Regulatory evolution, agriculture, and RNA – a possibly interesting intersection

Much of the interest and excitement in the field of “Evo-Devo” today centers on the roles that changes in gene regulation may play in the evolution.  This mechanism (altering when and/or where a particular gene is expressed during development) stands apart from that concerning changes in the actual structure and function of individual proteins.  A recent study from Steve Tanksley’s lab brings this phenomenon into focus for this blog, and may tie together some different themes.

This study (Cong et al., Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication, Nature Genetics 40, 800-804, 2008 ) deals with one of the two processes (cell cycle control and organ number determination) associated with the enlargement of tomato fruit size in the course of domestication of this crop.  Many years of QTL mapping have led researchers to regions of the tomato genome involved in these processes.  The study by Cong et al. describes the end result of the characterization of one of these QTLs, a locus that is a major contributor to organ number (specifically, carpel number).

As stated in the paper, carpel number determines the number of compartments in a mature fruit; the greater the number of carpels, the more the compartments, the larger the fruit.  This trait is controlled largely by two QTLs, and one of these (fasciated) has a larger effect than the other (locule-number).  The fasciated gene was isolated by positional cloning.  Because compartment number is a heritable trait, it was possible to perform crosses between large and small fruited cultivars and generate populations with a range of fruit sizes.  By simultaneously scoring individuals in this population for numerous molecular markers, it was possible to associate the variation of compartment number with specific markers, and thus to a rather small part of the tomato genome (on chromosome 1).   Exhaustive reiteration led to a narrowing to a small (ca. 300,000 bp) region of chromosome 1.

This region was sequenced and evaluated for possible candidates.  Two genes whose products may be regulatory – a YABBY-like transcription factor and a protein kinase – were studied in more detail.  While levels of expression of the protein kinase gene were similar in low- and high- compartment number varieties, YABBY gene expression was much higher in the high compartment number plants.  The money experiment was a complementation analysis – overexpression of the YABBY protein in a low compartment variety increased compartment number, demonstrating that this gene was responsible for the phenotype.

The question then arose – what is the basis of the phenotype?  The difference in expression levels suggest that regulation is important, rather than some feature of the YABBY transcription factor itself.  Sequencing of alleles in different backgrounds bears this out.  Thus, the YABBY protein-coding region of the genes was the same in different varieties.  Further analysis of numerous varieties and wild ancestors led to the final conclusion of the paper – that an insertion (of 6000 – 8000 bp) within the first intron of the YABBY-encoding gene is responsible for the increased expression of the fasciated gene, and thus to increased compartment number and fruit size in domesticated tomato.

While the authors do not discuss possible mechanisms, one of two general ones seem likely.  The insertion may have altered the functionality of a transcriptional repressor element, one resident within the intron.  This is, I suppose, the default explanation for this mutation, and possibly the correct one.  However, seeing as the nominal focus of this blog is RNA, I would be remiss if I did not mention a viable alternative.  Thus, the insertion may have altered an intron that inherently reduces gene expression in ways not directly associated with transcription initiation.  Precedent for effects of introns on gene expression such as this is provided by the work of Alan Rose and co-workers (see this recent report; I acknowledge that this precedent deals with enhancement of gene expression by introns, as opposed to the apparent inhibition seen in the fasciated gene, but also stress that it establishes post-transcriptional roles for introns in determining overall levels of gene expression).  This precedent should at least spur some additional characterizations of the fasciated locus, to establish if transcription initiation is the step in gene expression to which the differences in steady-state expression levels may be traced.

To wrap up, this study establishes a role for regulatory changes in an important evolutionary process, and it opens new avenues for the manipulation of fruits.  It also raises the tantalizing possibility that RNA processing may in some way be involved in all of this.

See also the write-up in ScienceDaily.

* – I use the term “compartment number” here so that readers do not get confused with the name of the QTL not studied in Cong et al., namely locule number.

Cong, B., Barrero, L.S., Tanksley, S.D. (2008). Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nature Genetics, 40(6), 800-804. DOI: 10.1038/ng.144

Rose, A.B., Elfersi, T., Parra, G., Korf, I. (2008). Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression. THE PLANT CELL ONLINE, 20(3), 543-551. DOI: 10.1105/tpc.107.057190