James and the Giant Corn Genetics: Studying the Source Code of Nature

March 8, 2010

Two classical maize genes, synteny, and the mystery of the missing gene

Filed under: biology,Genetics,genomics,Plants — Tags: , , , , , , — James @ 12:50 pm

Colored aleurone1 and Purple plant1 are both genes with long histories in maize research and are involved in the regulation of anthocyanin biosynthesis.The mutant version of purple plant1 does exactly what it sounds like. (In the proper genetic background) it has plants producing anthocyanin (a purple plant pigment) everywhere, resulting in purple plants. The mutant form of colored aleurone1 was identified from a mutant that changed the color of individual corn kernels. Guess which of these two classic maize mutants made it into the top 15 most published on genes in maize, and which fell barely short.

Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth).

More interesting, at least to me, is the fact that there is NO gene equivalent to colored aleurone1 and purple plant1 in the region we’d expect to find such a gene in Brachypodium (the only other grass species with a sequenced genome)*. From all the genes that line up perfectly on either side we can predict the exact location the gene equivalent to colored aleurone1 and purple plant1 should be found in the Brachypodium genome. But the gene isn’t there…

The GEvo panel shown here can be regenerated at: http://tinyurl.com/yddlwor

The original version of this image had Pl1 mislabeled as C1. This version corrects that error.

For a couple more examples of comparisons between the four sequences grass genomes check out the Cogepedia post I spent this morning pulling together.

*The publication of which I celebrated just a little while ago.


  1. this is interesting, James.. we tracked down a soft grain trait gene in wheat and brachy and found there is only gene relic in rice, and totally gone in sorghum. so that’d be a loss in the sorghum lineage.


    In your case it looks like a loss is in the brachy lineage. to me, it seems that many cereal traits (that humans value) have quite narrow phylogenetic context.

    Comment by Haibao Tang — March 8, 2010 @ 1:33 pm

  2. That’s a cool discovery Haibao. Genes like C1 and Pl1 are interesting, but it’s fascinating to learn about genes controlling traits that are actually important to feeding people.

    Would it be equally parsimonious to theorize that the gene was gained (or at least transpositioned) into it’s current location in in the rice-brachypodium lineage, and then became non-functional in rice vs being present in the ancestor of all grasses and then getting lost in sorghum and broken in rice? Each has two changes, but gene gain might be considered a bigger change than gene loss.

    Comment by James — March 8, 2010 @ 2:31 pm

  3. Is it possible the gene model is missing? I think I pulled up the equivalent region (http://www.brachybase.org/cgi-bin/gbrowse/brachy8/?name=Bd1:44873086..44965627) at my colleagues site brachypodium.org. They sequenced the transcriptome and have a transcript assembly pipeline that identifies splice junctions and builds exons. It does look like there are some small transcribed regions in the “gap,” nothing obvious though.

    Comment by Noah Fahlgren — March 8, 2010 @ 1:44 pm

  4. The final search was done against the whole genomic sequence. Normally we mask non-coding sequence (the purple regions of the first four panels, but when we can’t find the gene we default to repeat masked genomic sequence, and in this case I manually switched to completely unmasked sequence. So if there was any sequence in the region similar enough to qualify as a blast hit, we should be able to see it. If I switch to blastn ( http://tinyurl.com/yzmdz8j ) there are two hits within the region, but one is 24 bp long and the other 19.

    This dataset definitely can be used to identify missing or incomplete gene models. For example you can easily tell the brachy ortholog of the maize P1 gene is truncated, here:


    Comment by James — March 8, 2010 @ 2:10 pm

  5. Cool. Yeah, I wasn’t sure if the search had only included gene models or the whole genome sequence. Definitely sounds like the gene is not there then.

    Comment by Noah Fahlgren — March 8, 2010 @ 2:57 pm

  6. That’s the problem with working with in-house tools. I take WAY too much for granted with trying to explain an image like this to people outside of my own lab.

    Comment by James — March 8, 2010 @ 3:12 pm

  7. can u tell me about purple gen in maize? or purple gen controlled in maize…. Thank you a lot

    Comment by yefta — May 9, 2010 @ 7:38 am

  8. Purple corn kernels are purple because they contain lots of a pigment called anthocyanin. The genes that can make corn more purple are the ones that control the production of the anthocyanin pigment. The four classical genes involved in this process, although there are also others, are C1 (colored aleurone1), Pl1 (purple plant1), B1 (colored plant1), and R1 (colored1). Please let me know if you’re like to know more.

    Comment by James — May 9, 2010 @ 10:23 am

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