Wednesday, November 6, 2019

"Junk" DNA

One of the curious things about DNA is that very little of it has been linked to heritable traits. Only 2% of human DNA, for instance, is linked to heritable traits. The rest of the DNA has been called "junk" DNA or "non-coding" DNA. Scientists noted that the junk DNA looks "viral".

Scientists long speculated that the "junk" DNA had been inserted into the human genome by some mysterious process. An equal mystery is, why is it still in the human genome? If it caused even a slight evolutionary disadvantage, one would expect those carriers to be long gone.

Sharka Virus
Is there a more perfectly named virus than the virus that causes Plum Pox? SHARKA!

Traditional breeding techniques hit the wall when breeding for Sharka resistance. The virus emerged in the Balkans during WWI and there are no known sources of natural resistance*. How do you breed for resistance when you cannot find any parents with resistance?

Using genetic engineering, scientists at the Agricultural Research Station in West Virginia created a new plum named HoneySweet that is IMMUNE to Plum Pox.

How did they make HoneySweet immune?

They grafted Plum Pox Virus into the plum's DNA using naturally occurring bacteria.
The resistance is due to RNA silencing, which is a natural process in plants that gives them some adaptive protection against viruses. In the silencing process, the introduced PPV coat protein gene induces the plant to break down the coat protein, which prevents virus infection. This is a natural mechanism that plants use not only for virus resistance, but also to regulate many normal cell processes.
It is not much of a jump in logic to assume that the viral DNA we carry around was inserted into our cells by the same kinds of bacteria used by the ARS scientists. Remember, at the cellular and molecular level the numbers are astronomical and even very, very low odds events happen with regularity.

That inserted viral DNA gave us our great^10e6 ancestors resistance to those virus. The organisms competing with our ancestors lacked that resistance and our ancestors prevailed.

The irony is that the plum HoneySweet is failing commercially because consumers are freaked by the thought of eating viral DNA.

I got news for them. 98% of their DNA is "viral" DNA. 98% of the DNA in the free-range chicken they ate today was originally "viral" DNA. Probably ditto for the mesclun and almond salad.

Description of HoneySweet plum from the patent application:

Maturity when described.—Shipping ripe-eating ripe.
Average date of harvest.—Mid August to early September in Kearneysville, W. Va.
Size.—Medium to large; average size is 43 mm transverse diameter at right angles to the suture plane×45 mm transverse diameter in the suture plane×52 mm axial diameter; average weight is 60 grams.
Fibers.—Small, few, tender.
Juice.—Moderate at eating-ripe.
Flavor.—Very good.
Eating quality.—Sweet, excellent; brix of ripe fruit averages 21.5° depending on maturity at harvest.
Color.—Ranging from RHS 6 A to C to RHS151A, depending on stage of ripeness.
Pit cavity.—Color same as flesh color.

*Prunus domestica clutivar Jojo appears to have some resistance to Sharka but even when it is not shows symptoms of Sharka. Strange. Makes a fellow go "Hmmm!"

There are also some varieties that show modest qualitative resistance to Sharka. It may be that they are less attractive to aphids or other vectors than the more susceptible varieties. Example, cv "Vision" showed less Sharka infection (only 25%) when grown in an infected orchard for several years than many other cultivars.

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