species differences.…”

“…The first fact to emphasize is that the screen conducted by Correa et al (2012) covered less than 5% of the donor species’ genome. Furthermore, considering that with a false negative rate of at least 50%, only 2.5% of the donor genome was effectively screened.…”

“…But are the benefits to be gained likely to outweigh the work entailed in conducting evolutionary transgenomic experiments? In this paper we use evolutionary theory and data from prior interspecies transformation experiments and our published, pilot transgenomic screen ( Correa et al, 2012 ) to assess the approach and how it could best be implemented. We conclude that the time is ripe to develop transgenomics resources at least in Brassicaceae Burnett, a clade of flowering plants, many of whose species can now be transformed with high efficiency.…”