Sunday: 29 November 2009
The maize genome has been sequenced.
This beautiful figure summarizes the large scale features of the maize (Zea mays) genome. That’s corn, to us Americans - maize to everyone else. The sequence of its 2.3 billion nucleotides is pretty much complete now, and published in last week’s Science (subscription wall).
The black numbers on the outside of the circles identify each of the ten chromosomes of maize. Each concentric circle inward shows the presence of some kind of important feature. In addition, the correspondence with the already sequenced rice and sorghum genomes is shown in the innermost two circles.
I think the gray curves totally unify the portrait, don’t you? I don’t even want to get into it, because I only superficially understand it, but they represent duplications of DNA within the genome. Duplications are the fertile ground for new genes, and the maize genome is fraught with an enormous number of these events. I will note that the designers of this figure oriented the position of the chromosomes, not in numerical order, which would have produced a chaos, but in the order that would result in the minimal number of connections that reach across the figure and disturb the understanding of it. It’s a lovely piece of work.
It was a monumental effort - much more difficult than the sequencing of other genomes. The figure above shows why - there is a huge amount of repetition (circle E) in the genome. Actual genes (circle F) comprise only a very tiny portion of the maize DNA - the majority is composed of transposable elements (circle C). Because of the techniques used in sequencing, a high degree of repeated elements makes the process extremely difficult. Even with half again as much DNA, the human genome was a snap compared to maize.
Maize has always been thought of as a botanical monster, that is, something that is thoroughly unique. Its reputation as such is only enhanced by this new knowledge of its genome.
There are plenty of enthusiastic folks at work figuring out what all this means. Virginia Walbot has a characteristically very nice read on just a few of the major questions that have been around for years and will now be addressable. Some of these questions are fairly deep scientific issues, but others are very practical curiosities. Hybrid vigor, for instance, has always been something of a mystery, that the hybrid between two maize lines should be larger, more vigorous, and produce more fruit. Comparison between inbred lines of maize shows that many lines have genes that others completely lack, and vice versa. In fact, the statement is made that there is more genomic difference between some lines of maize than there is between humans and chimpanzees. Hybrids combine all the genes into one organism.
There is also the question of how maize survives such a huge amount of repetitive DNA, and not just that, but repetitive DNA that jumps around the genome and potentially disrupts crucial genes. Here’s an interesting discussion on that matter. I might add that it’s a curious thing that maize results from 10,000 years of breeding and domestication from a rather nondescript ancestral grass, teosinte. There will probably be lots of folks asking if it’s something about teosinte that led to maize’s extremely complex genome, or whether blind artificial selection for a food crop led to this bewildering morass of DNA that somehow works. It seems likely that we can only marvel at the job that native American geneticists did over the last 100 centuries.
No way can I do this justice - just mention a few things and sit back and wait for what’s going to come of it.
Here’s the author list - somewhere around 150 contributors from 33 institutions. They stand on the shoulders of giants - thousands of others, over the last sixty years or more, and then too the ones over the previous 10,000 years who contributed the genetics that made this possible.
Congratulations!
This beautiful figure summarizes the large scale features of the maize (Zea mays) genome. That’s corn, to us Americans - maize to everyone else. The sequence of its 2.3 billion nucleotides is pretty much complete now, and published in last week’s Science (subscription wall).
The black numbers on the outside of the circles identify each of the ten chromosomes of maize. Each concentric circle inward shows the presence of some kind of important feature. In addition, the correspondence with the already sequenced rice and sorghum genomes is shown in the innermost two circles.
I think the gray curves totally unify the portrait, don’t you? I don’t even want to get into it, because I only superficially understand it, but they represent duplications of DNA within the genome. Duplications are the fertile ground for new genes, and the maize genome is fraught with an enormous number of these events. I will note that the designers of this figure oriented the position of the chromosomes, not in numerical order, which would have produced a chaos, but in the order that would result in the minimal number of connections that reach across the figure and disturb the understanding of it. It’s a lovely piece of work.
It was a monumental effort - much more difficult than the sequencing of other genomes. The figure above shows why - there is a huge amount of repetition (circle E) in the genome. Actual genes (circle F) comprise only a very tiny portion of the maize DNA - the majority is composed of transposable elements (circle C). Because of the techniques used in sequencing, a high degree of repeated elements makes the process extremely difficult. Even with half again as much DNA, the human genome was a snap compared to maize.
Maize has always been thought of as a botanical monster, that is, something that is thoroughly unique. Its reputation as such is only enhanced by this new knowledge of its genome.
There are plenty of enthusiastic folks at work figuring out what all this means. Virginia Walbot has a characteristically very nice read on just a few of the major questions that have been around for years and will now be addressable. Some of these questions are fairly deep scientific issues, but others are very practical curiosities. Hybrid vigor, for instance, has always been something of a mystery, that the hybrid between two maize lines should be larger, more vigorous, and produce more fruit. Comparison between inbred lines of maize shows that many lines have genes that others completely lack, and vice versa. In fact, the statement is made that there is more genomic difference between some lines of maize than there is between humans and chimpanzees. Hybrids combine all the genes into one organism.
There is also the question of how maize survives such a huge amount of repetitive DNA, and not just that, but repetitive DNA that jumps around the genome and potentially disrupts crucial genes. Here’s an interesting discussion on that matter. I might add that it’s a curious thing that maize results from 10,000 years of breeding and domestication from a rather nondescript ancestral grass, teosinte. There will probably be lots of folks asking if it’s something about teosinte that led to maize’s extremely complex genome, or whether blind artificial selection for a food crop led to this bewildering morass of DNA that somehow works. It seems likely that we can only marvel at the job that native American geneticists did over the last 100 centuries.
No way can I do this justice - just mention a few things and sit back and wait for what’s going to come of it.
Here’s the author list - somewhere around 150 contributors from 33 institutions. They stand on the shoulders of giants - thousands of others, over the last sixty years or more, and then too the ones over the previous 10,000 years who contributed the genetics that made this possible.
Congratulations!
Wednesday: 14 September 2005
Americans call it corn, but the word “corn” is a generic term that just means “the grain that grows here”. In Norway, it’s barley (Hordeum vulgare) that’s called “corn”. In biblical Egypt “corn” meant what we call wheat (Triticum spp). Everyone else in the world calls our “corn” maize. It’s Zea mays.
This year we grew two varieties of corn, or maize, both “heirlooms” as opposed to hybrids, because I want to be able to propagate seeds next year and you can’t do that with hybrids. Well, you can, but the plants you get won’t produce the same kind of corn. There was a sweet corn, Golden Bantam (right), and a “dent corn”, Bloody Butcher (top left and bottom). The less colored Bloody Butcher is just a little less mature and the anthocyanin pigment hasn’t had a chance to fully develop:
And yes, the yellow sweet corn on the far right doesn’t look so great, but that’s because I was using later season cobs to save seeds with. We really enjoyed this one earlier in the season. You harvest sweet corn quite early before it has a chance to fully mature.
Dent corn on the other hand, the two cobs on the left, is meant for feeding to primary consumers, like pigs and cows, so that we as secondary consumers can eat those pigs and cows. That’s not all - it can be ground up as cornmeal and that’s why I had planted it. Isn’t it pretty! You wouldn’t believe all the molecular work that’s been done with the gene, the R-locus, that causes the red color!
Botanically, corn is a monster. That’s a real term; it means an organism that is unlike any other. The corncob is actually a multiple fruit - each kernel is a single fruit with an embryo inside; the majority of the fruit is starchy endosperm, which nourishes the embryo as it germinates. The cob is actually a highly thickened inflorescence stem. The pesky silks that you have to pull off are the leftover styles that caught the pollen and provided a pathway down to the baby kernels to fertilize the egg and make an embryo.
Part of maize’s monstrosity is that it has been highly bred from a “normal” grassy ancestor. Corn originates from South and Central America and is the result of Native American breeding that’s been going on for thousands of years. Its original ancestor is almost certainly teosinte, an unimpressive little grass that produces a few tiny kernels on an inflorescence that shoots out from the top of the plant. There’s several species of teosinte, including Zea diploperennis, and it can be crossed with maize. In teosinte, the female flowers are at the ends of the shoots and the male flowers shoot out from the sides. In corn, it’s the opposite. So not only has corn been bred to produce large numbers of large kernels all on a single cob, there’s been a sex change as well.
Here’s a neat pic of a cross between the teosinte on the left, the maize on the right, and the hybrid in the middle:
A lot of work has been done in using these wild teosinte species as sources of new genes to introduce into maize, and there have been efforts, some successful, to conserve habitats in Mexico and Central America where these wild plants live. It’s not clear that it would be a good idea to have a perennial maize, but the possibility exists. Insect and fungus resistance and so forth might be other valuable additions from outside wild species of the teosinte relative.
Maize is one of those organisms like E.coli bacteria, yeast, fruitflies, Arabidopsis, mice, and nematodes, that are heavily used as models for how organisms work. All of these organisms have had their entire genomes sequenced or in the process of being sequenced.
This year we grew two varieties of corn, or maize, both “heirlooms” as opposed to hybrids, because I want to be able to propagate seeds next year and you can’t do that with hybrids. Well, you can, but the plants you get won’t produce the same kind of corn. There was a sweet corn, Golden Bantam (right), and a “dent corn”, Bloody Butcher (top left and bottom). The less colored Bloody Butcher is just a little less mature and the anthocyanin pigment hasn’t had a chance to fully develop:
And yes, the yellow sweet corn on the far right doesn’t look so great, but that’s because I was using later season cobs to save seeds with. We really enjoyed this one earlier in the season. You harvest sweet corn quite early before it has a chance to fully mature.
Dent corn on the other hand, the two cobs on the left, is meant for feeding to primary consumers, like pigs and cows, so that we as secondary consumers can eat those pigs and cows. That’s not all - it can be ground up as cornmeal and that’s why I had planted it. Isn’t it pretty! You wouldn’t believe all the molecular work that’s been done with the gene, the R-locus, that causes the red color!
Botanically, corn is a monster. That’s a real term; it means an organism that is unlike any other. The corncob is actually a multiple fruit - each kernel is a single fruit with an embryo inside; the majority of the fruit is starchy endosperm, which nourishes the embryo as it germinates. The cob is actually a highly thickened inflorescence stem. The pesky silks that you have to pull off are the leftover styles that caught the pollen and provided a pathway down to the baby kernels to fertilize the egg and make an embryo.
Part of maize’s monstrosity is that it has been highly bred from a “normal” grassy ancestor. Corn originates from South and Central America and is the result of Native American breeding that’s been going on for thousands of years. Its original ancestor is almost certainly teosinte, an unimpressive little grass that produces a few tiny kernels on an inflorescence that shoots out from the top of the plant. There’s several species of teosinte, including Zea diploperennis, and it can be crossed with maize. In teosinte, the female flowers are at the ends of the shoots and the male flowers shoot out from the sides. In corn, it’s the opposite. So not only has corn been bred to produce large numbers of large kernels all on a single cob, there’s been a sex change as well.
Here’s a neat pic of a cross between the teosinte on the left, the maize on the right, and the hybrid in the middle:
A lot of work has been done in using these wild teosinte species as sources of new genes to introduce into maize, and there have been efforts, some successful, to conserve habitats in Mexico and Central America where these wild plants live. It’s not clear that it would be a good idea to have a perennial maize, but the possibility exists. Insect and fungus resistance and so forth might be other valuable additions from outside wild species of the teosinte relative.
Maize is one of those organisms like E.coli bacteria, yeast, fruitflies, Arabidopsis, mice, and nematodes, that are heavily used as models for how organisms work. All of these organisms have had their entire genomes sequenced or in the process of being sequenced.
