Clearing up some jargon

Monsanto’s press releases on Roundup Ready 2 Yield uses the term “advanced gene mapping and insertion process”. This sounds impressive, but what does it mean? A colleague asks: “can advanced gene mapping and insertion tech improve yield of the plant or would other factors like selection and crop physiology really be what’s improving yields?”
From the press release:

[David Nothmann, Monsanto’s Soybean Agronomic Trait Lead,] said Roundup Ready 2 Yield technology is based on an advanced gene-mapping and insertion process. “Through gene mapping, Monsanto has identified specific DNA regions in soybeans that have a positive impact on yield,” he explained. “Using these new insertion and selection technologies, the Roundup Ready 2 Yield gene is situated in one of these DNA regions.”

There has undoubtedly been decreased yield in Roundup Ready crops when compared to conventionally bred crops. This has two possible causes: lag “a temporary or transient problem associated with the introduction of a new technology” or drag “an inherent yield reduction associated with the technology itself”. There is a lot of evidence that the problem is in fact lag, but more research must be done. Some of the issues are discussed in Challenges in Comparing Transgenic and Nontransgenic Soybean Cultivars.
I covered the topic of yield lag/drag somewhat in my post Exposed, Indeed.

GM seeds are often “one hit wonders” that excel in one specific trait, but not particularly for increased yield. Non-GM lines, on the other hand, are improved every year, with the best yielding plants being used to produce the next year’s seed. I recently attended a seminar presented by a scientist from Pioneer where he said that they were working to develop better yielding lines that would work in conjunction with their primary transgenic traits. The companies are aware that this is a problem with their products, and are of course working to solve it, to avoid losing sales.

Back to the question at hand – as I understand it, advanced gene mapping is a selection tool.  The companies start with huge experimental fields (much larger than what an academic lab can afford) in multiple locations with different climates that include many varieties of the crop in question. They measure yield and determine genetic markers* for each variety/location combo, using known markers for yield as the starting point. The researchers are then able to see which varieties do and do not have certain markers. They cross varieties that have different markers, with the goal of a super high yielding plant that has all of the markers that are positively correlated with yield and none of the markers that are negatively correlated with yield. They have fields in multiple locations so they can choose the markers that confer an advantage in a variety of climates – ensuring that the plants will perform no matter what the location or conditions. There are a lot of benefits of this method over blind selection, the biggest of which (in my opinion) is that you don’t have to know what’s happening physiologically in the plant. Knowing what each gene does (and what each mutation to each gene does) is nice, but really not necessary for the purpose of breeding bigger better plants.
As for the “insertion process” part, I admit that I’m not 100% sure why positioning the insertion in an area of the genome that is correlated with high yield would matter (any readers who know, feel free to enlighten me!). I can think of a few reasons why the specific position of the transgene insertion does matter, but all of them are part of the normal process running up to a marketable genetically engineered crop. In fact, I’m in the process of some of those stages right now. Once the gene of interest is chosen, a compatible promoter must also be chosen. I imagine that a constitutive promoter (always on, in every cell) would be used for the glyphosate resistance trait. The gene construct is introduced into many plant cells that are then grown into individual adult plants. Each introduction is called an event. Each event is treated separately because the position of insertion is different each time. When the insertion lands in the middle of a gene, it can stop the gene’s normal expression – so many events are investigated to see which ones have the least effect on the plant’s normal gene expression while at the same time producing the desired trait. A video on Monsanto’s website says that they used Agrobacterium instead of biolistic transformation in RR2 because it is “gentler”, causing less damage to the surrounding DNA. They then screened many events using genetic markers to find the best ones – an expensive process that (to my knowledge) has not been done before. They say that having the insertion in one of the areas near a marker for high yield increases yield an additional 7 to 11 percent.
Edit: I don’t know why I was having a mental block on this! What I said in the last paragraph stands but I’ve figured out why having the insertion in a high yield correlated area would matter. If the insertion is near an allele for a gene that is correlated with poor yield, selecting for the trait of interest would bring along the area that you don’t want. Having the insertion in a  “good” area of the genome (assuming that it isn’t actually interrupting any genes) eliminates this problem.
*Here, markers basically correspond to alleles of a gene. Wikipedia has a decent explanation of genetic markers, but unfortunately requires the understanding of much more jargon. If you’d like a more detailed explanation of genetic markers, please let me know, and I will be happy to write a post on the subject.
Raymer, PL and TL Grey (2003). Challenges in Comparing Transgenic and Nontransgenic Soybean Cultivars. Crop Science, 43, 1584-1589.