​About 8-10000 years ago, probably in the Balsas River valley of Mexico, someone or perhaps several people, found a mutant teosinte plant in which the hard fruit casing did not extend fully around the enclosed single seeded grain, the kernel.  Someone realized that this made the kernel very edible and consequently propagated some of the seed.  It was recently discovered that a single mutation in the TGA1 gene in Teosinte, changed a single nucleotide in the DNA code of this gene.  This resulted in an amino acid change (asparagine instead of lysine) component of a protein critical to the development of the seed case in Teosinte and corn. Not only were the starch components of the seed more easily extracted by humans, but removal of the hard case allowed for greater growth of the kernels.  This was only one of several mutations that ultimately resulted in we know as maize but we are appreciative that people a very long time ago, recognized the advantage of this mutation. A description of the mutation is in http://phys.org/news/2015-07-tiny-genetic-tweak-corn-kernels.html.
 
Other mutations assisted humans as they moved from a plant with about 20 seeds per ‘ear’ encased in a hard covering, into a plant that were easily used for food.  It is notable that the initial mutation was to an annual plant version of Teosinte, thus allowing for selection of new genetics each year. A thousand years could equal 40-50 generations of humans but is 1000 generations of corn, allowing a lot of opportunity for genetic changes as humans made selections for adaptation to the environments and their food.
 
There is archeological data supporting that the early corn, although originating in a valley in south central Mexico, was moved to the highlands of Mexico.  From there it was spread eventually to all continents.

​Maize had already advanced from its teosinte origin in central Mexico 9000 years ago.  About 700 years previous to the 1620 event in Plymouth Rock, Massachusetts, people had moved, and adapted corn across the North American continent. As it was moved, different types resulting from mutations and diversity encouraged by the ease of cross pollination in this new species with separation of male and female flowers, more than only kernel pigmentation was selected.
 
Flint corns with hard, somewhat water repellant, pericarp and aleurone outer layers were probably favored by the Wampanoag tribe in Eastern Massachusetts. This seed not only did not germinate on the ear during fall rains but also maintained seed germination quality during cold wet winters.
 
The Wampanoag apparently had the custom of planting 5 seeds per hill, along with a herring fish in each hill.  After the corn emerged, bean and melon seeds were also planted in the hill. Beans adding to the nitrogen supply for the corn and the melons being a sweet extra treat. The ladies did the farming and that probably included the selection of the seed to save for the next season. They probably also ground the corn seed into a fine flour called nokehig.
 
This event and the many other interactions between people of the new and old world resulted in the movement of corn around the globe.  Genetic diversity further enhanced by the unique maize biology allowing selection of adapted varieties for northern Europe and tropical Africa.

​The aleurone layer of the corn kernel endosperm contains the water soluble anthocyanins, starch cells on the inner, yellow portion of this tissue is from carotenoid molecules. Two related molecules are xanthophylls and carotines.   Xanthophylls tend to give a light yellow color and the carotenes a darker orange color to the endosperm.  Function of these molecules in the corn kernel is not clear but they do have effects on the animals feeding on them.  Carotenes can include beta-carotene, a precursor to vitamin A.  Xanthophylls also contribute to the yolk color of chicken eggs. 
 
Carotenoids are produced in a series of synthetic steps but is especially dependent on the presence of the dominant Y1 gene.  If the recessive form of this gene, y1, is homozygous in the triploid endosperm, there is no yellow pigment and, consequently, the endosperm is white.  People have selected varieties with pericarp-aleurone colors, or absent of those colors as well as endosperm colors probably mostly by personal and cultural choice.  One can select for more carotene by simply choosing those ears with darker orange color.  White corn also can be selected, although maintaining purity of white endosperm being inherited by recessive genes requires adequate isolation from any yellow varieties. Corn’s ability to cross pollinate with wide distribution of pollen has allowed continual production of genetic variability, and people integrated this into their cultures long before Europeans immigrated into the new world.

​A dominant gene (Fl) causes more hard, vitreous starch to be deposited in areas surrounding the softer starch of the endosperm.  Much of the hardness is due to a hydrophobic protein called zein.  One of the effects for this protein surrounding the starch is repelling water and, consequently, germination is less likely to be affected by freeze or moisture after reaching black layer before harvest.  This character probably contributed to the wide use of flint corn types in the northeast USA by locals when the Europeans arrived and the continued use of New England flints by farmers in that area.  Flint corn also became common elsewhere and Argentine flint hybrids still are popular in Argentina.  Flint corn varieties are popular in Europe, especially in the northern area.   The initial breeding stock for much of Asia apparently came from flint corn types, with this character remaining among many current hybrids.
 
Popcorn is a flint corn, the hard starch with the hydrophobic protein contributing to the popping pressure in the kernel as the steam builds within the softer starch center of the endosperm.
 
The homozygous recessive form of the Fl gene results in more soft starch in floury types of kernels.  This became a feature of corn common in the southeastern USA and elsewhere that corn flour was used.  As the farmers saved seed up until the 1930’s, the flints tended to be most common in the northern USA and more soft starch (floury) types were in the Southeastern USA. Many of the latter were dented, being from crosses of soft types and Caribbean flints. A mix of local cultures use of food and tradition determined maintenance of many kernel types.

​Anthocyanin is a flavonoid compound produced in plants and giving color to the tissue.  It accumulates in the aleurone layer cells in corn kernels of varieties we commonly call Indian corn.  This pigment is water soluble and therefore easily extracted.  Although it’s total function in grain is not known, the compound does have some microbial inhibition character and perhaps is part of a pathogen resistance system.  Selection for purple corn was incorporated as part of the movement of corn to many parts of north and south hemisphere and remains as a mainstay among certain cultures who use the pigments.
 
Anthocyanin also is the purple pigment that occurs in seedlings of some corn hybrids when temperatures are low.  It is mostly a response to accumulation of sugars in tissue because the low temperatures slow down the movement of the sugars to growing points when under this condition. Phosphorus deficiency can be indicated by the purple leaves for the same reason. This functions to block light absorption by chloroplasts and thereby reducing photosynthesis.  Red and purple reactions in corn when sugar transfer is inhibited because of disruption of xylem tissue due to borers, or lack of sufficient developing kernels to draw the sugar from leaves also trigger production of anthocyanin.  Again, the function is to reduce light absorption in chloroplasts and therefore reduce photosynthesis and production of more sugar.
 
Genetics affect the occurrence and color intensity of anthocyanin in corn kernels. Although the major dominant gene is needed for purple corn kernels, the intensity of the color is affected by minor genes in the creation of the anthocyanin molecules.

​The colors of corn grain are basically purple, red, yellow and white.  Each pigment is produced through a series of metabolic processes.  Purple and red pigments are due to production of anthocyanin whereas yellow is a carotenoid and white is absent of all of these.  Anthocyanin is a flavonoid compound that is produced in an aleurone cells of the endosperm. Carotenoids, the yellow color, is produced in the starchy cells in the center of the endosperm.
 
A few genes of more than 20 involved in anthocyanin pigment production have major effects on anthocyanin as they are responsible for production of enzymes needed for the one of the steps in producing the pigment.  If the dominant gene Pr1 is present, a purple aleurone is the result.  If the recessive version of this gene (pr1), a red colored aleurone will be present.  However, another gene (C1), active in the kernel aleurone cells, functions as a promotor gene encoding for a protein that allows the production of the anthocyanin molecules.  A mutant of the C1 gene does not allow to produce the anthocyanin production and thus no purple or red color. Another gene (R1), also is needed for the anthocyanin production and the recessive version (r1), blocks the pigment formation.
 
Carotenes, affected by the Y1 gene are produced in the starchy cells of the endosperm. Carotenes are responsible for the yellow color of the endosperm.  The homozygous recessive version of (y1) gives a white starchy endosperm
 
Colorless aleurone combined with the recessive y1 will result in all white kernels.  Genetics of the endosperm is not simple because it includes two sets of genes from the seed parent and one from the pollen parent.  White kernels require recessive c1c1c1 in the aleurone cells of the endosperm and y1y1y1 in the starchy cells of the endosperm. Yellow flint and yellow dent corn has recessive c1c1c1 and Y1Y1Y1 genes.  It amazes me that people had already sorted out these types, without knowing genetics, before the Europeans arrived in the new world to see corn for the first time.

​Outermost covering of a corn kernel is the pericarp, a part of the female plant similar to the outer covering of any fruit.  Its genetics is that of the female plant.  It can range from 2 to 20 cell layers thick, mostly depending on the genetics of the variety.  Immediately inside and basically fused to the pericarp is a very thin wall of the actual seed coat.  These tissues surround the whole kernel, including the embryo and the endosperm.  Endosperm is mostly composed of large cells with stored starch molecules but surrounded by a few layers of living specialized cells, higher in proteins called the aleurone layer.  These cells’ activities become dormant as abscisic acid increases with seed maturity.  When exposed to moisture, the embryo produces gibberellic acid, causing activity in the aleurone cells to produce the enzyme amylase.  This enzyme migrates into the starchy endosperm cells, breaking down the starch into glucose molecules for use in the embryo growth metabolism.
 
Pericarp and aleurone layers become important contributors to insect and pathogen resistance.  They are also the location of major pigments affecting the color of the grain and are the main components of corn bran with the aleurone layer and the embryo as the main source of protein in corn grain.

​As corn got dispersed from its origin in Mexico it was eventually realized that some plants would delay the synthesis of starch in kernels leaving them with a creamy texture and a sweet taste.  This was caused by a recessive gene mutation that resulted in a sweet tasting substance, phytoglycogen. This was used by natives before the Europeans arrived in America.  This recessive gene is known as su.  In the 1970’s another recessive gene mutant was found that makes more sweetness, and tends to be associated with more easily digested pericarp. This sweetness enhanced gene (se) gives sweeter corn when combined with su gene but will also eventually become starchy.  Another recessive gene (sh2) was discovered in the 1950’s to have higher sugar content and a much longer shelf life before producing starch. As a consequence, the shrunken gene (sh2), the kernels do not become plump and with lack of starch reserve, may be vulnerable to poor emergence if planted too deep.
 
Endosperm genetics, being affected by the genetics of the pollen producer, and the sweetness genes being recessive requires isolation from field corn to express the sweetness.  Sweet corn hybrids tend to have large amounts of pollen, reducing the threat from other pollen but isolation in the seed production is imperative to assure that the seed is homozygous for the recessive gene(s). The best and purest sweet corn is produced with some distance away from field corn.

​Waxy and amylose corns are specialty corns influenced mostly by single gene mutations.  Popcorn genetics are more complicated, perhaps the consequence of a number of genetic changes that occurred in the early days of corn development in Mexico.  There is evidence that it was used by people in Mexico at least 5500 years ago. A major kernel structural factor causing popping is the ‘flint’ character of a hard pericarp, that is impervious to moisture passage.  Consequently, heating the kernel results in internal steam pressure. As the temperature increases the internal soft starch and protein resulting in a gelatin-like substance.  When the pressure finally breaks through the pericarp, the gelatin expands into a foam.

Pericarp thickness and endosperm starch type are two major characters affecting the successful popping.  Both characters are known to be affected by several genes, some major and some minor.  Other characteristics such as the size of the ‘pop’ are also genetically linked.  There are studies that have associated popping characteristics affected by at least minor genes on each of the 10 chromosomes of corn.
 
Those folks several thousand years ago didn’t need to know about molecular biology to understand the fun of eating popcorn and we really, really appreciate their persistence in passing along this feature of corn.