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Plant breeding

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

  • A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
  • Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
  • They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
  • While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
  • That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

The Color of Corn and Cultural Values

MAT_kinase has sparked an interesting discussion about the associations people have with corn of different colors. I’d previously heard that yellow corn (where pre-vitamin A carotenoids are produced in the kernels) isn’t popular in Africa, with the reason usually being given as its association with American food aid.* If yellow corn comes predominantely from food aid, it eventually becomes associated with being poor and/or starving, so that when people have a choice they eat other varieties of corn. I can’t find where I read it, but I vividly remember reading an interview with a woman who talked about the shame of eating yellow food-aid corn, knowing that it had originally been intended to feed livestock in the US, not people.

MAT points out another more pragmatic reason yellow corn may not be favored in Africa that I hadn’t heard of before. Apparently the extra carotenoids make yellow corn more susceptiable to spoilage than white corn varieties, a very pertenent issue in areas without access to the kinds of storage facilities we take for granted in American agriculture.

Jeremy at the Agricultural Biodiversity Weblog picked up the torch, highlighting a number of their own previous posts relevant to the discussion, including one by fellow blogger Luigi that relates the reaction of his own wife, originally from Kenya, on ordering polenta** at a restuarant and receiving a yellow dish.

Fortunately breeds of corn that contain even more beta carotene (the carotenoid most easily converted into vitamin A by our bodies) aren’t even yellow all the time. Although I wasn’t able to find a freely available picture, sometimes they’re ORANGE.*** While it turns out the correlation between color and beta carotene content isn’t perfect****, there’s still reason to hope varieties bred for the highest pre-vitamin A content will end up a striking orange color. For a visual examples of how orange corn can get, check out check out Dr. Rocheford’s lab website.

Will the distinction between orange and yellow***** be enough to get over the Africa’s lack of enthusiasm for yellow corn? Will the benefits of a diet with more vitamin A be enough to outweight the issues with yellow corn going “off” if stored improperly? I certainly hope the answers to both these questions are yes, but we won’t know for sure until we try. And there are some hopeful signs. For example this segment in a story from NPR: (more…)

“New” Cruciferous Vegetables

A stalk of brussels sprouts photo credit: cbmd, flickr (click for photo in original context)

Last week Greg over at Pie-ence was talking about the amazing variety of vegetable crops breed out of a handful of species within the genus Brassica, specifically Brassica rapa and Brassica oleracea.* I’m referring to these as cruciferous vegetables, which is actually a wider category including all the vegetables within the mustard family of plants (scientifically this is called the Brassicaceae). But one of the cool things about having so many kinds of vegetables within the same couple of species is that, because they’re the same species, they can still be interbreed with each other to create “new”** vegetables. (more…)

Genome Sequencing vs Genetic Mapping

There was a recent paper in Science about the mapping of the Artemisia annua genome. I’ve seen several people interpret this as another genome sequence. It’s hard to blame anyone for this confusion given headlines like “Scientists map the maize genome!” to describe the sequencing of the maize genome. So what’s the difference between a sequenced genome and a mapped genome? I’m glad you asked! (more…)

More on the Good Guys (CGIAR)

Tracked down a paper published just under a year ago in Food Policy (a peer reviewed journal). “The impact of agricultural research on productivity and poverty in sub-Saharan Africa” by Arega Alene and Ousmane Coulibaly.* 

CGIAR spending on research targeted at agriculture in Sub-Saharan Africa (178 million dollars a year in 2003) provides 1.3 million people with an escape from extreme poverty (living one dollar a day or less) every year. Simple division would indicate the agricultural research of the CGIAR centers is saving human beings from the trap of extreme poverty at a cost of just under 137 dollars per person. Of course it isn’t that simple, there are both economies of scale** and, eventually, diminishing margins of return*** to consider, but it seems the work of the CGIAR centers in Africa are big enough to have achieved those economies of scale, and, given their calculations on the elasticity on poverty to investment in agriculture, Africa is a LONG way from having to worry about diminishing marginal returns on agricultural investment.

Given the elasticity of poverty reduction to agricultural research spending they calculate (-.22) the marginal cost* of reducing poverty by another person in Sub-Saharan Africa through investments in agricultural research is only $71. (i.e. spending one billion dollars more on agricultural research would save an additional 14 million people from poverty.) This doesn’t consider the additional postive effects of improving local agriculture (for example reducing the incidence of famine).

Finally consider this quote from the paper for a sense of the work the CGIAR centers are funding and try not to feel as impressed as I do: (more…)

What is it about purple plants?

I’m really at a loss here, but there’s just something way cooler about eating a purple colored plant over a more regular color. I’m not sure what it is (I’m not particularly partial to the color purple in other contexts).

Consider the case of the cauliflower. (more…)

Not Genetically Engineered: Grapes

New York Grapes. Concords I believe, though it's been several years so I may be remembering wrong.

New York Grapes. Concords I believe, though it's been several years so I may be remembering wrong.

Scientific Name: Vitis vinifera

Supposed Genetically Engineered Trait: Large size/seedlessness

The Real Story:

Seedless grapes are descended from several different mutations that all result in the developing embryos of grape seeds to abort prematurely*. You can still find the tiny dead remnants of seeds in seedless grapes. Of course being seedless raises a new question: How do plant breeders work with seedless grapes? (more…)

Dr. Gebisa Ejeta on Investing in Agriculture

I mentioned Doctor Gebisa Ejeta before when he won the world food prize for his work developing striga resistant sorghum breeds. This is a man who began life… well his own words can say it better than I can paraphrase:

I was born of illiterate parents with little means and raised in a small village without schools in west-central Ethiopia. An only child, I was nurtured with with lots of love, but on a diet less than adequate even for body maintenance, let alone for growth and intellectual development. … I was rescued by a godsend from the United State of America…

I took that quote from his testimony before the Senate Committee on Foreign relations this past spring. It was a moving call to renew the international investments in agricultural research, and the training of plant scientists around the world, something the United State and the international community as a whole have let slide for the past two decades. The whole testimony is an excellent read (h/t to mary for pointing it out on the biofortified forums). If you have a few minutes, please take the time to read the whole thing here [pdf]. If you don’t, you surely have the time to read this single paragraph: (more…)

Not Genetically Engineered: Watermelon

I know I'm reusing images, but this is just a really gorgeous watermelon

I know I'm reusing images, but this is just a really gorgeous watermelon

Scientific Name: Citrullus lanatus

Purported Genetically Engineered Trait: Lack of seeds

The Reality:

Seedless watermelons grow on triploid (three copies of every chromosome) watermelon plants. Like the banana, triploid watermelons are seedless because it’s impossible to separate three copies of each chromosome into different different reproductive cells. Unlike bananas, seedless watermelons are grown from seed and must be fertilized by fertile (diploid) watermelons to produce fruit.

Where do farmers get seeds for a seedless plant? (more…)

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…)