​Corn seed is planted in complex environment with a mix of soil particle density, moisture levels and other organisms, some of which capable of digesting any carbohydrates they can reach. When seed does not emerge as expected we often look for a cause including fungi associated with the poorly emerging seed. This often is not simple.

Among the perplexing interactions in corn is that with corn and the fungus Fusarium verticilloides. This fungus was formerly known as Fusarium moniliforme and is the asexual stage of the fungus Gibberella fujikuroi. Many, (most?) seed samples germinated by paper methods will show at least a few seeds with this fungus growing from them, even with the appearance of normal seed germination. The fungus does produce a toxin called fumonisin that can cause rejection of grain by some livestock and grain elevators. This can occur in kernels showing not symptoms of infection.

The fungus can be found in corn roots, stalks and leaves as well, often without symptoms. It is not unusual to find this species growing from dead corn leaf tissue when moistened. It is as if it is an inhabitant of corn. Does it become transmitted to the next generation from infected seed? It is acknowledged that seed can be infected via growth of the fungus in the silk. Or does it become from infected debris in the soil? Or, perhaps entering thru injuries to plant tissue.

A study published at Appl Environ Microbiol. 2003 Mar; 69(3): 1695–1701 followed the spread of F. verticilloides from infected seed and from inoculated soil through corn plants using a carefully designed group of experiments using fluorescent strain of the fungus detected by fluorescent microscopy. They confirmed that this fungus can infect through the root to the mesophyll, often growing between cells. This can result in stunted seedlings, especially if grown under low light conditions. This growth can advance into the stalk tissue, in leaves and even into the seeds, sometimes without showing symptoms. More of the fungus was found in the plant if the soil inoculum load was increased. There was spread to the roots and to the rest of the plant from infected seed but the soil inoculum load appeared to be more significant.

Low light association with increased symptoms suggests that the metabolic health of the plant affects the defense against this fungal invasion. That also is consistent with the presence of this fungus in nearly all rotted stalks. If other stalk rotting fungi, such as those associated with Diplodia stalk rot, Gibberella stalk rot or Anthracnose stalk rot are not found, we tend to call it Fusarium stalk rot because it is always there. The low physiological state of stressed corn plants as they approach completion of grain fill increase the vulnerability the expansion of this fungus into the dead stalk tissue.

Microbes inhabiting the corn plant reflect the complexity that actually is affecting the biology of the corn plant.

​As corn seed is moved from a dry environment of storage encouraging slow metabolism to the wet, more complex environment of moist soil, germination and emergence becomes our next measure of success. 
 
It is difficult to sort out the real cause of seed not emerging or emerging much later than adjacent plants.  Seeds are planted in environments that vary every few inches for water holding capacity, organic content and microbes.  Furthermore, each individual seed varies slightly in its cellular membrane status.  With imbibition causing swelling of the membrane bound cell contents, some seed can have problems getting effective metabolism for early cell growth to push out the root and stem structures.
 
Cell metabolism includes producing the response to attacks by potential pathogens in the soil. These anti-pathogen chemicals (phytoalexins) are usually produced with a complex system of detecting the microbe and concentrating the phytoalexin into the area of the attack.  Weakened seed not only are likely to release more carbohydrates and proteins into soil because of membrane injury, but also be less capable of responding to the microbes invading root and mesocotyl tissue.
 
Diagnosis of seedling disease becomes complicated also.  Pathologists can isolate a fungus such as a Fusarium species or an oomycete like a Pythium species, but the actual cause probably involves some interaction between the microbes, metabolic quality for the ‘diseased’ seedling, and a complex environment not only providing potential pathogens but also affecting the seedlings metabolic rate. Soil organisms are affected by the environments as well.  Leakage of carbohydrates directs their growth toward the seedling roots but temperatures favor some over others.  Pythium’s swimming spores do well in cool wet environments but can be inhibited by certain seed treatments that have very little effect on fungi such as Fusarium species.  Other seed treatments can inhibit the latter group of microbes but are less effective against Pythium.  Corn seed genetics and seed quality can be greater factors than either group of chemicals.  Cold wet heavy soils for a prolonged time can overcome all methods of defense.
 
After the stress on the seedlings is reduced, remaining plants that emerge can give normal production especially if they are uniform in growth with adjacent corn plants.  The metabolism of these plants will promote the recovery and normal root growth.  Those plants that survive but emerge later than adjacent plants will have difficulty competing for light and mineral uptake which will be reflected in grain productivity.
 
Life for the corn plant, like for the rest of us, becomes more complex after we start living in our environments.
 

​Upon planting seed is exposed to an environment with many factors affecting the success of germinating and successfully producing a growing plant.  When corn seed, with its own biological potential problems, is placed in soil populated by multiple micro-organisms ready to feed on organic matter, multiple battles begin.  As the seed imbibes water, internal membranes swell, causing some leakage of stored sugars and proteins into the soil.  Many soil organisms grow towards the damaged seedlings, attracted by the leaked substances.  First tissue exposed to the potential invaders are the primary root and mesocotyl, two tissues that are later disposed when the secondary roots take over for the main root functions.  Invaders are detected chemically by the corn cells near the invasion, turning on local production of resistance antibiotics.  Success in suppression of the invaders is affected by aggression and intensity of the potential pathogens, environmental effect on pathogens and seedling and the biological vigor of the seedling.
 
Several fungal species are associated with seedling root rots.  Fusarium, Penicillium, Pythium and Rhizoctonia species are among the most prominent fungi found in diseased corn seedlings.  Fusarium species are common in nearly all soils with any organic matter.  Every corn seedling is exposed to this fungus and yet only a few show symptoms. The actual cause of the seedling disease is usually more complex than simply identifying the fungus present in the corn tissue.  Analysis of the cause should include consideration of environmental factors such as water concentration and temperature, and seed germination quality.  Vigorous seedling growth can quickly dispose of primary root and mesocotyl dependency as secondary roots develop and new leaf tissue produces the quantity of resistance factors needed to control potential invaders such as these fungi.
 
Seed treatments can give the seedling some temporary relief from fungal invasion pressures.  Genetic variability within the pathogen population can weaken its affect in some circumstances.  Vigorous early growth due to corn hybrid genetics and seed quality favor escape from seedling disease pathogens even when environments are not optimum for early corn growth.  Corn genetics and seed viability tests are strong deterrents to seedling diseases.  Favorable environments also contribute.
 

45 years ago, when pursuing the question of why one plant died early with stalk rot and the adjacent plant did not, I hypothesized that the dead plant was that one emerged late as a seedling.  When most of the plants in the test plots showed their 5th leaf, a tag was put near those that had only 3 leaves and another marking those with only a spike.  Notes were taken of these plants and their adjacent plant during the season.  At pollination, it was clear that even those tagged at three leaves were not silking in time with adjacent plants and tended to have more slender stalks.  Many of those tagged as spiking no longer were present, but those that survived were far off in pollination timing, had very small, narrow stalks and, eventually, small tassels.  Ears were harvested at end of season and kernel numbers were counted. Those tagged with three leaves had only 20% of kernels of adjacent plants and those tagged as spike only were barren.  Delayed emerging plants did not develop stalk rot but clearly the delay affected yield.
 
To eliminate the possibility that these delayed plants were not ‘selfed’ inbreds instead of hybrid plants, an experiment was performed the next season to confirm that emergence delay was the main factor.  Seed was planted with twice the normal plant-to-plant spacing.  When those seedlings spiked, the same hybrid seed was planted between the seedlings.  This would be an unusual delay but the effect was the same as the first observation.  Barren plants, skinny stalks, small tassels were characteristic of the delayed emergence.  Apparently plant competition for late emerging plants has a drastic affect. 
 
Others have done similar experiments, before and after these,  done by a young guy beginning to learn about corn.  My conclusion was that individual plants developing stalk rot were not the late emerging ones and that uniform emergence was an important factor in corn yields.  Also, it was interesting that those late emergers could be confused with selfs, as confirmed by the fellow who normally evaluated hybrid purity in winter growouts.  That eventually led to developing a different purity test method (Seedling Growout® test).
 
My experiments were done in the 70’s with hybrids and plant densities common at that time.  It would be useful if similar experiments were done with more recent hybrids selected for consistent ear development at the higher plant densities used today.  It is notable that experiments done by others have shown that among germination test methods, the cold test is the best predictor of field emergence and that it accounts for about 70% of differences among seed lots in field emergence. 
 
Corn plants in the field compete with each other for light, nutrition and water.  Although genetically identical, this small disadvantage of the late emerging plant can detract from the final yield in the field.

I am amazed when I see our grandchildren move with seemingly little effort.  Did I ever move that way?  Sadly, we do age and and it is not only in our minds but in all cells of our body.  The speed in which seed and us age is influenced by our genetics, and environments after our 'birth'.
​
The mechanisms between us and seed may be similar in that mitochondria are probably involved in all deteriorating living cells.  These organelles which can number a few hundred in a cell, are the main sites for transformation of stored carbohydrates into useable energy for other cell functions.  Mitochondria have their own DNA and are composed largely of membranes.  Dehydrated seed results in mitochondria functioning at a very low level resulting in being unable to repair deteriorating membrane structures.  While at very low kernel moisture levels (6-14%?) and cool temperatures (less than 50°F (?) further damage is limited.  Precise moisture percentage and temperature for best storage of maize seed probably varies for genotype and seed condition but the general concept remains.
 
Seed imbibition of water is a physical phenomenon with little inhibition from the pericarp or seed coat.  Seed treatments added to seed can slow down the imbibition, apparently giving the renewed mitochondrial function more time to repair damaged membranes.  On the other hand, only increasing kernel moisture slightly can cause more membrane damage to occur, but not repaired.  Increasing moisture more while at low temperatures (50°F) has the same effect.  Corn seed planted in cold soils will imbibe water, but the low temperature inhibits normal cell function, including repairing mitochondria.  Those individual seeds with the most mitochondrial damage are likely the ones that struggle to germinate when the soil temperatures do heat up.
 
Seed producers are aware of the significance of inadvertently adding a small amount of moisture, such as from a seed treater before bagging by designing their process to limit the water and allowing for drying after application.  I recall a case in the Thailand in which a new fungicide seed treatment was applied to control downy mildew, but the humid environment did not allow the seed to dry after application.  Seed germination quality quickly deteriorated as a result.  Accelerated aging test of corn seed is based upon placing seed in an environment of 100% humidity and 113°F for 3 days, then planting in germination test to record the reduced germination.  It is intended to predict the viability of the seed after storage.  It is notable that even under this condition, all seed within the sample are not equally affected.  Some germinated normally, some eventually and some not at all.  This is typical of normal, well treated aging seed lots.  Each individual seed is in a slightly different condition.  We expect maximum performance when emergence is uniform.  

​Energy for germination of a corn seed not only comes from stored carbohydrates but also from surrounding environment.  Heat energy is a major contributor.  Although imbibition is not inhibited by cool temperatures, heat energy allows the orderly repair of the membranes damaged during the dehydration of drying seed and then the hydration after planting. 
 
Very soon after the corn seed is planted, imbibition begins.  The H2O activates the membrane-bound mitochondria to respire, providing energy for protein production. The enzymatic proteins include those that digest the starch stored in the endosperm into more sugar molecules to be transported through the scutellum to other cells in the embryo, resulting in more energy available to produce structures for cell elongation.  Heat energy provides a regulatory function affecting the speed of this germination process.  Imbibition occurs at any temperature but metabolic activity in corn is generally thought to be very low if seed environment is below 50°F.  Speed of germination increases as the temperature increases.
 
Membrane integrity within the seed also affects the net speed of this process.  Those individual seed with more damage are slower to sufficiently activate the system and thus slower to activate the metabolism needed for cell elongation in root (radicle) and the shoot sections of the embryo.  Cool environments, delaying membrane repair, may result in death of the imbibed seed before the shoot can emerge from the soil.  Some of these seed, even after warmed manage only to extend the root through the outer wall for the kernel, the shoot never emerging.  Other weakened seed may finally get enough momentum to push through the soil surface but days after the healthier seed have emerged, resulting in a season-long competitive disadvantage.  Heat energy during germination affects the severity of the effect of membrane damaged seed.
 
Microbes in the soil are generally warded off by products of seed metabolism in healthy seed. Those individual seeds that are slow to generate sufficient energy for growth are also more easily attacked by microbes, further slowing the germination process.  Seed treatments are useful in giving the damaged seed more time to successfully germinate.  Healthy seeds can successfully produce normal seedlings despite surrounding common soil microbes but those weaker individuals need the extra protection.

 ​Corn seed planting time is approaching in the northern hemisphere. The processes of successful producing and storage of the seed will soon come to fruition.  The selection of seed parents, care in the seed field of the last season and then the drying, shelling and storage all have an affect on reaching the goal of getting a uniform emergence in this next stage of growing corn.
 
Cells in a developing embryo are sufficiently mature to germinate in only 15 days after pollination if separated from the endosperm.  Early germination (vipipary) is inhibited by the presence of the plant hormone, abscisic acid, in the endosperm which negates the growth stimulant hormone, gibberellic acid, in the embryo.  This allows normal seed desiccation as water is replaced with starch deposits and eventual seed germination inhibition because of low water content.  Seed producers know that each genotype differs in the percent moisture to be used to harvest for optimum seed quality.  Generally, for most corn dent hybrids, that moisture is higher (+/-36%) than normal black layer moisture of 32%.  From there the moisture level must be rapidly decreased to less than 13 % to prevent excessive aging caused by damage to the cell membranes.  It is the art and science of the seed producer to bring the moisture down rapidly without using excess heat which also could damage the membranes.
 
Intactness of the pericarp affects the speed of imbibition of water in the soil.  Allowing the membranes surrounding each cell as well as the cell internal membranes to swell back to normal size with minimum injury is essential to their functions.  Cell membranes being the main structural component of embryo cells needed for energy conversion from starch in the mitochondria and translation of DNA to proteins, have a major effect on the germination quality of seeds.  Genetics of mitochondrial membranes, at least partly affected by the mitochondrial DNA, are probably one of the major reasons that seed quality varies between hybrid parents.  Mitochondria of the seed are replications of those in the female parent.  This is the major reason why choice of which hybrid parent becomes the seed parent.
 
Another major factor affecting on seed quality is the growing environment in the seed production field.  Stress, from drought or disease during the seed maturation period shows later in seed germination quality.  Such seed often becomes evident in germination tests done 4-5 months after seed harvest, sometimes in contrast to tests done only a few months earlier.  It is as if these seed had some membrane pre-harvest injury that when added to normal aging during these 4-5 months surpassed the minimum for normal germination.  These individual seeds either fail to germinate or are slower to emerge than other seed in the same seedlot.

Not only is our species dependent upon diversity for survival as our environment, including pathogens, changes.  We are depended upon diversity among our crops as well.  Corn being naturally cross-pollinated and diploid provides this opportunity for the diversity that comes from naturally occurring mutations.  It is basic to providing the eventual variability that has driven and continually drives evolution.  It allowed the deviants in Teosinte that was selected by people in Mexico 10000 years ago and the multiple selections in corn as it was moved worldwide since then.  Most research has verified that most of these genetic mutations result in recessive genes and thus the presence of the mutation is not often expressed in a diploid present in which the dominant member of the paired gene is expressed. The su genes resulting in sweet corn is only expressed when the recessive gene is expressed in both members of the diploid plant.  Same is true of the mutants wx for waxy.  This is true for multiple other homozygous recessive traits.
 
Occurrence of mutations can be an advantage or a disadvantage.  In most cases, being recessive, the mutation may not be detected by performance of the hybrid.  Selfing to achieve homozygosity during the inbred development reflects the negative affect of making some recessive genes more homozygous.  This is reflected in reduction of plant size from the heterozygous parent used for inbred development. The selection process with each generation does allow elimination of some negative homozygous recessives.  Double haploid systems do not allow generational selection because the homozygous condition is fixed.
 
Expression of hybrid vigor when an inbred is crossed with another specific inbred is mostly due to dominant versions of the negative recessive genes of the inbred parents.  That is probably why prospective commercial hybrids are from crosses of inbreds with distinct ‘families’, each not likely to share the same negative recessive versions of important genes.  Corn has 40000 genes, including some negative recessives, perhaps due to mutations.  The seed industry uses hybrid testing, and inbred development to select for hybrid performance.  Further selection among those near-inbreds can allow for selection against the few negative traits found among some plants to improve inbred performance in hybrid production.  That has been consistent with our experience in our proprietary Rapid Inbreeding® program.  Diversity is good!

​Opportunities for mutations occurs with every cell division but those that really count are those that occur during meiosis, in which all cells dividing from the fertilized egg cell will lnclude the new DNA arrangement for that segment of the chromosome.
 
​Corn advanced from that first mutation in Teosinte, allowing and exposed kernel to be easily used as grain.  More mutations that occurred with each annual reproduction was utilized by people over the past 9-10000 years.  Mutations occur naturally in all organisms. For example, each new human baby, on average, has 100-150 new mutations different from either parent.  Majority of the human mutations are unnoticed and insignificant but a few can be drastic.  But human generation reproduction is once every 20 years whereas an annual plant such as corn produces new mutants with each seed generation.  Although the mutation rate per gene may be low in comparison with some organisms, having 32000 genes allows for a probability of some mutations to occur with each generation.  Not all of these mutations will be expressed because they will usually occur in one strand of the paired DNA strands, allowing the other dominant version of the gene to affect the trait associated with the gene.
 
Mutation causes are associated with errors that can happen during meiosis and recombination of gametes during reproduction.  Point mutations occur when a different nucleic acid is substituted during DNA replication. This small change can code for a different amino acid when placed in the eventual protein produced from the DNA-RNA-protein process.  This can lead to a difference in some biochemical process that the original protein, acting as an enzyme, would affect.  It may affect drastic and very visible differences in the plant but in most cases, it is insignificant and not noticed by most observers. Point mutations are probably the most common cause of mutations but a few other more drastic causes can be related to major errors in DNA duplication as part of meiosis. It is common, however for some breakage in one of the pair allowing a segment to be exchanged with a portion of the member of that pair.  This process, called a crossover, is utilized by corn breeders in backcrossing procedures in which the objective is to cross a specific gene, such as a BT gene, into a desirable inbred without disturbing most of the genetics of the original inbred. Backcrossing in a gene, long used as a breeding procedure before use of GMOs, has been relatively successful in recovering the essential genetics of the original inbred but now with the desired gene such as the Ht gene for resistance to the fungus causing northern leaf blight or wx (waxy corn gene).

​Corn growth is done by enlargement of cells, often with the assistance of water pressure before the cell walls have solidified and by cell duplication.  Cell division is is a remarkable process that first requires the duplication of the chromosomes within the nucleus by a process called mitosis.  This delicate process should result in exact duplication of each chromosome pair, followed by new membranes forming around each set of 10 chromosomes.  This process is called mitosis is nicely described and illustrated in https://www.nature.com/scitable/topicpage/mitosis-and-cell-division-205.
 
This process is not mutation proof.  During the chromosome duplication process a segment of a DNA string may not reattach properly, resulting in an important expression of a trait to be changed or missing in the resulting cells.  Because this new cell and other cells duplicated from this mutated cell will likely contain the same mutation it may become evident to our eyes like a long non- pigmented streak in a corn leaf.  Most such mutations are hidden from our eyes and have minor affect on the plant performance.
 
Mitosis in a corn plant occurs mostly in the root and shoot tips from the embryo stage completion of shoot and tassel formation.  Another remarkable process occurring mostly out of site in the corn field.

​Articles about the recent outbreak of the Covid19 often includes mention that this simple virus has its 15 genes tied to it’s mRNA.  I am pretty sure that RNA was not mentioned (or I wasn’t paying attention) in my college genetics course in 1960.  I recall teaching my secondary class in biology in 1963- and 1964 in Sarawak that the genes in the nucleus of the cell controlled the cell biology, but I could not explain how.  I became fascinated to learn of DNA and its interaction with mRNA and protein manufacturing in cells.  Lots has been learned since the 60’s and there is a lot more to come. Certainly, most of the younger readers of this blog have been educated on this but, as a review for some of the ‘oldies’ I will try to summarize.

Corn genes, like in all plants and animals, are organized in the nucleus in chromosomes.  Corn has 10 pairs and humans have 23 pairs.  Each chromosome of the diploid part has one strand of DNA from the male parent and one from the female parent.  Corn has 30,000 to 40,000 genes spread across the 10 chromosomes.  DNA code are a string of nucleic bases (adenine, cytosine quinine and thymine) attached to a sugar (deoxyribose).  The sequence of these four becomes a significant factor in the ultimate expression the gene.

When called upon to transcribe the gene, a molecule called RNA (ribonucleic acid) is constructed by transcribing the DNA of the gene, using its codes for the sequence of nucleic bases.  The gene has a start and stop code to stop the transcription.  This newly formed RNA molecule, now called mRNA (messenger RNA) migrates through the nuclear membrane into the cytoplasm of the cell.

mRNA enters the cell ribosome, a small organelle of the cell.  The mRNA now become translation RNA (tRNA). Each set of 3 consecutive nucleic baes signal for a specific amino acid to be attached within the ribosome creating a long string which becomes a protein.  The specific arrangement of the aminos acids dictate the potential action of the protein as an enzyme in cell activity.  This enzymatic activity becomes most important determinant of the cells, and therefore the organism’s, behavior.

Many viruses, such as the one causing Covid-19, have relatively few genes, no DNA, that is coded to invade human cells, codes for the ribosome to produce the protein that allows formation of the virus spike to penetrate the cell.  The host cell thus produces more of the virus.

The response of the corn plant to its environment is ultimately tied to those small DNA codes in every living cell of the corn plant.

​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.