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A Home for Genomic Information of Weed Species

In 2014, my grad student at the time Shu Chen, and I began contemplating the idea of an online repository for weed species genomics information.  We were neck deep in assembled transcriptomes — most of which we  assembled  to find only one gene associated with herbicide resistance.  To us it seemed like a waste of resources just to let the data sit around not being used.  Of course we uploaded data to NCBI TSA, but this data is of little use to those who do not work with transcriptomes, in bioinformatics, or with large text files (these files are also available on our site by the way).  What we saw as a need was a search able database that would allow for searching of any keyword to find genes of interest.  But who would use such a site?

Introducing WeedGenomics

WeedGenomics was developed for non-genetics researchers in mind. With the keyword search, researchers could easily find target-site herbicide resistance genes such as “acetolactate synthase” or “psbA”, or any other gene for that matter. Users can search transcriptomes by nucleotide sequence as well with sequences presented in order of most similar. Results can be downloaded in FASTA format allowing easy use of data. Sequences can also be subjected to BLASTn at NCBI or BLASTp via local Uniprot Virdiplantae protein database. Once sequences are identified they can be downloaded in FASTA format or our new trinBank format. I also offer a python script that can be used to create an object from the trinBank file, thus making it easy to use sequences in programs such as Biopython.

Just getting started

The Weed Genomics repository is just getting started. The goal is to grow WeedGenomics into an online community of users that allows for uploading of user data including capillary sequence data, transcriptome assemblies, and genome assemblies. Tools are being developed that allow users to search for SNPs associated with herbicide resistance on the site, with complimentary command line tools for processing large numbers of sequences. See my GitHub site for further information on command line tools (MutationFinder command line). Other tools and information are being added to the site in the coming months. Please let me know what you find useful, what you would like to see developed, and any other ideas for the development of the site. I am always open to new ideas.

So check out the site and let me know what you think.



Growing Degree Days in Southeast are Double Two Years Ago

I ran an analysis of the growing degree day accumulation for Auburn, AL for this year and 2015 up until February 6.  I used a 0 degree base temperature to keep it simple.  The figure inset is very telling of what has occurred– basically over the first ~35 days of the year the number of growing degree days in 2017 is almost double 2015 with approximately 450 accumulating in 2017 and 250 in 2015.  Basically the two weeks in January of warm-weather experienced across the US are the cause for the high accumulation up to this point.  auburn-2015-vs-2017

Here is one last thing to think about — what if we experience a two to three cold period or if we dip below freezing?  Does that mean all growing degree days should reset?  Even worse, what if we do not dip below freezing again?  Does this mean we should not reset and we should count all growing degree days since January 1?  This is why, in my opinion, that accumulation of growing degree days starting January 1 in the Southeastern US and other similar regions might need to be rethough.

Goosegrass and Compaction

I have been working on goosegrass biology and control for a couple years and I found this article previously published in turfgrass trends.  The article is title “Goosegrass Shows No Tolerance to Compaction.”  Not to bemoan the work– it is good work, but it misses a few crucial points.

First, just because a plant declines in measured variables does not mean it does not tolerate the condition.  Lots of weeds/plants in general will decline in root growth and general biomass when under a stress– such as compaction or low fertility.  Such species are not “obligate” to the condition they are “facultative”.  In other words, the species does not necessarily like the conditions, but they tolerate it in order to survive.

Second, tolerance to a condition is better measured in terms of fecundity– especially with an annual species.  Fecundity is simply reproductive success.  So if it produces seed, even if lower than normal amounts it can “tolerate” the conditions.

Third, goosegrass does not have to have similar rates of growth and development when compared to compacted and not compacted, it just has to have less in a decline than the species it is competing with.  It is like the joke- if we are being chased by a lion, I don’t have to out run the lion, I just have to out run you.

The full scientific paper – Goosegrass and Bermudagrass Competition under Compaction — was published in Crop Science in 2009.  Very well written article but it basically says the same thing– goosegrass does not tolerate compaction.  I have to disagree with their assessment– one problem is they did all their studies in high sand soils — almost pure sand and a 91% sand native soil.  Second, compaction can vary with soil depth.  In a sand soil, compaction can occur at the surface layer but traffic may not cause compaction at lower depth.  Another problem is that I cannot find where they reported where they got their goosegrass seed for the study.  There are definite ecotypes of goosegrass that have been selected for greater compaction tolerance just like there is herbicide resistance selection.

Certainly I have a bias since I find goosegrass being the only species that will survive in highly compacted, concrete type soil.  I will post goosegrass growing in strange places later.


Specticle (Indaziflam) Movement into Perennial Ryegrass Overseed

I viewed a few courses yesterday with Specticle movement from non-overseeded bermudagrass to bermudagrass fairways overseeded with perennial ryegrass.  The movement was substantial in places and creates a jagged look to the fairway edges.  Here is the kicker though– the supers I spoke with do not mind the injury.  To them this is not a big deal.  The annual bluegrass control is so good that they said they can live with the movement injury.  The amount of play is limited this time of year so as the bermudagrass begins to green up in March these areas will begin to mask themselves. Don’t get me wrong — this type of injury is not “acceptable” per se.  It is, however, tolerable.

In most cases the injury is only a few feet, but in one instance it moved across an entire fairway.  See the pictures below.

2015-02-10 13.40.19 2015-02-10 13.58.13 2015-02-10 13.49.43 2015-02-10 13.03.03

Warm-Season Turfgrass Winter Kill

I really should have wrote about this about two months ago.  But such is the way of things.

Whether the winter of 2013/2014 was one of below average temperatures or if it was a return to what winter conditions should actually be in the southeast is debatable.  What is not debatable however, is the negative impact that the winter had on warm-season turfgrass– especially on golf courses.

Note the winter-kill on the southside of the fairway where there was greater shade.

Note the winter-kill on the southside of the fairway where there was greater shade.

Of all the winter kill I have seen on golf courses this spring there is only two factor that jumps out at me with respect to where winter-kill occurred– Shade and low mowing height.  Bermudagrass fairway and greens that were in 90 to 100% shade throughout the winter were the areas that were most likely to not green up in the spring, displaying typical winter kill symptoms.

The question remains — was it the winter shade or was it the shade in spring/summer/fall that did not allow the turfgrass stand to develop adequate root system/rhizome-stolon density/carbohydrate pools to survive the winter?  Probably a little bit of both.  Certainly winter shade areas are going to be colder for longer during the day, preventing the soil from thawing or remaining frozen longer during the day.  Shade during the growing season would put the turfgrass in a weakened state with no buffer for survival during the winter.

Note the winter kill of bermudagrass on the southside of this bermudagrass fairway.  Much less kill on rough height cut and as fairway moves north.

Note the winter kill of bermudagrass on the southside of this bermudagrass fairway. Much less kill on rough height cut and as fairway moves north.

The low mowing heights on greens and fairways just exacerbates the potential for winter kill because the root/rhizome/stolon system simply does not develop to the extent that higher mowing heights do.

No covers were used on these bermudagrass greens.  Golf course is in the southern transition zone.

No covers were used on these bermudagrass greens. Golf course is in the southern transition zone.

One other note:  I have heard a lot of comments out of North Carolina that TifGrand bermudagrass has not faired well following this winter.  TifGrand is the best shade tolerant bermudagrass I have ever seen.  Thus it has spread rapidly around the southeast and is being planted in shaded or semi-shaded areas.  From what I have heard TifGrand planted in North Carolina in shaded areas was wiped out.  Perhaps someone has a comment on this?  I admit this is only from one source.  It may not be the case with all TifGrand in North Carolina.


Sureguard (flumioxazin) lateral surface movement onto a bentgrass putting green.

I have been holding back writing about lateral movement of flumioxazin, aka Sureguard, on to a bentgrass putting green.   I wanted to see if other movement scenarios would happen of in an incident in Alabama was a freak occurrence.  Since an incident happened in December 2013 in Alabama I have heard of other situations of movement in the Carolinas.  Considering it is the summer it seems like an opportune time to discuss the potential for movement of herbicides applied normally for Poa annua control in the green surrounds to damage bentgrass if the herbicide moves onto the green.

Sureguard is a single active ingredient herbicide containing flumioxazin, a protox inhibiting herbicide that is primarily used as a preemergence herbicide but also can be used for postemergence burndown in dormant to semi-dormant warm-season turfgrass.  In my evaluations it is an excellent preemergence herbicide for annual bluegrass and crabgrasses.  The problem is that if one applies Sureguard to green bermudagrass, “chemical induced dormancy” will quickly occur.  In other words it will turn the bermudagrass brown.  This is not a problem if it is late fall and bermudagrass would be going dormant anyway.  In fact, I see it as a positive because Sureguard causes the bermudagrass to develop a lighter, blonde coloration to the turfgrass instead of a normal darker brown.

But the topic at hand is lateral movement.  Lateral movement is the movement via surface water, foot traffic, or machine traffic from a treated area to an adjacent non-treated area.  Sulfonylurea herbicides, atrazine, simazine, and Kerb (pronamide) are well known for their ability to be move with surface water or tracked to non-treated areas.

Let me set up a typical scenario for lateral movement.  In the vast majority of cases it is the movement of a herbicide applied to warm-season turfgrass such as bermudagrass or zoysiagrass on to a cool-season bentgrass putting green, perennial ryegrass overseeded into a fairway, or a tall fescue rough area. Very simply, lateral movement most often occurs when herbicides are applied to warm-season turf and move on to cool-season turf.  Golf courses are the ideal situation for movement because of multiple different turfgrass species.  Of course movement can occur in other turfgrass situations, but if a sensitive species is not close by then the injury will not be observed.

I’m going to make a broad statement about lateral movement in turfgrass– any herbicide can move laterally short distances in a turfgrass environment.  Most information regarding the potential for lateral movement is based on the potential for herbicide soil binding and water solubility.  If a herbicide binds to soil and is not water soluble, it is thought that it will not move laterally.  To the contrary, if a herbicide does not bind tightly to soil and is water water soluble, it is thought that it can move laterally.  This is true in an agricultural environment where the herbicides are applied to the crop and directly to the soil surface.  But in a turfgrass environment the herbicide is first captured by the turfgrass leaf material and then the undegraded turfgrass mat layer which lies above the soil or constructed rootzone.  Leaf material and undegraded organic material have very low binding compared to degraded organic material and soil.

Consider the application of a herbicide, or any pesticide for that matter, to the turfgrass surface.  If the herbicide is allowed to stay on the surface and a large rain event or irrigation event occurs, the material can be “washed” from the leaf surface and move laterally along the turfgrass surface before it has time to percolate into the soil.  The infiltration rate would be an obvious factor influencing potential lateral movement with factors such as saturated soils, smaller particle size, and hydrophobic soils increasing the likely hood of lateral movement.

Tracking is another possibility in a turfgrass environment.  Herbicides can be picked up after a herbicide application by foot traffic or equipment tires.  Allowing the herbicide to dry on the surface can decrease the potential for tracking. But the herbicide can be redissolved by dew allowing for tracking days after application.

Based on these standards for gauging a herbicide lateral movement and tracking, Sureguard seems to have low potential for movement.  In addition, creeping bentgrass is more tolerant to Sureguard than sulfonylurea herbicides like Monument, Revolver, Tranxit, or Katana and it is a contact herbicide with minimal translocation throughout the plant.  Based on all these factors, Sureguard would be considered to have low movement potential.  But the fact remains that this is a turfgrass environment and in my opinion, in turfgrass, anything can move.

And that is exactly what happened at a golf course in Alabama.  Sureguard moved laterally following a heavy rainfall and damaged a bentgrass putting green (see images).  To make matters worse, herbicide was picked up by foot traffic and damaged the green in footprint patterns.

Lateral movement of Sureguard across a bentgrass putting green causing injury.

Footprint damaged caused by tracking of Sureguard onto a bentgrass putting green.

Footprint damaged caused by tracking of Sureguard onto a bentgrass putting green.

Preventing Movement

The key to reducing the potential for lateral movement and tracking is to not apply herbicides that can injure bentgrass above the putting green and do not apply within 15-20 feet of the green.  But if applications must me made, to reducing lateral movement and tracking is light, successive irrigations following application can aid to move the herbicide off the leaf surface and into the soil.  The majority of herbicides need only 1 to 2 hours on the leaf surface to have an adequate amount absorbed in.  Following this, two light irrigations can aid to first wash the herbicide from the leaf surface and second push the herbicide into the soil surface where it will be degraded, bound, or remain available for plant uptake.

These best management practices are the best way to prevent lateral movement.  But in the Sureguard movement case in Alabama, these irrigation practices were followed and the herbicide still tracked and moved.  So the best practice is to keep a safe distance and do not apply up slope.

Additives improve winter performance of Revolver and other SU herbicides.

The following is from some work conducted a few years back.  Often SU herbicides can underperform when temperatures are consistently below 50 to 55 F for an extended period of time.  While not completely understood, the addition of methylated seed oil and ammonium sulfate can improve winter activity.  Note: Revolver was applied at 17.4 fl oz/a, additives were applied at listed rates per acre, and all treatments were applied at 30 GPA. -SMImageImageImage