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November 14th, 2009:

The top two good keywords for this site are James and Corn!

Looks like the search engine is finally letting me put the annoying hacking of this site over the summer behind me.

Marker Assisted Breeding

Some traits are easy to select for. It’s easy to tell which plants have a gene that turns them purple, or one that turns a single stalk of corn into a, for lack of a better word, corn bush. (links) When I was an undergrad some of the world I did was with a gene that (when it wasn’t knocked out by a transposon) turned corn kernals dark purple. Traits like that one (the R gene) that can be identified just from looking at a seed are the easiest of all.
Other traits are not so easy to select for. How do you pick out which plants in a row carry a gene variant that increases yield by 6%. Or worse yet, yields 6% more under drought conditions, but has no effect otherwise? For improving crops a plant breeder will need to track gene variants for many generations under in all sorts of growing conditions.
The solution, made possible by modern genomics and molecular biology, is to use differences in the genetics code between individuals in the same species to track what what happens to different pieces of DNA from one generation to the next.
Today a plant breeder can take a piece of leaf from every plant in his field, and find out a huge amount about which parts of their genomes they inherited from which parents. So even if it’s not a dry year, he or she can still tell which plants carry the gene variant previously identified as better surviving drought. A breeder can check for dozens or hundreds of of different genes in each plant from that same small piece of leaf.
Some companies are even setting up systems to scrape little pieces off of individual corn kernals and do the same kinds of analysis. Then only the kernals with promising combinations of gene variants are planted, either further study or breeding with other kinds of corn carrying other promising traits identified and mapped by breeders.
The system can also work to discover useful new traits, something called quantitative trait mapping. A bunch of plants that are the mixed descendants of two known breeds are measured for some trait, for this example let’s use flowering time. The same plants are also analyzed using known genetic varations between their two ancestors to see which parts of their genomes come from which of the ancestral breeds. A region of the genome that contains a gene that effects flowering time will show a pattern. More of the plants which flower earliest will have inherited that region from one of their ancestors, and more of the plants which flower later will have inherited that region from the other ancestor. Regions of the genome what don’t contain genes that have an effect on when plants flower will be randomly distributed between the earlier and later flowering plants
Doing some complicated math that I don’t even want to think about can reveal regions on individual chromosomes which contains genes that control flowering time.  Depending on how much they’re able to narrow the region down, breeders will often use the regions they identify (called QTLs: quantitative trait loci) to bread improved crops without ever having to identifiy the exact gene responsible. (And flowering time can be important for breeders, for example when adapting a breed of soybeans grown in Georgia to be grown in North Dakota, a breeder will want to select for soybeans that flower faster because the growing season is shorter farther north.)

Some traits are easy to select for. It’s easy to tell which plants have a gene that turns them purple, or almost any of the mutants seen in the mutants of corn garden at cornell. When I was an undergrad some of the world I did was with a gene that (when it wasn’t knocked out by a transposon) turned corn kernals dark purple. Traits like that one (the R gene) that can be identified just from looking at a seed are the easiest of all.

Other traits are not so easy to select for. How do you pick out which plants in a row carry a gene variant that increases yield by 6%? Or worse yet, yields 6% more under drought conditions, but has no effect otherwise? For improving crops a plant breeder will need to track gene variants for many generations under in all sorts of growing conditions. (more…)

Genetically Engineered Crops: Rice

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Rice photo: flickr,毛利人

Scientific name: Orzya sativa

Genetically Engineered Traits: Herbicide tolerance, insect resistance (bt), increased vitamin A content

Details of Genetic Engineering:

Rice genetically engineered to be resistant to glufosinate (developed by Bayer CropScience) has been approved (deregulated) in the US but is not yet for sale commercially as the company attempts to get approval in countries which import rice from the US as well.

As far as I know, no company in the US has produced bt rice, which has less to do with consumer fears than with the small amount of rice production in the US rather than consumer rejection, but that’s just a guess. The Chinese government has developed breeds of bt rice, but doesn’t grow them commercially because of the risk to their export markets, which is primarily to countries that reject genetic engineering (although Chinese rice exports are declining drastically as more and more of their production is needed to feed their own people).

White and Golden Rice Respectively

White and Golden Rice Respectively

Golden rice, which has betacarotene, which human bodies need to make vitamin A, was developed by in Swizerland in the 1990s. Almost all plants produce carotenoids like betacarotene in their leaves as part of the biological machinery that makes photosynthesis possible. Breeders can sometimes identify and propogate natural mutations which lead to the expression of carotenoids in other parts of the plant, two key examples are orange carrots* and orange cauliflower. Vitamin A deficiency is a major issue** in many countries were rice is the primary crop, so breeders have searched for decades for natural mutations at would create orange rice, without success.*** The initial breed of golden rice which used two genes, one from daffodile to promote the expression of carotenoids in the grains of rice was attacked as requiring people to eat more than a dozen bowls of rice a day to get their daily recommended vitamin A intake, new versions that replaced the gene taken from daffodil with a version of the same gene taken from corn have more than twenty times as much beta carotene. Golden rice is also not currently grown commercially as it, like ringspot resistant papaya, doesn’t have a powerful for-profit corporation to shepherd it through the complex approval processes of various nations.

About Rice:
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