​Pythium and Fusarium species get the most attention as being associated with seedling rot.  These fungi are only marginally aggressive, however, mostly infecting plants that are weakened either from damage to the seed or from environmental stress. 
 
Each seed within a lot has a separate experience as it develops in the production field.  Position on the ear and synchrony of silking on the female parent and pollen production from the male parent affects the shape of the corn kernel.  Resulting shape and size influences the vulnerability to damage during harvest, drying and handling within the production facility. Genetics of the female parent also affects the vulnerability to imbibition damage as well.
 
Environmental factors affect the duration from germination to eventual independence upon the transport of nutrients from the seed endosperm and water and minerals via seminal roots. Water is needed but too much water can limit oxygen supply to the submerged cells and thus limiting growth.  Heat energy greatly affect the speed of metabolism and resulting cell elongation of the mesocotyl cells.  Heavy soils with high clay content can present physical barriers.  Feeding by soil insects and nematodes can offer avenues for soil fungi to enter the mesocotyl tissue.
 
Nearly everyone involved from the beginning of seed production to planting the seed can affect the establishment of a good final stand in the field.  Good luck with the uncontrollable environmental factors also helps.

​Several Fusarium species infect corn at all stages of the host’s life cycle.  These fungi often are not aggressive pathogens in the sense of attacking vigorous cell tissue but are ubiquitous in soils and on decaying plant materials allowing opportunity to invade living, weakened plant tissue.  Among those are senescing silks still attached to freshly pollinated corn ovules.  This can result in obvious kernel rot on the ear but also some internal infection of developing seed.  The fungus remains in the seed after drying and revives after seed is moistened.  This seed may not be sufficiently damaged by the fungus to inhibit germination.  Imbibitional damage to embryo cell organelles may allow more damage by the fungus, especially if cold stresses inhibit membrane repair, but germination, although delayed, may still proceed.
 
Cool soils during germination also gives advantage to Fusarium species in the soil to invade weakened seminal roots and mesocotyl tissue as the coleoptile is being pushed to the soil surface.  If sufficient damage is made to the mesocotyl, cutting off the supply of nutrients from the seed endosperm and seminal roots, coleoptile and enclosed new leaves will die, as the very young seedling wilts shortly after emergence.  If the young plant survives this early infection, the Fusarium can continue to spread within the growing plant, perhaps having no visible effect on the plant.
 
The genus Fusarium is the asexual stage of certain members of fungi known for their sexual stage as Ascomycetes.  Asexual stages of these fungi often reproduce and spread through asexually produced spores called conidia. They allow aerial spread of the fungus but also can move within the vascular system of the plant.  Sexual reproduction in most ascomycetes requires the combination of two mating types and thus is less frequently found.  Consequently, often a fungus is identified by its asexual stage, such as Fusarium, and only associated with its sexual stage after study by specialists.  Fusarium graminearum, commonly identified in seeds is the asexual stage of Gibberella zeae and Fusarium verticilloidessexual stage is Gibberella fujikuroi.
 
Gibberella zeae is associated with Gibberella stalk rot because the sexual stage (perithecia) is expressed at the outside of the dead stalk.  On the other hand, fusarium stalk rot is associated only with the asexual stage of a different species, Fusarium verticilloidesbecause that is the stage most frequently found in the dead stalk.
 
Ubiquitousness of Fusarium fungi in corn often allows them to be associated with dying or dead tissue although they may not be the main cause.  This is true of seedling rots and of stalk rots of mature plants often involves environment stresses but these fungi quickly spread to damaged tissue and thus become associated with the problem.

​Corn seedlings are most vulnerable to damage before the emergence of the secondary roots.  Pythium species are the most frequent pathogens at this stage, especially invading the mesocotyl tissue and thus interfering the transfer of minerals and carbs to the coleoptile before in emerges.
 
Pythium looks like a fungus, but it differs in structure and chemical constituents, making it have a closer relationship to brown algae.  Among the distinctive features are swimming spores.  Another feature common to Pythium and its relatives is an oospore produced after fertilization of the egg cell.  Oospores develop thick walls allowing the organism to withstand dry and cold conditions in soil until water returns.  Oospores germinate when exposed to water, producing filaments similar to fungal hyphae except Pythium filaments are mostly without septa that wall off individual cells. While exposed to water, sporangia form within the filaments to produce swimming spores called zoospores.  These spores feature two flagella allowing them to swim towards potential host roots, assumedly stimulated by exudates from potential host roots.  
 
Many Pythium species infect grass roots, including corn with a range of ability to overcome host tissue resistance.  A study in southeastern Iowa in 2012 Showed Pythium torulosumas the most frequent Pythium species found among the nine found associated with seedling disease in season favoring the disease (https://crops.extension.iastate.edu/cropnews/2013/04/nine-species-pythium-associated-corn-seeding-blight-southeastern-iowa).
 
Mesocotyl tissue is generally most vulnerable to attack by Pythium species.  Cool wet weather delays the elongation of the mesocotyl to the surface, prolonging the potential exposure and damage from this pathogen and yet encouraging Pythium to produce zoospores.  After infecting the seminal roots and mesocotyl tissues, basically causing collapse of the tissues.  Results could be seedling death or weak growth.  It is a primary cause of weak corn stands and uneven growth in areas of fields that have prolonged early season wetness.
 
Although Pythium species can invade more older corn plants when flooded for some time, it is mostly a seedling pathogen.  Seed treatments can protect the germinated seedling from Pythium, but there are isolates that are resistant to most seed treatments.  Although these pathogens are common in soils, conditions for significant damage is not common.

​Cell elongation in the area of the apical meristem results in the upward growth of the area between the seed and seminal roots and eventual emergence of the first leaf from within the coleoptile.  That mesocotyl tissue functions as a passage for energy (glucose) and minerals supplied by the seed endosperm and seminal roots to the newly forming upper tissue.
 
Mesocotyl growth continues until the coleoptile emerges from the surface of the soil where reactions from light, especially the blue wavelengths, results in more lignin deposition in the cell walls of the mesocotyl, essentially stopping its elongation.  The mesocotyl continues to function as a conduit to supply the development and emergence of the first leaves developing in the tightly wrapped coleoptile.
 
Metabolism in the mesocotyl cells is greatly affected by heat energy.  Growth is slower in colder soils and could also be slowed with low oxygen supply when in fully water saturated soils. Heavily encrusted soil surfaces may also interfere with ability of mesocotyl ability to cause the coleoptile to emerge, resulting in twisted mesocotyl and even leaves to push through the tip of coleoptile before emergence.
 
The secondary roots, also called nodal roots, form at the base of the coleoptile just below the soil surface as it releases the first new leaves.  This new source of carbohydrates along with the minerals and water absorbed the new roots as the utility of the kernel, seminal roots and mesocotyl is reduced.  The relatively short performance of these seedling parts is essential in establishing timely starts to the crop affecting not only number of plants but also the uniformity of the crop.

​Corn embryo cells are stimulated with imbibition as chemical energy in the form of ATP, allows for the production of complex molecules for elongation of existing cells and production of new ones.  The radicle, located near the tip of the kernel, breaks through the pericarp to form the non-branching, seminal root.  It is attached to the scutellum at a node.  As this seminal root pushes away from the kernel, tropism from gravity, causes the root to go downward. 
 
As the stem apical meristem elongates to form the first leaf tissue, the node at the base of the coleoptile, remaining in the soil, allows the growth of the lateral seminal roots. These roots branch, forming branches of a fibrous system.  These lateral seminal roots also turn downwards because of tropism. 
 
Energy for growth of seminal roots mostly comes via the scutellum from the endosperm.  These carbs are moved to mitochondria for ATP production and to other cell organelles to form the new cytoplasm contents and cellulose cell walls as these roots grow.  Residual carbs and ATP in the embryo are sufficient to get some germination, however, as shown when embryos excised from the endosperm germinate.  The growth is limited, however, unless carbs are supplemented by artificial media.  
 
Seminal roots absorb water and minerals from the soil further supplying the early growth of the seedling.  After the apical meristem pushes the green leaf tissue through the soil surface, allowing photosynthesis to produce the carbohydrates, new nodal roots develop at base of the first several leaves.  With this development, the seminal roots stop growing and start to senescence.  Dependence on the stored carbohydrates in the endosperm ends as new sources are now available.  Nodal roots now take over the role of water and mineral absorption for the plant.

Imbibition of water into dry maize seed occurs within a few hours after exposure, initiating cellular activity, initially in the mitochondria.  Examination of mitochondria structure using electron microscopy show poor developed membrane structures in the dry seed.  Mitochondria in dry seed have very low amount of oxygen uptake and low activation of enzymes.  These characters change with imbibition.  
 
Following 24 hours of imbibition, the mitochondrial membranes show more normal structures.  Among the mitochondria, however, there are some that appear to not recover normal structures and function.  It is easy to conjecture that these not recovering were either inadequately formed or were damaged during drying process.  This may be related to either the nuclear genetics or mitochondrial genetics of the seed parent.  Enzymes needed for membrane synthesis in the mitochondria is synthesized in ribosomes and thus dependent upon nuclear DNA and thus indicative of the significance of both hybrid parent genetics, but the mitochondrial DNA is only from the female parent.
 
 These numerous organelles in each cell activated after imbibition become drivers of cell elongation to push the first root tissue to emerge from the seed.  More info on this initial activity can be found at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64868/
​

​Imbibition of water into the seed leads to activation of the cytoplasm within cells.  Most of those processes occur along membranous components of mitochondria, ribosomes, plastids and the endoplasmic reticulum.  Hydrated proteins now acting as enzymes in break down starch molecules stored in the endosperm and glucose and sucrose molecules are moved thru the scutellum to embryo cells.  Diffusion of these sugars through pores of these cells, with cooperation of the cellular membrane and endoplasmic reticulum, these complex molecules composed of carbon, hydrogen and oxygen atoms are transported to mitochondria where they are further metabolized to create the ATP energy needed for other cellular activity.  This cellular respiration process allows further cell construction as cells divide in the root and shoot meristems. Elongation of hypocotyl cells, as well as meristem cell division pushes the tissues from the kernel.
 
Heat energy helps in driving these metabolic activities, including repairing damage to membranes occurring during seed production and storage, as well as those enhanced by hydration of membranes after planting.  
 
ATP (adenosine triphosphate) results from the energy transfer from electrons holding the glucose atoms together to form ATP, releasing CO2 and H2O.  This process occurs in the mitochondria.  These membrane-intense organelles apparently vary in number and efficiency among corn varieties.  Mitochondria, having their own DNA, and yet is dependent upon the rest of the cell for its structural components, are transmitted to the next generation only through the egg cell.  This is probably why different female parents of corn hybrids vary in time for seedling emergence and vulnerability to imbibition chilling damage.
 
It is amazing to see a near-perfect emergence of corn seedlings in a field, given all that had to happen at the cellular level.

​Corn seed is vulnerable to damage from soon after pollination in seed field until planting in the field.  Each cell in the embryo has membranous tissue that could be damaged from insufficient moisture during embryo formation.  Fungal pathogens can infect the seed as it develops.  Delaying harvest, perhaps because of weather problems, can result in initiating an aging process of cytoplasm of cells.  Too slow a drying process, perhaps because of inadequate dry air movement within the seed facilities can also contribute to cell aging.  Excess heat during that drying also affect the membranes within the cells.  Rough handling of the seed can result in breakage of the pericarp, allowing faster imbibition of water when in the field.  Genetics of the female parent affects vulnerability to each of these factors.
 
These damages rarely affect all the seed within a lot.  There is a tendency for the damage to be greatest at both ends of the ear, with the flat sizes generally having the least damage.  It is not clear of the cause but perhaps the embryos in rounds have less physical damage protection.  It appears that the damage is not evenly distributed in all cells of the embryo. Individual plants that show malformation during germination often show major injury in shoot meristem, resulting in radical growth but no stem. Injury to cells in the hypocotyl area is believed to be the cause of shoot finally emerging but twisted and clearly behind in growth compared with adjacent seedlings.
 
Imbibition, in which water allow the dehydrated membranes to swell and activate will allow some damage to repair.  Adequate heat is important to generate the energy generated by undamaged cytoplasm to promote repair. Generally, temperatures below 50°F (10°C), inhibit membrane damage in the embryo.  Imbibition chilling can result in lowering emergence in the field.
 
Corn breeders select for multiple performance characteristics, including tolerance of potentially damaging seed production stresses.  Combining all the favorable characteristics is never perfect.  Seed production methods aim to reduce stresses but nature does not always cooperate.