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	<title>Comments on: &#8220;New&#8221; Cruciferous Vegetables</title>
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	<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/</link>
	<description>Genetics: Studying the Source Code of Nature</description>
	<lastBuildDate>Thu, 29 Jul 2010 05:49:10 +0000</lastBuildDate>
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		<title>By: James</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4651</link>
		<dc:creator>James</dc:creator>
		<pubDate>Mon, 08 Feb 2010 16:03:30 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4651</guid>
		<description>I didn&#039;t know there were varieties of B juncea grown for their roots, clearly I&#039;ve been neglecting indian mustard in my recent reading on the Brassicas. An oversight I&#039;ll now be sure to correct. Thanks!</description>
		<content:encoded><![CDATA[<p>I didn&#8217;t know there were varieties of B juncea grown for their roots, clearly I&#8217;ve been neglecting indian mustard in my recent reading on the Brassicas. An oversight I&#8217;ll now be sure to correct. Thanks!</p>
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		<title>By: Toby Hodgkin</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4649</link>
		<dc:creator>Toby Hodgkin</dc:creator>
		<pubDate>Mon, 08 Feb 2010 10:51:32 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4649</guid>
		<description>If I remember rightly from surveys 20+ years ago (some of which were published in a journal called Cruciferae Newsletter) Brassica juncea has even more different agromorphological forms that B rapa or B oleracea. For example B. oleracea never really produced any crop in which the root is the edible portion and B rapa lacks the sprout type and one or two other &quot;oleracea&quot; types while I think you can find some of these in B juncea.</description>
		<content:encoded><![CDATA[<p>If I remember rightly from surveys 20+ years ago (some of which were published in a journal called Cruciferae Newsletter) Brassica juncea has even more different agromorphological forms that B rapa or B oleracea. For example B. oleracea never really produced any crop in which the root is the edible portion and B rapa lacks the sprout type and one or two other &#8220;oleracea&#8221; types while I think you can find some of these in B juncea.</p>
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		<title>By: Science Report &#187; Blog Archive &#187; Nibbles: Amman again, DNA hype, Blight-resistant spuds, Seeds, Sorghum, Brassicas, UK Food Security</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4613</link>
		<dc:creator>Science Report &#187; Blog Archive &#187; Nibbles: Amman again, DNA hype, Blight-resistant spuds, Seeds, Sorghum, Brassicas, UK Food Security</dc:creator>
		<pubDate>Tue, 02 Feb 2010 14:15:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4613</guid>
		<description>[...] sprouts off on brassicas [...]</description>
		<content:encoded><![CDATA[<p>[...] sprouts off on brassicas [...]</p>
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		<title>By: Nibbles: Amman again, DNA hype, Blight-resistant spuds, Seeds, Sorghum, Brassicas, UK Food Security</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4612</link>
		<dc:creator>Nibbles: Amman again, DNA hype, Blight-resistant spuds, Seeds, Sorghum, Brassicas, UK Food Security</dc:creator>
		<pubDate>Tue, 02 Feb 2010 14:11:30 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4612</guid>
		<description>[...] sprouts off on brassicas [...]</description>
		<content:encoded><![CDATA[<p>[...] sprouts off on brassicas [...]</p>
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		<title>By: Matt</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4573</link>
		<dc:creator>Matt</dc:creator>
		<pubDate>Wed, 27 Jan 2010 22:09:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4573</guid>
		<description>My boss told me that at one of the recent plant molecular biology meetings, the salad on the final day of the conference included arabidopsis leaves.</description>
		<content:encoded><![CDATA[<p>My boss told me that at one of the recent plant molecular biology meetings, the salad on the final day of the conference included arabidopsis leaves.</p>
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		<title>By: James</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4572</link>
		<dc:creator>James</dc:creator>
		<pubDate>Wed, 27 Jan 2010 19:55:18 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4572</guid>
		<description>&quot;a large, highly redundant genome would probably be an argument against being a model organism, not for.&quot;

I agree with your point. This is why I&#039;m in awe of the people who manage to do genetics in wheat. I just have two caveats related to the different between recent tetraploids (plants like wheat, potato and octoploid strawberries) and ancient ones (which, if you look far enough back, includes every plant genome sequenced so far).

1. An ancient tetraploid doesn&#039;t necessarily have a large genome (relative to grape, arabidopsis has gone through two whole genome duplications, yet the grape genomes is ~3 times as big) and it certainly isn&#039;t highly redundant. Very few genes get retained by chance over tens of millions of years in plants, generally if there are still two copies it is because there is a fitness cost of losing either one, either because the two genes have specialized in somewhat different functions and losing either one will make the plant less fit, or as a result of dosage (if the plant loses one copy of gene X or gene Y but still has two copies of the other gene the balance of X and Y is off causing problems and, presumably, reduced fitness).

2. Reading back over what I wrote, I see that it wasn&#039;t clear that I wasn&#039;t suggest that arabidopsis or maize became popular model systems because people knew the species were ancient tetraploids. For one thing I don&#039;t know that anyone suspected arabidopsis was an ancient tetraploid back when it was first becoming popular. I meant to convey was that if ancient tetraploids have a higher incidence of interesting non-lethal mutant phenotypes when mutagenesis knocked out members of gene pairs retained for the reasons I mention above (pure conjecture), the result might be to attract interest in working with the system from more plant researchers (not knowing that the plant was an ancient tetraploid something that would make life complicated for genomics researchers when the genome was sequenced decades later), contributing to a species becoming a popular model system.</description>
		<content:encoded><![CDATA[<p>&#8220;a large, highly redundant genome would probably be an argument against being a model organism, not for.&#8221;</p>
<p>I agree with your point. This is why I&#8217;m in awe of the people who manage to do genetics in wheat. I just have two caveats related to the different between recent tetraploids (plants like wheat, potato and octoploid strawberries) and ancient ones (which, if you look far enough back, includes every plant genome sequenced so far).</p>
<p>1. An ancient tetraploid doesn&#8217;t necessarily have a large genome (relative to grape, arabidopsis has gone through two whole genome duplications, yet the grape genomes is ~3 times as big) and it certainly isn&#8217;t highly redundant. Very few genes get retained by chance over tens of millions of years in plants, generally if there are still two copies it is because there is a fitness cost of losing either one, either because the two genes have specialized in somewhat different functions and losing either one will make the plant less fit, or as a result of dosage (if the plant loses one copy of gene X or gene Y but still has two copies of the other gene the balance of X and Y is off causing problems and, presumably, reduced fitness).</p>
<p>2. Reading back over what I wrote, I see that it wasn&#8217;t clear that I wasn&#8217;t suggest that arabidopsis or maize became popular model systems because people knew the species were ancient tetraploids. For one thing I don&#8217;t know that anyone suspected arabidopsis was an ancient tetraploid back when it was first becoming popular. I meant to convey was that if ancient tetraploids have a higher incidence of interesting non-lethal mutant phenotypes when mutagenesis knocked out members of gene pairs retained for the reasons I mention above (pure conjecture), the result might be to attract interest in working with the system from more plant researchers (not knowing that the plant was an ancient tetraploid something that would make life complicated for genomics researchers when the genome was sequenced decades later), contributing to a species becoming a popular model system.</p>
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		<title>By: Joseph Tychonievich</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4571</link>
		<dc:creator>Joseph Tychonievich</dc:creator>
		<pubDate>Wed, 27 Jan 2010 17:56:52 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4571</guid>
		<description>Oh, I&#039;m not suggesting the small genome size is the only reason -- I think short generation time and small over all size are probably the biggest ones (floral dip transformation, I think, was discovered after it was well established as a model) my point was that a large, highly redundant genome would probably be an argument against being a model organism, not for.</description>
		<content:encoded><![CDATA[<p>Oh, I&#8217;m not suggesting the small genome size is the only reason &#8212; I think short generation time and small over all size are probably the biggest ones (floral dip transformation, I think, was discovered after it was well established as a model) my point was that a large, highly redundant genome would probably be an argument against being a model organism, not for.</p>
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		<title>By: James</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4570</link>
		<dc:creator>James</dc:creator>
		<pubDate>Wed, 27 Jan 2010 17:03:28 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4570</guid>
		<description>Tiny arabidopsis vegetables! I love it.

Surely the importance of Arabidopsis can&#039;t rest solely on having a sequenced genome. I&#039;d at least include the floral dip method of plant transformation, being sexually self compatible and an incredibly short generation time to the list, although you&#039;re right it probably didn&#039;t become THE plant model system until it became the first plant to have its genome sequenced. 

As far as gene redundancy, I was picturing cases of partial subfunctionalization (the arabidopsis tetraploidy is tens of millions of years old) where there&#039;s still enough over lap in function to moderate the effect of mutant phenotypes. But since no examples of this happening are coming to mind, I can&#039;t make much of an argument for the point.</description>
		<content:encoded><![CDATA[<p>Tiny arabidopsis vegetables! I love it.</p>
<p>Surely the importance of Arabidopsis can&#8217;t rest solely on having a sequenced genome. I&#8217;d at least include the floral dip method of plant transformation, being sexually self compatible and an incredibly short generation time to the list, although you&#8217;re right it probably didn&#8217;t become THE plant model system until it became the first plant to have its genome sequenced. </p>
<p>As far as gene redundancy, I was picturing cases of partial subfunctionalization (the arabidopsis tetraploidy is tens of millions of years old) where there&#8217;s still enough over lap in function to moderate the effect of mutant phenotypes. But since no examples of this happening are coming to mind, I can&#8217;t make much of an argument for the point.</p>
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		<title>By: Joseph Tychonievich</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4568</link>
		<dc:creator>Joseph Tychonievich</dc:creator>
		<pubDate>Wed, 27 Jan 2010 13:51:16 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4568</guid>
		<description>The &#039;new&#039; crop I&#039;d like to create is: vegetable arabidopsis! I know they have the mutants to make it into mini-cauliflower, I&#039;m betting you could do cabbage and so forth pretty easily too. Wouldn&#039;t they be cute little tiny vegetables?

While I&#039;m speaking about arabidopsis, whoever suggested to you that arabidopsis became a model due to lots of redundancy in the genome is wrong. Arabidopsis has a TINY genome -- which was a reason for it being a model -- easy to sequence. Corn became a model just because it is an important crop, and probably because the bajillion transposons make mutation common. Redundancy in the genome actually makes genes much harder to study -- because more mutants have no effect whatsoever.</description>
		<content:encoded><![CDATA[<p>The &#8216;new&#8217; crop I&#8217;d like to create is: vegetable arabidopsis! I know they have the mutants to make it into mini-cauliflower, I&#8217;m betting you could do cabbage and so forth pretty easily too. Wouldn&#8217;t they be cute little tiny vegetables?</p>
<p>While I&#8217;m speaking about arabidopsis, whoever suggested to you that arabidopsis became a model due to lots of redundancy in the genome is wrong. Arabidopsis has a TINY genome &#8212; which was a reason for it being a model &#8212; easy to sequence. Corn became a model just because it is an important crop, and probably because the bajillion transposons make mutation common. Redundancy in the genome actually makes genes much harder to study &#8212; because more mutants have no effect whatsoever.</p>
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		<title>By: James</title>
		<link>http://www.jamesandthegiantcorn.com/2010/01/26/new-cruciferous-vegetables/comment-page-1/#comment-4566</link>
		<dc:creator>James</dc:creator>
		<pubDate>Wed, 27 Jan 2010 05:44:19 +0000</pubDate>
		<guid isPermaLink="false">http://www.jamesandthegiantcorn.com/?p=1256#comment-4566</guid>
		<description>Oh I&#039;m certain the triplication played a major role. Someone once suggested to me that the reason maize and arabidopsis ended up as such major model systems (before the arabidopsis genome was sequenced), was that in both there&#039;s still enough redundancy from previous whole genome duplications that knocking genes out tends to create interesting, but non-lethal, mutant phenotypes. (Note: I don&#039;t even know if this is a biologically sound argument, let alone logically sound, but it was cool to think about)

Dozens or hundreds or thousands of weird, but non-lethal, mutant phenotypes piled on top of each other seems like a reasonable explanation for how a couple of species have been bred to create such a wide range of forms.</description>
		<content:encoded><![CDATA[<p>Oh I&#8217;m certain the triplication played a major role. Someone once suggested to me that the reason maize and arabidopsis ended up as such major model systems (before the arabidopsis genome was sequenced), was that in both there&#8217;s still enough redundancy from previous whole genome duplications that knocking genes out tends to create interesting, but non-lethal, mutant phenotypes. (Note: I don&#8217;t even know if this is a biologically sound argument, let alone logically sound, but it was cool to think about)</p>
<p>Dozens or hundreds or thousands of weird, but non-lethal, mutant phenotypes piled on top of each other seems like a reasonable explanation for how a couple of species have been bred to create such a wide range of forms.</p>
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