​Single cross corn hybrids are made by crossing two homozygous inbreds, in theory, resulting in each plant of such a hybrid being genetically identical. A few mutations along the way and a few impurities occurring during seed increases and hybrid production are probable, but most of the 32000 genes in each plant of a single cross hybrid are identical to the adjacent plant.
 
Close observation during the season shows slight differences in growth among those plants. Not each one emerged from the soil at the same time.  Perhaps this was due to planting depth, or soil consistency or differences in individual seed germination quality.   Each plant may not reach exactly the same plant height due to differences in soil water or nutrient supply.  Slight differences in silk growth and timing is especially obvious if the field had moisture stress.  Most of these differences are easily observed during the growing season when comparing regions or pockets of the field and are associated with soil differences.
 
It becomes a little more confusing when one plant suddenly wilts while adjacent plants are still green.  Seemingly same genetics in what would seem the same environment as the plants are a few inches away but one dead and one alive.  The wilted plant gains a gray appearance, with all leaves, including the ear husks turned downwards.  The change in the affected plant’s appearance occurs within a few days.  A few days later the stalk outer color changes from green to yellow and then brown. Adjacent plants maintain green leaves and green stalk color.  The dead plant’s inner stalk tissue becomes separated from the outer rind as the pith cells shrink from desiccation.
 
It is tempting to blame the problem on one of the fungi found in the deteriorating cell tissue.  We can call it Fusarium, Gibberella, Diplodia or Anthracnose stalk rot but still why that plant and not the adjacent ones.  These fungi are ubiquitous in a corn field with near uniform exposure to each plant.  The plants are genetically the same with the same exposure to potential pathogens.
 
Dead plants, usually, have more kernels than adjacent plants.  This is most obvious with the 2-earred plants near a plant gap on outside rows of a field but also can be clear when counting kernels of single eared plants.  All plants were genetically alike but some had a slight environmental advantage resulting in additional number of kernels.  If the later environment, or stress, did not allow sufficient fulfillment of the daily demand for movement of sugars to the developing kernels, the root cells of that plant died from starvation.  When the roots could no longer transport enough water from the soil to meet the water loss via transpiration from the leaves, the continuous chain of water in xylem tissue was broken and the plant wilted.  What was an advantage of a favorable environment for that individual plant becomes a disadvantage.  It has a larger ‘sink’ for carbohydrates but if not sufficient photosynthesis to fill the sink, the resulting kernels will not be completely filled for the 50-60 days after pollination.  Additionally, this weakened stalk will probably lodge. All plants of the single cross hybrid may have the same genetics but not exactly the same environment.

Annual plants such as maize are genetically programmed to salvage nutrients from leaves after pollination, resulting in senescence of the leaves.  One study (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115617) maintained that it begins in the ear leaf of corn as early as 14 days after pollination. These authors found at least 4500 genes involved in the biosynthesis of the senescence process as degradation of leaf cell components and new proteins were made, resulting in the regulated movement of nutrients and sugars from the leaf to the developing ear.

​This phenomenon is not unlike the reabsorption of leaf nutrients that occurs in many plants species and is being expressed in the Northern Hemisphere currently in deciduous trees, as the senescing leaves lose nutrients and chlorophyll, eventually abscising from the branch. The similar process in corn begins with the degradation and removal of leaf cellular contents, transportation to the fruit (grain) and eventual development of thickened cells at the base of the leaf, cutting off all movement of water and nutrients in and out of the leaf. 

​Varieties of corn surely differ in the timing and effectiveness of this senescence process.  These differences may be reflected in leaf cellular activity such as leaf disease resistance or drought stress.  The modified leaves composing the ear husk undergo the same senescing process, eventually effecting the opening of the husk needed for the evaporative drying of pre-harvest grain.  Eventually, the senescing leaves are cut off from the rest of the plant by the development of thick walls in the parenchyma cells at the base of the leaf similar to the abscission layer known as the black layer at the base of a mature kernel.  The cutting off of the water into the leaf after the abscission layer is evidenced by the sagging of the leaf.

​Basic gene function must be effective in all living corn plants except in those few with major mutations.  Corn breeders attempt to select individuals that have the characteristics, and thus, the genetics, preferred by the ultimate use of the hybrid. Unseen gene products carry out most physiological functions without our intentional interference. Thousands of genes are regulated and activated for the growth and function of all corn plants without our direct genetic intervention.  We do, however, attempt to select those relatively few genes that affect the products most desired by the user of corn.  Each of these traits are inherited by relatively few genes.
 
We can select for flowering timing, relative ear and plant height, grain quality characteristics from the variability present within a breeding population.  Resistance to each potential corn disease usually only involves 3-4 genes available in some genetic source within corn.  Grain quality characteristics are mostly affected by only a few genes.   The challenge is to select for these relatively simply-inherited characteristics within the background of those other physiological and morphological functions influence by those thousands of other genes.  Furthermore, the expression of those genes must be relative to the varied environments faced by the growing crops.
 
Added to this breeding difficulty, we must stabilize the genetics by selfing to make inbreds and then match inbreds to make a hybrid combination for repeatable performance in the field.  It is no surprise to find appearance differences among hybrids within a variety display plot. Each hybrid exhibited desirable product performance to be commercialized.  Each got there by slightly different genetic pathways and because of the necessity of having homozygous parents, each plant within a hybrid will appear identical to each other but different from the other hybrids.  Characters such as shape of canopy, length of leaves, and color and shape of tassel are inherited and uniform within a single cross hybrid as the result of uniform homozygosity of the hybrid parents.
 
Homozygosity of hybrid parents results in uniform and identical genetics for each plant of the hybrid.  This applies to each morphological character when the plants are grown in a uniform environment.  This applies to corn seedlings as well.  PSR has utilized this concept for 30 years assisting seed companies in assuring seed genetic purity of each lot of new seed production. Genetics affect all function and appearance of corn at all development stages.

​It was recognized more than a century ago that crossing unrelated corn varieties often resulted in increased vigor in the progeny.  It was known that self-pollinating corn plants a few generations resulted in smaller plants.  Heterosis, that boost in plant size coming from the combination of genetics from two unrelated parents, allows the preferable version of a gene result in production of some metabolic product either more efficiently or in greater quantity, than the version in the other parent.  It is assumed that this is usually a dominant form of the gene that overcomes the recessive form in the new hybrid.
 
Realizing that inbreeding would lead to depression of the plant size and grain production but that combining with the right other parent would not only restore these characters but could produce plants more productive than the original breeding stock. The large number of genes of corn, genetic diversity due to its history and cross-pollination biology, natural mutation rate, annual life cycle and human’s affecting phenotype selection, has led to huge opportunities for occurrence of detrimental versions of genes. 
 
The commercial plant breeder’s dilemma in inbreeding must be done to obtain uniform, dependable genetics in parent stalk inevitably resulting in some negative versions of some genes and yet identify another inbred that will essentially cover up the weakness of the other hybrid parent.  A traditional method of inbreeding is to grow and evaluate each selfed generation for desirable characters until the breeder is satisfied that the material is almost completely homozygous.  Most of the hybrid performance can be indicated by making crosses with other parents in earlier generations but lack of complete homozygosity can lead to problems of maintaining the inbred genetics with increasing of seedstock.  Waiting to test for heterosis until 6, or more, generations of selfing has led to disappointment as a homozygous inbred with excellent phenotypic characters can be identified but no other parent can be identified to cover up its few genetic deficiencies.  Several seasons of breeding but no commercial product is disappointing.
 
Complete homozygosity can be made quicker by crossing with pollen onto silk of corn genetic source in which the female plant makes no genetic contribution to the seed.  Instead this seed contains only one set of chromosomes, those of the male.  But the plant being haploid is weak, However, usually a specific chemical, a low percentage of haploid embryos can be doubled, resulting in totally homozygous plants.  This results in a very low percentage of plants becoming homozygous but the occurrence is genetically random and not always successful with every genetic background.  It is quicker than the traditional method of several generations of selfing but must accept the lack of ability to adjust and select for minor changes.
 
A third way invented by PSR Inc. is to select and self plants from a large population of genetically segregating plants of those that are most homozygous.  This is done by applying years of experience of evaluating corn seedlings in controlled environments.  These selections are sufficiently homozygous for evaluation in hybrid performance, while continuous selfing generations are used to reach the final level of homozygosity.
 
The large number of genes and the diversity allowed by corn’s biology has allowed this crop to be productive in multiple environments. Continual fluctuation of crop environments will forever require new genetic combinations to meet demands for this amazing carbohydrate producer.

​At least 32000 genes in the ten chromosomes plus the independent DNA of mitochondria and chloroplasts in corn plants.  We know the function of relatively few of these genes. We have selected genetics based upon field performance for the traits that we desire for the most part but we don’t know the actual genes involved in establishing grain yield and standability. Certain physiological processes such as photosynthesis can be studies, discerning the enzymes that can be traced back to a genetic code. Based on mutations we can determine the genes involved in endosperm starch formation. Resistance to some diseases can be linked to specific genes.
 
But how about the genetics that determines number of stomata, allowing for passage of CO2 into the leaves, or loss of water.  Do genetics influence the photosynthesis in stomata guard cells determining when they open or close?  Chloroplast and mitochondria DNA influences the membrane structure of these organelles.  Replication of chloroplasts and mitochondria must involve the interactions of genetics of these organelles with that of the host cells.  Movement of minerals into cells and photosynthetic products out is partially determined by cell wall structures as influenced by genetics.  Size and number of vascular bundles must be important to movement of water from roots to leaves and ears as well as carbohydrates from leaves to roots and ears.
 
Genetics influence corn stalk rind thickness, duration of life in pith cells and carbohydrate storage capacity.  Root branching, formation of root hairs and ability to absorb water and minerals from the soil are affected by products of the corn plant’s DNA.  Kernel number and size also limited by genetics. It is no wonder that corn has a lot of genes.
 
Many of these genes had to have been established in those Teosinte plants that humans tapped several thousand years ago.  Natural occurrence of mutations and human selection of traits expressing adaptation to their environments and desires provide us with large genetic variability.  Despite modern molecular techniques to study corn DNA, the complexity of interactions within the corn plants, we are still stuck with our somewhat crude method of field testing in several environments for the best hybrids.  We do this with the knowledge that many unknown genes are influencing the final performance and the hope that there remain new genetic combinations that will lead to better performance in the future.

​The eleven corn genes affecting the nature of starch synthesis in corn grains illustrates how much, and how little we know of genes in corn.  Much of what we know of location and function of corn genes is based upon occurrence of mutants, such as the waxy gene affecting corn starch synthesis. Maize Genetics Cooperation Stock Center was formed in 1932 as a means of collecting unique mutants and sharing with corn genetics researchers.  It is currently located at University of Illinois and can be found on internet at maizecoop.cropsci.uiuc.edu
 
Genetic studies using mutants has allowed some understanding of relationship of specific genes to some structures and activities in the corn plant but there remains a lot left to learn.  Careful analysis of mutations through breeding methods has even allowed location of these genes not only as to on which of the 10 chromosomes of corn but in relation to other mutants.  Mutant genetic studies have contributed considerably to our understanding of corn genetics and has been limited to only a few hundred genes.
 
Chromosomal DNA is a string of units, each of which are composed of 3 of a possible 4 nucleic acids. Most possible combinations code for one of 20 amino acids.  A gene is a string of these amino acid codes that has a start nucleic acid combination not related to an amino acid and a stop combination that also does not translate to an amino acid.  Actual translation of the DNA gene occurs when the section between the start and stop portion transcribed into a RNA molecule which is moved to the ribosome organelle in the cell.  The codes are then translated into corresponding amino acids which are connected to each other to form very specific proteins. The arrangement and sequence of amino acids have significant effects on their enzymatic activity in biosynthesis of structure and function of the plant.  A mutation may be only a single nucleic acid change in the DNA change that results in the substitution of a different amino acid in the final protein that affects the enzymatic activity.
 
Analysis of corn DNA of a single inbred (B73) by counting those with Start and Stop codons concluded that there were at least 32000 genes in that corn plant.  We have a very limited knowledge of which ones are most significant in terms of final corn production.  Surely some affect some structures and functions that are not related to grain production, at least in some environments.  On the other hand, having at least 32000 genes provides plenty of opportunity to select for features that lead to successful growth of corn across many environments.

Most ‘normal’ corn hybrids have endosperm content that is about 70-80% starch and 8-10% protein after the grain is dry.  Much of the protein is a storage protein called zein. Like most proteins, minerals such as nitrogen and phosphorus are major components.  Proteins, other than zein, are major contributors to the multistage biosynthesis of starch, linking the sugar molecules into the amylose and amylopectin components of starch. These proteins, functioning as enzymes, are major factors in quickly reducing the sugar content of the endosperm, thus improving the osmotic pressure to move more carbohydrate into the endosperm.
 
The zein protein in ‘normal’ corn is devoid of two amino acids, lysine and tryptophan, essential to animal nutrition. These two amino acids can be increased by recessive mutations to two corn genes designated as Pbf and O2, resulting in a reduction in zein proteins and increase of non-zein proteins.
​
Opaque corn, as the mutant o2 has been called because of its grain appearance, has been used for increased lysine and tryptophan amino acids.  It consistently has less starch and thus less grain yield than normal corn.  It has been shown that the gene O2, codes for proteins essential to the starch biosynthesis in the endosperm, probably with a regulatory function affecting the rate of conversion of sugar to starch (www.pnas.org/cgi/doi/10.1073/pnas.1613721113)
 
The complexity of starch synthesis in corn endosperm cannot be overlooked. Studies indicate that more than 1000 genes are involved in this process.  Although we have reduced many of the most detrimental mutants by yield testing and selection, remaining variability is reflected with every field yield test.

​Excessive storage of carbohydrates in plants used by humans for food has been selected over time by moving sugars into starch.  Kernel endosperm is the main site for starch storage in corn. At least 11 major genes have been characterized in corn by the enzymes that they code (Maydica 50(2005):497-506).
 
The enzyme Adenosine dipbospbate glucose pyropbosphorylse (AGP) affects the rate of starch synthesis and is coded by at least two genes.  This enzyme is also found in other plants, such as potatoes with the same function determining the rate the starch synthesis.  The enzyme is located mostly in the liquid surrounding the cell organelles (amyloplasts) where the starch is ultimately stored.  The recessive mutant of one of these two genes (shrunken2) reduces the rate of starch synthesis, resulting Supersweet corn. The dominant form of this gene (Sh2) thus was found to regulate the rate of synthesis of starch in the corn endosperm.
 
Other genes affecting starch synthesis in corn kernels have been found after mutants were identified. Recessive mutant form of the Sugary1 (Su1) gene reduces the branching of the starch molecules resulting in more sugars in the endosperm.  This led to the conclusion that the dominant form of the gene is associated with starch synthesis.
 
Corn starch is composed of highly branched strings of carbohydrate molecules (amylopectin) and non-branched molecules (amylose). The recessive mutant form of the Waxy gene (wx) results in only the amylopectin form of starch in the corn endosperm.  Amylose starch stains blue when exposed to iodine.  A recessive version of the iodine affinity gene (ia) increases the amylose portion of starch in the endosperm.  The amylose-extender gene recessive (ae) further increases the amylose portion from 25% found in most corn varieties to 50-80% of the starch in high amylose corn varieties.
 
Genetic diversity of corn is expressed in nearly all aspects of its production.