understanding corn genetics

[DarJones]

I spent quite a bit of time studying corn genetics trying to figure out why a given trait kept doing strange disappearing acts. I finally located some information on the web that helped to understand. I'm going to try to reduce it to simple terms so others can grasp the way it works. If you want to look up some of the detailed steps, Meiosis, Mitosis, Gametophyte, Pollen, Egg, and Oogenesis are some good words to look up for meaning. To make this understandable, I am not going to talk about exceptions. Several of the statements below are true most of the time, but there will be times that they are not true because more than one gene is involved in a given effect.

1. Production of the embryo starts with a single megasporocyte. This is a massive cell that develops from a regular diploid cell near the surface of the cob. This cell goes through the preliminary stages for division by fully duplicating both sets of chromosomes. (has 2 complete centromere joined copies of the dna of the maternal plant, i.e. fully duplicated and ready to divide). The megasporocyte then divides and divides again (this is meiosis which reduces the total number of chromosomes per cell) to form 4 haploid megaspores. Here is where it gets tricky. Three of the megaspores disintegrate and disappear. One of them begins to divide again ( this is mitosis which results in duplication of a complete cell) first forming 2 duplicate haploid cells, then divides again forming 4 duplicate haploid cells, then divides again forming 8 duplicate haploid nuclei but they are in only 7 cells because two of the nuclei are held in a single large cell that will become the endosperm.

2. The protoembryo now contains 7 cells with 8 nuclei of which one is a germinal cell, one has 2 nuclei and will become the endosperm, two are synergids which attract the pollen nucleus, and three are antipodal and inactive. All nuclei have a single identical set of chromosomes that are chosen more or less at random from among the double set that makes up the nuclear dna in the maternal corn plant. If the plant has 1 gene for yellow kernels and another for white kernels, then the ovules on the cobs on that stalk will more or less have equal numbers of white gene and yellow gene protoembryos.

3. One of the single nucleus cells formed in the protoembryo can be fertilized by pollen. This cell will become the future plant when the corn kernel germinates and grows. One large cell has two nuclei and can be fertilized to become the endosperm of the developing kernel. The endosperm cells will form the part of the kernels that you can see. They have absolutely nothing to do with the genetics of the resulting embryo which will grow, but they have everything to do with the kernel of corn you will see on the cob.

4. In the tassels, a similar process (meiosis to turn one megasporocyte into 4 haploid pollen cells) forms each pollen grain with only 1 set of chromosomes. When pollen lands on the silk, a tube develops down the silk to the ovule. As the pollen grain moves down the silk, it splits into two identical sperm cells, one moves to the embryo and fertilizes it, the other merges with the endosperm cell giving it 3 complete sets of chromosomes. The two synergid cells are vital to the process of pollination. Once pollination is complete, they degenerate and disappear.

Now lets look at the genetics. The embryo is diploid which means it has 2 sets of chromosomes, one from the mother (ovule), and one from the father (pollen). We can figure out the genetics fairly easy because there are only two sets of chromosomes. Using the yellow/white example, if an embryo has two genes for yellow, then if you grow that kernel into a plant, it will produce yellow corn seed unless some other dominant color comes from the pollen plant. If it has two genes for white, then the offspring will always have at least one gene for white, but it may be masked by a gene for a color such as yellow or red because these colors are dominant. If the embryo has one yellow and one white chromosome, then the offspring could be either color depending on the pollen parent. And this is important, the corn ear will have a mix of colors, some with white and some with yellow.

The endosperm is a different ballgame entirely. It is triploid. It has 3 sets of chromosomes. You have to do a different kind of math to understand it. For example, the maternal plant may have two genes for red kernels. If the endosperm receives a sperm from pollen that has yellow, then the resulting endosperm will have some yellow and some red making it look yellowish red. The genetics will be red/red/yellow meaning that there are three chromosomes, two have genes for red and one has a gene for yellow. While this example is pretty cut and dried, the effect of having different combinations in the endosperm can be crucial in sweet corn breeding. For example, the "dull" gene can make a kernel of corn slighly sweeter all the way up to supersugary depending on whether the endosperm contains one du gene or three du genes.

Now lets see what we will find if we make a cross with corn using some diverse genetics. Lets say we grow some white dent corn and we cross it with a yellow sweet corn. We can use either variety as the female parent in this example. Lets say we use the sweet corn as the female and let the white dent corn produce pollen. The sweet corn kernels will be fertilized by a dent corn which happens to have the gene to produce starch. Therefore when we save the seed from our sweet corn ear, it will not look like sweet corn. It will look more like dent corn with normal starch formation.

Lets plant some of our F1 seed which genetically has a chromosome for sweet paired with a chromosome for dent and another chromosome for white paired with a chromosome for yellow. How will these segregate? We grow the corn to maturity letting it self-pollinate. The resulting kernels will have embryo's that are in a ratio of 1:2:1 or one yellow/yellow, 2 yellow/white, and 1 white/white. But we CAN'T SEE this by looking at the endosperm, it is just in the embryo. The endosperm will have the following combinations.
1 - white/white pollinated by white - w/w/w
1 - yellow/yellow pollinated by white - y/y/w
1 - white/white pollinated by yellow - w/w/y
1 - yellow/yellow pollinated by yellow - y/y/y
You can usually tell a slight difference in the kernels because the colors will grade from white to pale yellow, medium yellow, and to deep yellow.

What about sweet vs dent? The same type genetics apply.
1 - sweet/sweet/sweet - s/s/s(shriveled sweet kernel)
1 - sweet/sweet/dent - s/s/d(looks dent)
1 - dent/dent/sweet - d/d/s(looks dent)
1 - dent/dent/dent - d/d/d(looks dent)
Notice that this time you can't really tell the difference between the kernels because the gene for dent completely masks the su gene for sweet corn. So what do we see on the ear of corn for the above? 3/4 of the kernels will be dent and 1/4 will be sweet. Of the 1/4 that are sweet, 3 will be shades of yellow and one will be white in a ratio of 1:1:1:1. Of the 3/4 that are dent, 1/3 will be homozygous dent and will breed true, but 2/3 will have a hidden sweet gene that can show up in future growouts. The color genes will follow the 1:1:1:1 ratio same as for sweet kernels.

There are 4 commonly used genes in sweet corn breeding and a few others that can be used.
se - chromosome 2 commonly called Sugar Enhanced
sh2 - chromosome 3 commonly called Shrunken 2
su - chromosome 4 commonly called Sugary
bt - chromosome 5 commonly called Brittle
du is a minor gene that can be used to enhance sweetness but is rarely used. It is on chromosome 10.

DarJones


Links to help understand what is happening:
books.google.com/books?id=qtboPf9eeUkC&pg=PA109&lpg=PA109&dq=meiosis+polar+nuclei&source=bl&ots=Ri94SOsP-c&sig=xG0iI1Om--5qlyRwKnG9Lbi1QuM&hl=en&ei=QIHBTOq0H9j9lAe63pjPDA&sa=X&oi=book_result&ct=result&resnum=9&ved=0CDUQ6AEwCA#v=onepage&q=meiosis%20polar%20nuclei&f=false

This one is about paramutation. Really really odd! www.biology-online.org/articles/purple-corn-rna-break-genetic.html

And here are the transposons. From the description, Cherokee Squaw is an excellent example of transposons in action. www.carolina.com/category/teacher+resources/classroom+activities/corn+genetics+hip+hop+genes.do

This one will keep you reading for hours. www.maizegdb.org/

Here is a patent that makes fabulous reading once you understand the terminology. patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=4,630,393.PN.&OS=PN/4,630,393&RS=PN/4,630,393

This one is a sweet corn breeders handbook. www.globalsciencebooks.info/JournalsSup/images/0706/IJPB_1%281%2927-30o.pdf

This discussion of gama grass teosinte maize hybrids is an excellent resource. www.maiscoltura.it/maydica/articles/51_315.pdf

A reasonably up to date monograph about corn's origins. Still has quite a few errors repeated from years past, but overall gives an excellent picture of corn today. Click the "preview" link to see the book. books.google.com/books?id=eDJ3NjHh8H8C&printsec=frontcover&source=gbs_atb#v=onepage&q&f=false

This one is a phenomenally good discussion of the origin of corn from a genetic basis. www.bio-nica.info/biblioteca/Buckler2005MaizeOrigins.pdf

Here is a good general discussion of corn vs teosinte morphology and origin. sfmatheson.blogspot.com/2007/10/they-selected-teosinteand-got-corn.html

And this link will get you to an excellent resource covering maize and its relatives. teosinte.wisc.edu/

Here is an outstanding link covering the cross of maize and tripsacum and resulting genetic segregation. www.genetics.org/cgi/reprint/78/1/493.pdf

[Joseph Lofthouse]

The three haploids that are provided by the mother are identical. (The nucleus splits and then one haploid is duplicated...) So while the endosperm is triploid, and the embryo is diploid there are only two halploids involved: one from the pollen and one from the mother. There is not a hidden haploid.

The pericarp is maternal tissue.

[DarJones]

I'm adding a link to the above list with some of Mary Eubank's work with gama grass teosinte maize hybrids.

[keen101 (Biolumo / Andrew B.)]

Keen, I've read about the work at Duke several times, originally because I was reading about aerenchyma in gama grass (tripsacum dactyloides). The error that Mangeldorf made was to propose a "triparte" origin for corn. Meaning that teosinte, tripsacum, and some proto corn hybridized. Another of his theories was that teosinte may have derived from a cross of zea and tripsacum. Genetics show this is not correct. Teosinte is a unique species and did not derive from maize, rather, it was maize that derived from teosinte.

It is a real pleasure to read an article about corn breeding and the name of a person who is involved. One of the names I started bumping into recently is David Galinat. When I saw the name, it rung a bell, but I couldn't figure out where I had heard it. Finally I remembered.
www.mesamaize.com/


DarJones

I've decided a reply in this thread is more appropriate than the density one.

Okay, now i understand what you were trying to say. I agree with you. I thought you were trying to discredit that Tripsacum was involved at all, and misunderstood.

I'm adding a link to the above list with some of Mary Eubank's work with gama grass teosinte maize hybrids.

Great! The articles i got from Duke University were obtained from Mary herself. I have paper copies of "comparative analysis of the rio balsas and tehuacan models for the origin of maize", "the origin of maize: evidence for tripsacum ancestry", "economic botany" (vol. 55 no. 4) (october-december 2001), and "an interdisciplinary perspective on the origin of maize".

I have no idea if there are online versions available.

[DarJones]

Since genetics fits better in this thread, I'll expand on the Mangelsdorf/Beadle dog fight here.

Mangelsdorf published the tripartite theory of corn origin in 1939. The tenets of the theory were that a primitive variety of corn hybridized naturally with Tripsacum (a mexican variety, not Gama Grass) and from the segregating offspring, Teosinte and modern corn came into being. Mangelsdorf was a very well known and highly respected professor at Harvard. He defended the tripartite theory successfully for about 30 years.

Beadle was a geneticist who won the Nobel prize for work unrelated to corn. Arguably, he is the only person who could have successfully challenged Mangelsdorf's position. He had worked with corn in the 1930's and was strongly opinionated that teosinte was in fact the ancestor of corn, not the other way around.

The evidence available to Mangelsdorf at the time he published the theory was limited. He was aware of one species of teosinte. He could see the visual differences between teosinte and corn. As a biologist, he was aware that many - if not all - major crop plants are the result of cross species hybridization. He found a putative ancestor in tripsacum which is the closest relative species to corn.

Beadle as a geneticist was not focused on the biological traits. He focused like a laser on the genetics involved. His writings indicate a ready acceptance of teosinte to corn gene alignments.

For three years now I've been accumulating evidence, mostly from F2 and BC hybrids of various teosintes and corns. The recovery of good corns and good teosintes says no more than 4 or 5 independently segregating units. I agree that these are in some instances clusters of linked genes but that is to be expected from the repeated transfer of genes from teosinte to corn over the last 7000 plus years in the areas where they coexist.

Beadle and Mangelsdorf argued over a period of roughly 20 years about the true position of teosinte in the corn family. In the end, Beadle's position was vindicated. However, Mangelsdorf was not entirely wrong either.

Mary Eubanks made hybrids on a perennial teosinte with tripsacum and found them to be fertile among themselves and backward to both parent species. This was the evidence needed to finally place corn into a valid position in the family tree. She went on to do significant - if still somewhat limited - genetic analysis of the corn genome and compare it to both tripsacum and teosinte. The results she obtained are easily repeatable and highly thought provoking. The DNA of corn is highly aligned with teosinte with roughly 36% identity. But there is also about 12% that is unique to tripsacum. Please note the meaning of "unique". It means that the genetics in question are ONLY found in a particular species. In the case of corn, to have 12% alignment with tripsacum was a partial vindication of Mangelsdorf's position.

What is not proven? Well, if 36% of corn is from teosinte and 12% is from tritacum, where did the other 52% come from? The bulk of this portion of the genome is shared with multiple other related species as would be expected from a member of a rather large family. However, a significant amount is from mutations unique to the corn genome. I am suspicious of using these statements as the sole explanation. There is still a possibility that some other unknown ancestor is involved or that some other explanation will be found. I need to verify the 12%, 36%, and 52% numbers used here, I'm going from memory.

The long and short of it is that Mangelsdorf was proven wrong on at least 2 primary tenets of his tripartite theory of corn origin.
1. The ancestor of cultivated maize was a primitive pod maize. <No putative primitive corn species has been found and evidence to date is that it never existed>
2. Teosinte is derived from the hybridization of maize and tripsacum. <Genetics prove that teosinte pre-dates corn and is more specialized than corn>
3. Many varieties of maize have undergone genetic introgression from teosinte, tripsacum, or both. <That tripsacum is an ancestor of corn is reasonably proven, however, no recent evidence of introgression has been found. There is clear evidence of introgression with teosinte.>

Anyone who cares to is welcome to critique, I'm more interested in getting the facts right than in worrying about whether I made a mistake!

A good book to demonstrate parts of the above is "George Beadle, An Uncommon Farmer" by Berg and Singer. You can find copies online or purchase the book on Ebay.

DarJones

[DarJones]

I'm adding a couple of articles to the list above that are outstanding resources to understanding the origins of maize.

DarJones

[flowerpower]

Oct 22, 2010 1:08:28 GMT -5 DarJones said:

1 - white/white pollinated by white - w/w/w
1 - yellow/yellow pollinated by white - y/y/w
1 - white/white pollinated by yellow - w/w/y
1 - yellow/yellow pollinated by yellow - y/y/y
You can usually tell a slight difference in the kernels because the colors will grade from white to pale yellow, medium yellow, and to deep yellow.

I have a dumb question. In the above example, the y/y/w & w/w/y would not be bicolor, right?

Thanks for all the info and links. Little by little, I am learning more about corn breeding.

[DarJones]

flowerpower, The designations refer to the genetic makeup of the endosperm of a single grain of corn. If there is a yellow gene present, the seed color will be yellow. If all three duplicate chromosomes code for yellow, then the seed will be darker yellow. The four possibilities from above will only permit one white seed because yellow is dominant.

To get a bicolor corn, all you have to do is plant a yellow corn beside a white corn and save the yellow seed that grow on the white corn plants. These seed will grow to produce a mix of colors based on the genetics as above.

DarJones

[DarJones]

I've gradually worked through several decades of research on Maize origins and eventually located the following items. This will partially answer the questions about 5 differences between maize and teosinte.

teosinte glume architecture1 ( tga1 ), has been identified that controls the development of the glume, a protective covering on teosinte kernels that is mostly lacking in maize

This is the gene that changes the hard outer shell of teosinte into a soft paperlike remnant in corn. This gene is a single genetic switch that controls a huge amount of genetic machinery in teosinte and the turns off the machinery in corn.

teosinte branched1 ( tb1 ), which dictates a difference in plant architecture (long lateral branches terminated by male tassels in teosinte vs. short lateral branches tipped by female ears in maize)

This gene changes from teosinte's multiple tassel tipped branches to a single stalk with short branches which become ears in corn. This is another example of a single genetic switch with a major effect.

While each of these genes has a major effect, keep in mind that other modifier genes are required to make the change useful. For example, tb1 causes shortened branches that turn into ears, but it does not determine how long the ears will become.

I'll add more as I have time!

DarJones

[flowerpower]

Nov 1, 2010 12:27:49 GMT -5 DarJones said:

flowerpower, The designations refer to the genetic makeup of the endosperm of a single grain of corn.

Thanks, now I get it. My mistake. I thought it was referring to entire ears of corn.

[DarJones]

Added a link to the first post which covers maize/tripsacum hybrids and resulting genetic segregation.

[keen101 (Biolumo / Andrew B.)]

Oct 27, 2010 10:28:17 GMT -5 DarJones said:

Since genetics fits better in this thread, I'll expand on the Mangelsdorf/Beadle dog fight here.

Mary Eubanks made hybrids on a perennial teosinte with tripsacum and found them to be fertile among themselves and backward to both parent species. This was the evidence needed to finally place corn into a valid position in the family tree. She went on to do significant - if still somewhat limited - genetic analysis of the corn genome and compare it to both tripsacum and teosinte. The results she obtained are easily repeatable and highly thought provoking. The DNA of corn is highly aligned with teosinte with roughly 36% identity. But there is also about 12% that is unique to tripsacum. Please note the meaning of "unique". It means that the genetics in question are ONLY found in a particular species. In the case of corn, to have 12% alignment with tripsacum was a partial vindication of Mangelsdorf's position.

What is not proven? Well, if 36% of corn is from teosinte and 12% is from tritacum, where did the other 52% come from? The bulk of this portion of the genome is shared with multiple other related species as would be expected from a member of a rather large family. However, a significant amount is from mutations unique to the corn genome. I am suspicious of using these statements as the sole explanation. There is still a possibility that some other unknown ancestor is involved or that some other explanation will be found. I need to verify the 12%, 36%, and 52% numbers used here, I'm going from memory.

Apr 9, 2011 7:00:24 GMT -5 DarJones said:

I've been in contact with Mary as recently as a couple of months ago.

There is one major hurdle that has caused confusion re her work. That is the claim that zea mays is a result of a prehistoric cross of zea diploperennis with tripsacum. This was first propounded by Mangelsdorf back about 1930. Genetics are hard to argue with, especially when you can get seed of zea mays parviglumis and zea mays mexicana and tripsacum dactyloides and compare the genomes with the genome of zea mays mays (our modern corn). Doebley has enough genetics mapped to prove that there are no signs of recent introgression from tripsacum. There is however a significant overlap of genetics between the two species which validates the known relationship between zea and tripsacum (first cousins). The actual disagreement is a bit more complex than this, but if you want details, due diligence is required.

I'm finally getting back to reading all your replies Dar. This really is all fascinating stuff. I need to go back an dig through all the links you provided. I guess my interest was rekindled after seeing that my Zea mexicana plant was really close to producing mature seeds this week.

I was reading through Mary Eubanks article again (Economic Botany, Vol 55). Today i focused on reading about the genetics testing. On page 507 it says that they did RFLP genotyping and restriction enzymes to determine how much of Maize is unique to Teosinte or Tripsacum and the amount shared by both (common ancestor).

The results say:

"Bands are shared between Tripsacum and Zea at 129 of the 140 molecular marker loci. Thus, 92% of the loci tested yield evidence of Tripsacum introgression in Zea. out of all 140 loci , maize has a total of 456 polymorphisms that are present in teosinte and/or Tripsacum. Of those 456 polymorphisms, 92 (20.2%) are unique to maize and Tripsacum; 166 (36.4%) are unique to maize and teosinte, and 198 (43.4%) are present in both Tripsacum and teosinte. It can be inferred that polymorphisms uniquely shared between Tripsacum and maize were likely derived from a Tripsacum ancestor, and polymorphisms uniquely shared between teosinte and maize were apparently inherited by a teosinte progenitor. Polymorphisms shared among all three taxa could have derived from either a teosinte or a Tripsacum ancestor."


So what does this data mean? is this pretty conclusive evidence that a Tripsacum ancestor contributed at least 20% to the evolution of maize?

[DarJones]

Mary's tests are still unduplicated and highly questionable. Her conclusion that some polymorphisms are unique to tripsacum ignores the possibility of a teosinte X teosinte cross where the genes in question were conserved in one of the teosinte lines. Keep in mind that a teosinte x tripsacum cross has been made under highly artificial conditions. The result is genetically unstable with extra chromosomes gradually being removed from the artificial genome.

My view is that we should wait for more concise and detailed results from genetic tests to draw a conclusion.

DarJones

[steev]

Very dense and chewy stuff, here. Really challenging for my attention span, but I'll get it down and digested eventually.

[keen101 (Biolumo / Andrew B.)]

Oct 22, 2011 2:29:23 GMT -5 DarJones said:

Mary's tests are still unduplicated and highly questionable. Her conclusion that some polymorphisms are unique to tripsacum ignores the possibility of a teosinte X teosinte cross where the genes in question were conserved in one of the teosinte lines. Keep in mind that a teosinte x tripsacum cross has been made under highly artificial conditions. The result is genetically unstable with extra chromosomes gradually being removed from the artificial genome.

My view is that we should wait for more concise and detailed results from genetic tests to draw a conclusion.

DarJones

Ok, that actually helps a lot. I didn't know that this data has yet to be reproduced. Yeah i was aware or the extreme artificial conditions, and the large amount of unstable chromosomes.

It is my current understanding that when hybrids are unstable like that genetically that they are usually sterile, and if they are fertile, that usually after several generations that the plants somehow know about this instability and spontaneously loose many of the chromosomes that are causing the problem.

But, i think your right. There really isn't enough good evidence to come to any definite conclusion any time soon.