​When a poor stand is apparent as the seedlings emerge, we search for a cause. Seed treatments include control of Pythium. After eliminating soil compaction, freezing and insect damage, seedlings can be submitted to a pathology lab for microscopic examination. It is probably that the fungus Fusarium will be found.  But that is not a simple answer to the problem. 
 
The fungal species of the genus Fusarium have a complicated relationship with germinating corn seedlings. The most studied species, Fusarium verticilloides (formerly known as Fusarium moniiforme and its sexual stage as Gibberella fujikuroi commonly is found in germinating corn seeds.  It often is found in corn plants without symptoms of damage and therefore is characterized as an endophyte because it appears to live within the plant tissue but does not always cause symptoms.  It is not uncommon to see growth of this fungus from germinating seed in paper germination test. A study published in 1997 (Plant Dis. 81:723-728) compared seedling growth from seed artificially infected with this fungal species with those that were not infected.  There was no difference in germination percentage between infected vs uninfected seed. There was a slight size difference favoring the uninfected seedlings at 7 days after planting but at 28 days those growing from the infected seedlings were slightly bigger and with more lignin in cell walls. Is this because of a hormone (gibberellin?) produced by the fungus or because of some defense compound produced by the plant? The fungus was easily recovered from the seedlings but less from the older leaves. Infected plants showed no symptoms of disease. 
 
It is clear that Fusarium verticilloides can be damaging to germinating seed sometimes but I don’t think all the factors are clearly understood.  Is the difference caused by the strain of the fungus, the host plant or the environment?  I know from experience that it is so common to find Fusarium growing from a dead leaf sample that one tends to ignore it.  It seems to live in much of corn plant’s tissue.  It often leads to confusion with diagnosis of problems including stalk rot, almost as if one cannot find other fungi usually associated with rotting stalks, there is always Fusarium. 
 
It’s complicated!

​At about the V3 stage of development, the primary root function begins to be replaced by the nodal, secondary roots.  Energy provided by photosynthesis in young leaves, and heat, drive the production of the metabolites for cell division and cell elongation in these young root tissues.  Whereas auxin hormone causes increased cell elongation in stem and leaf cells, auxin reduce this activity in the root cells.  Consequently, although the nodal roots initially emerge horizontally from the stem nodes beneath the soil surface, gravity causes more auxin to accumulate on the lower root epidermal cells.  This results in longer epidermal cells on the upper side than on the lower side, effectively turning the root growth downwards.
 
Root tip meristem cells rapidly divide, producing the root cap cells below to protect the dividing cells as it pushes through the soil and functioning root cells above the dividing cells.  Outer layer root cells composing the epidermis are thin-walled and porous to water via osmosis.  A short distance from the meristem of the root tip, epidermal cells form protrusions (root hairs), effectively expanding the surface area exposed to water and minerals of the soil.
 
Cells in the core of the new root differentiate to form vascular tissue that connects to the stem vascular tissue through the nodes.  This vascular tissue allows transport of water and minerals upwards through the xylem and carbs downwards through the phloem. A few cells in this vascular portion of the young root maintain cell division capability, becoming stimulated by another group of hormones (cytokinins) to increase cells laterally, pushing through the epidermal cell layer becoming lateral roots with their own root meristems.
 
As with all aspects of corn growth a combination of genetics and environment influences the growth of the root system.  Total volume of roots and depth of root growth tendencies will vary among genotypes. The fibrous nature of corn roots not only increase absorption from the soil but also provide support for the stalk as it elongates. 
(CornJournal 6/6/17)

​Most corn seed planted in the USA has a seed treatment that includes at least one fungicide intended to reduce damage from Pythium.  But effectiveness is complicated by differences among Pythium species and environments.  A publication in Plant Disease (http://dx.doi.org/10.1094/PDIS-04-15-0487-RE) indicated that 3 of the 4 species isolated from Iowa fields in 2014 were favored by lower temperatures (55-62°F) but one species favored a little warmer temperature of 73°F.  Although the fungicides were generally effective there were situations in which the pathogen still effectively infected the seed or seedling root.
 
It has to be complicated down there.  There are the dynamics of the biology of a germinating seed, with some less vigorous than others, soils with varying water holding capacities and organic matter, and competing microorganisms.  The latter generally produce chemicals to ward off others as well.  Cell contents are leaked into the environment surrounding the seed as the seed swells and begins germination, attracting not only the zoospores of Pythium species but also numerous fungi.  The plant responds to invaders by producing phenols that can stop or slow down further invasion.  The fact that the germinating seed environment has many complicated interactions makes any attempt to give exact characterizations is difficult and contradictions to conclusions are often seen.
 
With favorable temperatures, moisture and oxygen levels, we know high quality corn seed generally overcome the potential problems with fast root and shoot growth.  We also know that every seed can be slightly different in cell membrane status because of factors that includes genetics, maturity, drying, handling, and storage conditions.  Field conditions vary in soil type, temperatures and moisture levels.  Pathogen intensity and seed treatment effectiveness may vary with all of the above conditions.  It is a wonder that we actually usually get 90+% stands in the fields.  It is to the credit to everyone from the corn breeder, seed producer, seed quality workers, public and private researchers and the grower that this happens. (Corn Journal Blog 3/7/2016)

​Corn is often planted in temperate zones as early as possible to take full advantage of the warmth of spring and summer.  The spring weather is not always predictable, and temperatures affect the growth rate and metabolism of the seedlings.  A battle begins between potential pathogens and corn plants.
 
The field environment of corn germination includes many organisms.  One group active in early spring are the Oomycetes.  These organisms were once classified as fungi but now their distinctiveness has most specialists agreeing that they are more closely related to brown algae.  Fungi have chitin cell walls whereas Oomycetes have cellulose walls.  Oomycetes have swimming spores, zoospores, whereas this is not a feature of most true fungi.  This is the feature that makes Oomycetes genera such as Pythium so significant to corn seedling survival.
 
Pythium species reproduce with swimming sperm cells fertilizing egg cells, while in infected live or dead plant tissue.  These then form a thick-walled oogonium that persists during stress, including winter temperatures.  When in water, and spring temperatures in the 50’s, sporangia growing from the oogonia release the swimming zoospores.  Attracted to sugars released by primary roots and the mesocotyl of corn seedlings.  In some cases, the oogonia produce filaments (hyphae) that infect the roots also.  Infection of these tissues can cause the seedlings to die, cutting off water to the emerging leaves.  If the seedlings survive this early infection of the primary root and mesocotyl, secondary roots emerging from the crown area bypass the infection and outgrow the damage.  Low temperature and oxygen deficiency because of water-soaked heavy soil contribute to the seedling vulnerability to damage.  Seeds with previous membrane damage resulting in slow early seedling growth are often the most vulnerable, perhaps because they are slower to produce the more resistant secondary roots.
 
There is evidence that the same Pythium species infecting corn also infect soybeans and several grasses as well. Pythium species do exist in a competitive environment with other microorganisms capable of inhibiting Pythium success.  Apparently low oxygen, cool environment of water-soaked heavy soils favor the Pythium species.  Seed treatments on corn (and soybeans) are often aimed at not allowing the seedling infection.  Races of Pythium are known to overcome some of the treatments.  It is unfortunate that genetic variability works for all organisms!
 

Primary roots supply water to the mesocotyl and energy from the endosperm via the scutellum stimulates the elongation of shoot cells in the embryo.  Outer layer of embryo leaves is a modified one called the coleoptile, essentially enclosing the other leaves in the emerging shoot.

​Elongation of cells in the mesocotyl pushes the corn seedling coleoptile towards the soil surface.  Cells in the coleoptile are also elongating as it grows upward but cell function changes drastically when light strikes the emerging coleoptile.  Meanwhile the immature leaves encased by the coleoptile are also slowly enlarging.  Almost immediately after the coleoptile is exposed to light, hormones are produced that essentially shut down the mesocotyl growth. Other plant hormones, auxins, are produced in the shoot tips and transported to the node at the bottom of the coleoptile, stimulating the growth from root primordial cells to produce the secondary root system.  Movement of this auxin in the opposite direction of the flow of water from the soil requires energy, as it must go from individual cell to cell.  That energy is now being supplied by photosynthesis occurring initially in the emerged coleoptile and then by the new leaves that pushed out of the coleoptile enclosure. Previous to emergence, energy for growth was supplied by the seed endosperm and influenced by heat.  Water supplied by osmotic pressure in the primary root tissue allowed for cell elongation in the mesocotyl. Now with exposure to light, a new source of energy moves the seedling to new phases of development above and below the soil surface.  Mesocotyl significance to the seedling reduces as the above soil structures take over the physiology of the young corn plant.  This transition does allow the plant to be vulnerable to negative temperature, moisture and pathogen affects but if everything goes right, the mesocotyl remains intact until the secondary roots function as the main supplier of water and nutrients for above ground growth of the seedling. 
 

​The corn embryo is alive but dormant until water is imbibed. The water causes membranes in the cells to activate.  Mitochondria absorb the surrounding carbohydrates and those coming from the endosperm via the scutellum. RNA, some of which is newly transported from being coded by the DNA in the nucleus is translated in the proteins needed for processing the sugars into the chemical energy ATP.  This energy, and that provided by heat, is utilized for cell division and elongation in the root and shoot meristems.
 
Root tip cells are surrounded by a special layer of cells (coleorhiza) that act as a protective covering when the root tissue, also called the radical, pushes through the pericarp of the seed. Root tips include special cells with organelles (statoliths) that are heavier than other parts of the cell.  Consequently, they accumulate on downside of the outer layer cells of root tissue.  These cells lead to production of hormone-like chemicals (auxins) that inhibit root cell elongation on the lower side of the emerging root.  With greater cell length on the upper side, the root grows downwards, regardless of the orientation of the seed when planted.
 
This initial root is called the primary root.  It is usually unbranched and relatively short lived as secondary roots grow from the lower nodes of the stem portion of the embryo.  Between the two major parts of the corn embryo between these two is the mesocotyl.
 
The shoot portion of the embryo already has several nodes, each with undeveloped leaves. Energy and water stimulate cell growth and division in the meristem causing the shoot to push through the pericarp usually after the primary root has emerged and begins absorbing soil moisture and minerals from the soil to be transported to the shoot.
 
Shoot tips cells also produce similar organelles also affected by gravity.  They also produce auxins, but these hormones have the opposite affect on shoot cell elongation.  Those cells on the gravity side with more auxin become longer than those on the upper side.  Consequently, the shoot grows upwards.
 
Affect of gravity on plant growth direction is called geotropism.  After shoots emerge, phototropism becomes dominant, causing the plant to grow towards light because cells on the shaded side produce more auxin and consequently longer cells.
 
When all works as planned healthy seedlings begins the season.

​Corn, like other grasses, is a monocot- the seed has a single cotyledon as part of the embryo. Unlike the dicot species, such as soybeans, in which the two cotyledons emerge and photosynthesize, the corn cotyledon remains underground. The shape of this thin structure led to the name scutellum, which is Latin for ‘small shield’.  It attaches to the rest of the embryo by a small channel with vascular tissue and is positioned between the shoot-root portions and the endosperm. The scutellum has its own enzymes that are activated with imbibition to digest the starch and oils stored in the scutellum as well as assist in the movement of sugars from the endosperm.
 
The scutellum is a storage location although much smaller than the endosperm.  Efforts to select for high oil corn, carried on for many years at the University of Illinois, resulted in larger scutellum for more storage of oils, and smaller endosperm. Other parts of the embryo also were larger in high oil corn seeds as compared to the original ‘normal’ varieties before selections. Having a carbohydrate storage capacity and having a vascular connection with the shoot and root parts of the embryo makes it a target for infection by pathogens.  This connection has been utilized by scientists to transmit trait DNA via infection by the symbiotic bacterium Agrobacterium tumefaciens carrying the DNA into the scutellum when excised from the embryo. Activity in the scutellum is turned on with imbibition as germination begins. (Corn Journal Blog  4/5/2017)

​The corn ‘seed’ appears as a single entity, but its parts have distinct origins and functions.  The outer layer, the pericarp, is completely derived from the female parent and does not include genetics from the male parent.  Immediately inside the pericarp is a product of the union of both parent.  Aleurone cells are biologically active and include anthocyanin and carotenoid pigments affecting the color of the corn kernel.  Pericarp and aleurone cell layers surround the the embryo and and endosperm of the corn kernel.
 
Most of the grain’s carbohydrate is stored in the endosperm.  The embryo includes tissue adjacent to the endosperm called the scutellum that is rich in mitochondria and therefore ready to produce the energy needed to make enzymes such as amylases that break down the starch into it’s glucose components that will be moved to the other embryo cells.
 
Mitochondria show only slight activity in the dry seeds. Many apparently are only partially formed but a little respiration is occurring.  However, once exposed to water, and the seed imbibes, the cells and its components, including mitochondria, swell. Partially formed mitochondria are not only activated but gain the more membranes needed to get the glucose transformed into the chemical energy needed for germination. 
 
Studies have shown that temperatures affect this transition.  Not surprising to anyone experienced with growing corn, the mitochondrial activity is higher at 77°F than at 57°F.  Some of that activity is responsible for the membrane reproduction and repair not only in mitochondria but other membranes in the cells of scutellum and other embryo cells.
 
Another site of activity in cells of the embryo are the ribosomes, also inherited from the female parent.  Ribosomes are the site of protein manufacturing.  RNA molecules, as coded by the nucleus DNA, migrate through the nuclear membrane to ribosomes in the cell. Chemically energy from the mitochondria provide the power for import and combination of amino acids in the ribosomes for production of proteins to become the enzymes and structure of cell replication and growth in the germinating seed.
 
A lot of things are going on in that seed after it begins germination.