Friday, March 4, 2016

In the News: Soybean Cold Stress!

In the Midwest US it is not uncommon to have a frost or snow event in early spring. My Mom's gardening practice is wait until after Mother's Day to be sure a cold snap won't kill her plants. Soybean are sensitive to cold, especially in the young seedling stage.  But why is this? And is there anything that can be done about it? Last week an important paper came out that shines some light on this subject.

Impact of cold on soybean seedlings (Pers. Photo)

The article looked at the CBF cold responsive pathway, which is known to play a very important role in cold acclimation and tolerance in other plants. This multi-step pathway is well documented in cold tolerant species, especially the labrat plant Arabidopsis. In this pathway, CBF (also called DREB, as it is in this paper) is the main transcription factor. A transcription factor is the cell's version of a foreman, going into the nucleus and telling the cell what genes need to be activated.

Cold stress in plants, personal illustration
Turns out, soybean also has these same genes. And that CBF turns on when soybean is exposed to cold much in the same way that it does in Arabidopsis. The researchers were able to draw a line in the sand between working and non-working portions of the CBF cold responsive pathway within soybean. Turns out only half the pathway is non-functional, the other half is working just fine! You might wonder how they figured that out, great question!

The first question that they examined was, does soybean have similar genes to Arabidopsis CBF cold pathway? By examining the soybean genome, they were able to compare gene sequences with the Arabidopsis genome to generate a list of potential homologs (genes that are the same between species). This is only good on paper, just because the sequences match does not guarantee the functions match.

But once you narrow an entire genome down to less than a dozen genes, it is easy to examine functional responses. Toss the soybean in the cold, use quantitative PCR to get a measure of the gene expression amount before and during the cold. When the authors did this, they found that the CBF transcripts (mRNA) increased drastically and transiently. This is the same response that is seen in Arabidopsis. From this they concluded that all the steps in the cold response are active in soybean, and the "problem" lies between CBF transcription and cold responsive gene translation.

Perhaps the "problem" is that CBF itself has mutated in soybean and is damaged so that it can no longer interact and activate the cold responsive genes. The researchers set out to test this by taking the soybean CBF and moving them into Arabidopsis. This new genetically modified Arabidopsis will always be expression the soybean CBFs. If soybean CBF works, it should turn on the Arabidopsis cold responsive genes without having to expose the Arabidopsis plants to cold.

Simplified Fig 5 from Yamasaki & Randall 2015, provided by S. Randall
And that is exactly what happened! The downstream cold responsive genes COR47, RD29a, and ADH1 all increased in the transformed Arabidopsis. This told the researchers that the soybean CBF are indeed functional, at least they are capable of activating their target genes when expressed in Arabidopsis.

So what is the "problem" with soybean's cold responsive pathway? We still do not know. But we do know that it is not upstream of CBF transcription. Thus this article allows us to focus in on part of the pathway as the "problem" area. Hopefully these researchers are still examining this and will find the solution!

Yamasaki, Y, and Randall SK, 2015.  Functionality of soybean CBF/DREB1 transcription factors (paywall)

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