The English often call a fruit seed other names, like pip. A large pit could be called a stone.  Avocado usually has a seed, and if not it turns out to be a small fruit, called a "cuke".  Well that's a different story.  Sometimes little hard stones form in the flesh that are unrelated to germination.  These stones are unpredictable and uncommon. A friend has said that if an avocado gives you a stone, turn it into a pearl.  These stones are that rare.  Art Schroeder from UCLA described them without much attribution to their cause, but gave them a good name - sclerocarpelosis.  You can read his description in the 1981 California Avocado Society Yearbook which is available at Avocado Source:

http://www.avocadosource.com/CAS_Yearbooks/CAS_65_1981/CAS_1981_PG_125-132.pdf

Sclerocarpelosis in Avocado Fruit
C. A. Schroeder
Department of Biology, University of California, Los Angeles.

A rather unusual case of malformation in avocado fruit has been noted recently. The
aberrant tissue structure is not detectable from external examination of the fruit. Upon
cutting the mature or nearly mature fruit, the aberrant tissue becomes evident in the
form of a stony layer of various degrees of development located in the otherwise soft
fleshy pericarp wall. A tentative name of sclerocarpelosis is used to describe this
condition. The term sclero refers to hardness of the stone cells, or sclereids, which are
the basic structural elements involved. Carpel refers to the fruit wall, and osis implies a
disease or disturbance of the plant or plant tissue.

The fruit is sometimes affected to an extent that it becomes inedible. Still other fruits
may contain small clusters of stone cells which would not be detected even if eaten.
Extremely affected fruits can have a stony layer 1 to 5 mm in thickness completely
surrounding the seed. This structure is suggestive in many ways of a peach pit which
envelops the peach seed.

The affected fruits have been observed on several trees at various locations in a very
large (1300 acres) avocado planting in Orange County, California. The orchards
involved are situated on gently rolling hills. The major portion of the trees bearing
abnormal fruits are found in low elevations or "pockets" where the effects of local
radiation frosts were observed to severely affect the trees during the 1979-80 winter
season. Many of the trees exhibited responses to frost injury such as unusual resprouts
and development of main structural limbs at points near the soil, severe bark and
sunburn injury due to unusual exposure as the result of loss of leaf canopy by frost, and
a general weakened appearance of the entire tree in comparison with nearby unaffected
trees.

Mandarins, also known as “zipper skins” and “easy peelers” can have very fragile peels/skins/rinds/exocarp that make them easily subject to more damage than most oranges and lemons. Some are a bit tougher skinned than others, but some are so fragile that any rough handling often prevents them from going through conventional packing operations.

These skins were recently put to the test in the recent fires in Ojai. There was a mix of different varieties - ‘Pixie', ‘Gold Nugget', ‘W. Murcott', ‘Yosemite Gold', ‘Tahoe Gold' and others. Some of them were more sensitive than others, some were closer to the fire, all were affected by smoke to some degree. In Matilija Canyon where smoke was present for many more days than in the east of the Ojai Valley and possibly more ash, the trees have started flowering sooner. That might be temperature difference, either cooler or warmer, so it is hard to say how much effect the smoke has had versus, the ash and/or heat. Smoke has many different gasses in it, one of which is ethylene which is a naturally occurring ripening agent. Smoke not only has gasses, but it occludes the sun so less or more or altered light might have an effect on these fruit. It's not a controlled experiment, so some little scientist is going to have to come along and wriggle out these different effects. Whatever. Fire and smoke have an effect on mandarins as we have seen in other crops, such as cherimoya, avocados and other citrus.

Heat damage. Fruit facing the fire.

Ash effects on fruit coloring. Fruit was covered with ash for several days until rain washed it off. Might be a pH effect (ash is alkaline), temperature effect, uneven light radiation, or other…….

Same sort of uneven coloring, that actually looks like an ashy color, but the ash has washed off the cluster by rain

And here's something interesting where fruit facing the fire is much lighter colored than fruit facing away from the fire. Here are two pieces of fruit, one from the side directly facing the fire, and the other from the other side of the tree. The side of that fruit facing the fire was also lighter colored. So, it had an effect through the canopy (small tree). The canopy was otherwise intact, unaffected heat or flames.

Oh yeah, and there is the characteristic fruit drop from either the heat, smoke gases, water stress or ….

And then there's the fruit that looks like it had actual embers on the skin.

If the tree survives and keeps its green leaves, sometimes the fruit is affected in ways that don't appear for a while. The peel may be affected, but in many cases the fruit is just as sweet as it could be. It just looks terrible. That might even be a selling point. "Here have a wonderous piece of history that braved the horror of the Ojai fires."

There have been some complaints about satsuma mandarin fruit having problems. These are prone to a rind/skin/peel breakdown when the fruit is not picked promptly. It's not clear what the cause is - wet winter, warm winter - but it is less of a problem if the fruit is picked when it is mature. A lot of the time in southern California, satsumas will develop good flavor and sweetness, but for lack of cool weather, they don't turn bright orange, a hallmark of the fruit. So growers will leave the fruit on longer, hoping for color, but the fruit becomes over mature, and more susceptible to breakdown. This weakening of the peel then opens it up to infection by fungi, such as Alternaria. In warm winters, the peel matures more rapidly and is more susceptible. Early maturing varieties like ‘Okitsuwase' are especially prone to breakdown later in the season, since their rind matures earlier. They end up being a mess, as can be seen in the photo below.

Navels can have a similar problem in these winters with erratic rainfall. Common wisdom is you don't irrigate in the winter, right? Wrong. With no, low and widely spaced rain events, the tree roots dry out, and rewet with rain. Navels are building their sugar in the winter and they become suction balls for water as the sugar increases. The fruit will continue to grow as the tree takes up water. When the roots run out of water, and then are suddenly rewetted during this period, the fruit can suck up water so rapidly that the skin cant expand fast enough and will split. So this is what happens with uneven irrigation or rainfall this time of year.  One of those abiotic problems in citrus.

Diseases, disorders and other plant problems are critical concerns for the wholesale nursery.  These include biotic problems — caused by living organisms such as pathogens, nematodes, and insects and other arthropods — as well as abiotic problems — caused by factors such as temperature and moisture extremes, mechanical damage, chemicals, 
nutrient deficiencies or excesses, salt damage and other environmental factors. Many plant problems, especially biotic problems, if not recognized and controlled early in their development, can result in significant economic damage for the producer.  Therefore, timely and accurate diagnoses are required so that appropriate pest and disease 
management options and other corrective measures can be implemented.

Definition of Plant Diagnosis and Steps

Diagnosis is the science and art of identifying the agent or cause of the problem under investigation.  When one renders a diagnosis, one has collected all available information, clues and observations and then arrives at an informed conclusion as to the causal factor(s).  Hence, plant problem diagnosis is an investigative, problem-solving process that involves the following steps:

1. Ask and answer the appropriate questions to define the problem and 
   obtain information that is relevant to the case under investigation.

1. Conduct a detailed, thorough examination of the plants and production areas.

1. Use appropriate field diagnostic kits and lab tests to obtain clinical information on possible causal agents and factors.

1. Compile all the collected information and consult additional resources and references. 

1. Finally, make an informed diagnosis.

Throughout this process compile all notes, observations, maps, laboratory results, photographs and other information.  This compilation will be the information base for the present diagnosis and can also be a useful resource for future diagnostic cases.  Keep an open mind as the information is analyzed and do not make unwarranted assumptions.
 

Distinguishing Abiotic and Biotic Problems

The first step is to determine whether the problem is caused by an infectious agent, and this can be difficult. Plant symptoms caused by biotic factors such as infectious diseases and arthropod pests are oftensimilar to damage caused by other factors.  Leaf spots, chlorosis, blights, deformities, defoliation, wilting, stunting and plant death can
be common symptoms of both biotic and abiotic problems; therefore, the presence of these symptoms does not necessarily mean the problem is a disease. Some general guidelines for distinguishing abiotic and biotic 
problems follow and are summarized in table 1.

Biotic problems. Identifying biotic problems is sometimes facilitated if signs of a pathogen, primarily the growth of a fungus, are present.  The most obvious examples of such signs are the mycelium and spores produced by rusts and powdery and downy mildews.  However, in other cases nonpathogenic fungican grow on top of damaged plant tissues and appear to be signs of a pathogen, resulting in possible misdiagnoses.

Biotic problems often affect one species or cultivar of the same age and typically are initially observed in random or irregular locations; symptoms appear at varying times, and severity varies among affected plants. Biotic problems are infectious, spreading when environmental conditions are favorable, and may be associated with pests that have affected the crop. This infectious aspect is important, as biotic diseases will many times be progressive and continue to affect 
additional tissues and more plants.

Abiotic problems. In contrast to biotic factors, abiotic problems often affect several species or plants of various ages; typically, damage is relatively uniform, doesn't spread and is often not progressive. Abiotic problems are not associated with pests. They are often caused by a single incident and are related to environmental or physical factors or cultural practices. Once the responsible factor has dissipated and is no longer affecting the plant, the plant may grow out of the problem and develop new, normal appearing foliage.

Diagnosing Biotic Problems

Infectious diseases. To confirm if a problem is caused by a pathogenic fungus, bacterium, nematode, or virus, it is often necessary to have symptomatic tissues analyzed by a trained horticulturalist or plant pathologist.  Such experts will attempt to microscopically observe the agent and recover it, if culturable, through isolation procedures.  Lab analysis is particularly important to determine if multiple pathogens are infecting the plant. A downside is that obtaining a diagnosis from lab analysis is not a fast process. However, quick test kits (fig. 1A) are available that can be used to rapidly identify many common diseases in the field.

                                                        A                       B

Fig.1. Diagnosing biotic 
problems. Plant pathogens can sometimes be rapidly diagnosed using 
commercially available quick tests, such as these test strips for 
viruses (A). Arthropod pests such as Cuban laurel thrips (shown here on Ficus) cause feeding damage, which can help in pest identification (B). Photos: S.T. Koike (A), J. K. Clark (B).

It is worthwhile to emphasize that diagnosing plant diseases requirescareful examination of the entire plant specimen.  Symptoms on leaves, stems, or other above ground plant parts might lead one to suspect that afoliar pathogen is involved.  However, these symptoms could also resultif the roots are diseased.  Therefore, it is important to conduct a 
complete examination of the symptomatic plant. 

Because biotic diseases are caused by living microorganisms, the collecting and handling of samples is particularly critical.  Samples that are stored for too long a time after collecting or that are allowedto dry out or become hot (if left inside a vehicle, for example) will sometimes cause the pathogen in the sample to die, making pathogen recovery and identification impossible.  Plants that have been diseased for a long time and that are in the late stages of disease development will often be colonized by nonpathogenic saprophytic organisms.  If these tissues are collected, it will be difficult to recover the primarypathogen of concern because of the presence of these secondary decay organisms.  Root samples should be collected carefully as diseased rootsare sometimes difficult to dig out of the potting mix or soil, are 
usually colonized by the pathogen as well as secondary agents, and are very sensitive to high temperatures and drying conditions.

Arthropod and other invertebrate pests. Insects,mites, slugs and snails cause damage while feeding on the plant (fig. 1B).  Feeding damage is usually associated by the type of feeding characteristics and mouthparts of the insect or pest.  For example, mites and insects such as whiteflies, aphids and mealybugs have tubular sucking mouthparts that suck plant fluids, causing buds, leaves, or flowers to discolor, distort, wilt, or drop. Thrips have rasping mouthparts that result in dried out, bleached plant tissue. Caterpillars, weevils, snails and slugs have chewing mouthparts that 
make holes and cuts in foliage or flowers.  They can also prune plant parts and sometimes consume entire plants.

If present, these pests are visible with the naked eye, a 10 X hand lens, or stereomicroscope, all depending upon their size.   An assessment of whether the identified arthropod or invertebrate matches the plant damage it is associated with must be determined.  Sometimes the identified arthropod or invertebrate may not be the sole problem or 
could, in fact, be a beneficial organism or insignificant pest.

Aphids, whiteflies, thrips, leafhoppers and some other insects that suck plant juices may vector pathogens such as viruses and phytoplasmas (and to a lesser extent fungi and bacteria).  They can feed on infected plants, acquire the pathogen, feed on healthy host plants and transmit the pathogen to the new host.  The insects do not necessarily have to bepresent in large numbers to cause a significant disease outbreak.  The insect vectors are not always present at the same time the disease symptoms are being expressed.

The excrement and byproducts from these pests can also provide clues that the pests have been or are actively present.  Caterpillars and other chewing pests produce dark excrement or droppings.  Greenhouse thrips and plant bugs produce dark, watery, or varnish-like droppings onfoliage.  Aphids, whiteflies, soft scales, and some other sap-sucking insects excrete excess plant fluids as honeydew, a sticky sap, which provides a medium for the growth of sooty mold.

Diagnosing Abiotic Problems

Nutrient deficiencies and toxicities. Nutrientdeficiencies and toxicities reduce shoot growth and leaf size, cause leaf chlorosis (fig.2A), necrosis and dieback of plant parts. However, nutrient deficiencies cannot be reliably diagnosed on the basis of symptoms alone because numerous other plant problems can produce similarsymptoms.  There are general symptoms that can be expressed by deficiencies of nutrients but usually leaf and/or soil samples are 
needed to confirm the problem.

                                                                 A                       B
Fig. 2. Examples of abiotic problems. Iron deficiency on sweet gum (Liquidambar styracifolia) showing interveinal chlorosis (A). Chorotic spots on Hedera caused by a miticide application at a higher dosage rate than specified on the pesticide label (B). Photos: E. Martin (A), S. A. Tjosvold (B).

Herbicide, insecticide and fungicide phytotoxicity. Herbicidesused to control weeds in crops or in non-cropped areas sometimes injureornamental crops when they are not used in accordance with label instructions. Examples include when an herbicide is used in or around sensitive non-target crops, when an herbicide rate is increased above tolerable limits, or when an applicator makes a careless application.  By understanding the mode of action of the herbicide, one can determine if the symptom fits an herbicide application. Herbicide detection in affected plants is possible with the help of a specialized laboratory but the analysis can be expensive. To minimize the cost of testing, the laboratory will need to know the suspected herbicide or its chemical group to narrow the analysis. Pesticides and fungicides occasionally cause obvious plant damage. 

Symptoms can vary widely.  Generally, flower petals are more susceptible to damage from pesticide applications than are leaves.  The younger and more tender the leaves the more susceptible they are to pesticide applications.  Hot weather can exacerbate the damage the chemicals cause.  Pesticides that have systemic action can have a more profound effect.  Some active ingredients can adversely affect the photosynthetic mechanism or other physiological processes and can resulti n a general leaf chlorosis, interveinal chlorosis, leaf curling and stunting.  Emulsifiable concentrate (EC) formulations, soaps and oils can adversely affect the waxy surface layer that protects the leaf from desiccation.  Applications with these products can result in the loss ofthe shiny appearance of a leaf, leaf spotting and necrosis.  Pesticidesapplied as soil drenches can cause poor germination, seedling death, or
distorted plant growth.

Check label precautions against use on certain species. Make sure thepesticide is not applied more frequently or at a higher rate (fig. 2B) than recommended, or that the pesticide is not mixed with incompatible pesticides.  When in doubt as to whether the plant species is sensitive to the pesticide, spray a few plants and observe them for several days to a week for any signs of damage before spraying any more of the plants. 

Physiological and Genetic Disorders

There are numerous disorders that can occur because of environmental extremes — too much or too little of an environmental element such as light, temperature, water, or wind.  Sunburn is damage to foliage and other herbaceous plant parts caused by a combination of too much light and heat and insufficient moisture.  A yellow or brown area develops on foliage, which then dies beginning in areas between the veins.  Sunscaldis damage to bark caused by excessive light or heat.  Damaged bark becomes cracked and sunken.  Frost damage causes shoots, buds and 
flowers to curl, turn brown or black and die.  Hailstones injure leaves,twigs, and in serious cases even the bark.  Chilling damage in sensitive plants can cause wilting of foliage and flowers and development of dark water-soaked spots on leaves that can eventually turn light brown or bleached, and die.  Physical and mechanical injury can occur when plants are mishandled during transport or routine cultural practices.  Wounds might serve as entry sites for plant pathogens and can attract boring insects to woody stems.

In closed environments such as greenhouses and nursery storage areas,plants can be exposed to toxic levels of ethylene gas. Sources of ethylene include improperly functioning or unvented greenhouse heaters; exhaust from engines of forklifts and vehicles; cigarette smoke; damaged, decaying, or dying plants; and ripe or decaying fruit.  Toxic levels of ethylene gas can cause premature abscission of flower buds, petals (fig. 3) and leaves.  Other symptoms include wilted flowers, chlorosis, twisted growth or downward bending of stems and leaves and undersized or narrow leaves.

                                                        A                       B

Fig. 3. Poor air quality can 
lead to physiological disorders. Shattering (petal drop) on geranium was
caused by plant exposure to low levels of ethylene in the greenhouse or
during postharvest storage (A). Yellowish and brownish patches on 
Japanese maple leaves are damage caused by ozone (B), an outdoor air 
pollutant. Photos: J. K. Clark.

Outdoors, exposure of nursery plants to air pollutant gases such as ozone (fig. 3), carbon monoxide, nitrous oxides and sulfur dioxide can cause damage.  Typical symptoms vary widely, but include slow growth anddiscolored, dying, or prematurely dropping foliage.  Damage is often found where plants are located near sources of polluted air such as near
freeways or industries or where weather and topography concentrate the pollutants.

Sometimes plants or plant shoots exhibit an unusual and sudden changeof color producing discrete markings of variegation.  For example, a plant with entirely green leaves suddenly produces a shoot that has leaves with edges lacking green pigment, stripes, or blotches.  A new shoot such as this is probably a chimera (fig. 4).  It is produced when a genetic mutation occurs in a specific region of the growing tip resulting in a section with genetically different cells.  The ostensible result of the genetic change is dependent on the arrangement of the genetically different cells in the shoot tip and their expression.  This can lead to sometimes bizarre variegation forms or sometimes forms thatare quite desirable.  Sometimes variegation can be caused by viruses.  Viruses usually cause non-uniform chlorosis, such as mosaics, while 
chimeras usually produce patterned forms such as variegation of color onleaf margins, stripes, or complete loss of pigment. Some viroids may also cause bleaching of pigments in leaves; such symptoms, however, are generally produced throughout the plant and are not restricted to a single shoot.  Some nutrient disorders can cause variegation but these disorders usually do not arise from a specific shoot as with chimeras.

Fig. 4. Genetic disorder. 
Growing points with variegated leaves can sometimes arise spontaneously 
from some species such as this Origanum. Genetic variants such as this are sometimes confused with plants with virus disease or nutrient deficiency symptoms. Photo: S. A. Tjosvold.

Steve Tjosvold is Environmental Horticulture Advisor and 
Steve Koike is Plant Pathology Farm Advisor, UC Cooperative Extension, 
Santa Cruz and Monterey counties.

This article was condensed from: Diagnosing Plant 
Problems, Chapter 11.  In Newman, J. (ed) Container Nursery Production 
and Business Management. Univ. of Calif. Agric. and Nat. Resources. 
Publication 3540. Richmond, CA.

References

Boxer P, Sandmann G. 1989. Target sites of herbicide action. Boca Raton, FL: CRC Press.

Costello L, Perry E, Matheny N, Henry M, Geisel P. 2003. Abiotic 
disorders of landscape plants: A diagnostic guide. Oakland: University 
of California Division of Agriculture and Natural Resources Publication 
3420.

Derr JF, Appleton BL. 1988. Herbicide injury to trees and shrubs: A 
pictorial guide to symptom diagnosis. Virginia Beach, VA: Blue Crab 
Press.

Dreistadt SH. 2001. Integrated pest management for floriculture and 
nurseries. Oakland: University of California Division of Agriculture and
Natural Resources Publication 3402.

Eagle, DJ. 1981. Diagnosis of herbicide damage to crops. New York, NY: Chemical Publishing Co.

Grogan RG. 1981. The science and art of plant disease diagnosis. Annual Review of Phytopathology 19:333–351.

Ratzinger EJ, Mallory-Smith C. 1997. Classification of herbicides by 
the site of action for weed resistance management strategies. Weed 
Technology 11:384–393.

Schubert TS, Breman LL. 1988. Basic concepts of plant disease and how
to collect a sample for disease diagnosis. Plant Pathology Circular No.
307. Florida Department of Agriculture and Consumer Services, Plant 
Pathology Circular No. 307.

Sharma MP. 1986. Recognizing herbicide action and injury. Alberta Environmental Centre, Alberta Agriculture. Agdex 641–647.

Shurtleff  MC, Averre  CW. 1997. The plant disease clinic and field 
diagnosis of abiotic diseases. St. Paul, MN: American Phytopathological 
Society Press.

Stewart TM, Galea VJ. 2006. Approaches to training practitioners in 
the art and science of plant disease diagnosis. Plant Disease 
90:539–547.

Tickes B, Cudney D, and Elmore C. 1996. Herbicide injury symptoms. 
Tucson, AZ: University of Arizona Cooperative Extension Publication No. 
195021.