2024 Plant Disease Issues to Watch Out For: Seed and Seedling Issues

Unfortunately, plant diseases that occur early in the growing season can be difficult to diagnose.  At this stage the focus is typically on issues affecting seed germination, emergence, stand establishment, and general crop appearance.  Plant diseases such as seed rots, damping off, wirestem, and seedling blights are the main diseases that can be associated with early season issues.  It is important to recognize that these common names may be used interchangeably and often describe any symptom from seed decay to seedling death.  It may be useful to think of early season disease issues in terms of the seedling disease complex, which consists of seed rot (various agents) damping off (Pythium spp.), seedling blight (Rhizoctonia solani and Fusarium spp.), and wirestem (Rhizoctonia solani).  Symptoms caused by these diseases can be similar and it is difficult to identify causal pathogens in field; this necessitates the need for timely collection of plant samples and assessment by a diagnostic laboratory. 

  

Impacts of early season plant disease issues: 

·       Reduced seed germination, poor emergence, and non-uniform/unthrifty stand establishment;

o   Poor stands can make it more difficult for the crop to compete with weeds;

§  Herbicide performance may suffer due to reduced crop competition and because significant weed populations develop there may be an increased risk of herbicide resistance;

o   Non-uniform crop development can make it challenging to schedule subsequent herbicide, fungicide and insecticide applications, especially where they are growth stage dependent;

o   Uneven crop development can also complicate harvesting operations later in the season when several growth stages are present;

·       Overall crop performance and yield are directly or indirectly compromised.

  

General descriptions of early season plant disease issues aka the seedling disease complex: 

·       Seed rots;

o   Seed doesn’t germinate, with subsequent softening and disintegration of seed and discolouration (e.g. blackish or brownish);

o   Can result from pathogens (e.g. Pythium spp.) or saprophytic or opportunistic fungi and bacteria;

§  Note the seed may already be dead due to factors related to harvest and subsequent grain handling;

·       Seedling blight;

o   General and rapid killing of the entire seedling or particular tissues (e.g. roots);

§  Can be before or after emergence;

·       Damping off;

o   Destruction of seedlings close to soil surface;

§  Seedlings topple over at soil line;

§  May have slimy, blackish, rotted appearance;

o   Causes decay or watery rot of fine feeder roots;

o   Sudden wilting and death before or after emergence;

§  Plant killed prior to emergence versus after;

·       Pre- vs. post-emergence damping off.

·       Wirestem (mainly in canola);

o   Symptoms first appear water-soaked;

§  Develop into sunken reddish-brown lesions;

§  Infections typically remain firm and “dry”;

o   More of a “pinching off” along the hypocotyl;

§  May extend up to the cotyledons and down to the roots;

·       Root rots;

o   Softening, discolouration, and disintegration of root tissues;

§  Early season issues can result in poor stand establishment;

§  Mid to late season root rot issues;

·       Early infections can then be followed by progression of root rot pathogens on root and crown tissues;

·       The impact on yield is exacerbated by dry conditions during the grain filling period;

o   Remaining healthy root tissues (if present) are unable to keep up with water and nutrient demands.

  

Key risk factors for seed and seedling diseases include: 

·       Tight or non-existent rotations, which facilitate the build up of infected crop residues and soil-borne survival structures;

·       The host range of some pathogens can be quite wide depending on crop species.  For example, various Fusarium spp. may attack a range of pulse crops as well as canola, while Fusarium graminearum is a concern for various cereal crops; 

·       Deep seeding prolongs exposure to soil-borne pathogens, while also resulting in stressed seedlings that may increase risk;

·       Seed-borne pathogens are a key concern early in the season with cereal pathogens such as Fusarium graminearum and the spot blotch pathogen, Cochliobolus sativus being particularly damaging at moderate to high infection levels (e.g. well over 10% seed infection);

o   Other seed-borne issues may result in a source of disease affecting crop productivity and grain quality later on in the season;

o   The cereal smuts and bunts are classical examples of this, while net-form net blotch seed infection in barley can result in leaf infections and a source of inoculum for the remainder of the season;

·       Nutrient imbalances may cause issues, such as browning root rot in barley due to Pythium spp., which is exacerbated by phosphorus deficiency.  Fortunately, routine use of phosphorus fertilizers has reduced the risk over the last 50-75 years;

·       Prolonged exposure to wet soil conditions with moderate temperatures.  Cooler temperatures are often blamed for an increased risk of seed and seedling diseases, but the optimal temperature range for many seed and seedling pathogens is 15-25^oC; 

o   Note cool dry conditions may increase the risk of dry seed rot in cereals caused by Penicillium and Aspergillus spp.;

·       Damaged or highly weathered seed can increase the risk of seed rot and damping off;

o   Cracking of the seed coat due to mechanical damage can directly compromise seed embryo viability or as the seed takes on water it may leak sugars that attract pathogens;

o   Weathering of plants around harvest or storage issues may lead to poor seed and seedling vigour which can slow germination and emergence, thus increasing risk. 

When scouting for early season seed and seedling disease issues, symptoms may be scattered throughout the field or may be associated with field knolls or depressions.  With suspected issues it is very important to dig the seed and seedlings up and look at below-ground plant tissues.  Above-ground plant symptoms can be similar to other issues related to soil nutrient deficiencies, water-logged soils, herbicide residues and even insect damage.  Saprophytic microorganisms or opportunistic pathogens will often colonize insect- or abiotic stress damaged tissues resulting in brownish-blackish discolouration of below-ground seedling tissues.  Don’t wait too long to scout as secondary infections by saprophytes or opportunistic pathogens may mask the real cause of emergence and stand establishment issues.

  

Stand establishment issues can also be related to: 

·       Poor seed quality due to mechanical damage during harvest and grain handling/storage or excessive weathering of the crop prior to harvest.  Note this may be the primary reason for problems, while weak/opportunistic plant pathogens may take advantage of these non-disease related issues;

·       Herbicide residue issues, or for some crops (e.g. pulses) preharvest glyphosate application, especially when applied too early;

·       Deep seeding;

·       Poor seedbed preparation, seeder/opener issues and lumpy soil resulting in poor seed to soil contact;

·       Excessively dry soil conditions, especially under conventional tillage;

·       Too much seed-placed fertilizer or poor separation of seed and fertilizer at the time of seeding;

·       Insect damage;

·       Pinching off of stems at the soil surface may be caused by other factors;

o   High winds;

o   Heat canker;

o   Frost canker.

  

Management of early season seed and seedling issues:`

 

• Try to use rotations of at least two years between host crops to reduce the build up of infected crop residues and soil-borne survival structures;
• Watch out for seed and seedling disease issues where the causal agent attacks a range of crop species;
• For example, various Fusarium spp. may attack a range of pulse crops as well as canola, while Fusarium graminearum is a concern for various cereal crops; 
• Monitor seed quality and use seed with high germination and vigour and no to low levels of seed-borne pathogens;
• Be mindful that combine settings and weather conditions may affect seed quality;
• Low seed moisture at harvest together with increased combine cylinder and wind speed can increase the risk of mechanical damage;
• Grain handling/conveying equipment may be a factor; for some crop types, e.g. pulses, it is recommended to use a belt-type versus screw-type auger;
• Excessive post harvest processing of grain can damage seed, e.g. hulless barley and removal of hulls;
• Dry seed and increased wind speed with larger seeders may increase mechanical damage and decrease seed germination and vigour, especially in pulses;
• Avoid seed with elevated levels of seed-borne pathogens;
• Seed-borne Fusarium graminearum and the spot blotch pathogen Cochliobolus sativus are particularly aggressive on cereals;
• Seed-to-seedling transmission of some pathogens can result in a source of disease during subsequent crop development;
• E.g. cereal smuts and bunts, net-form net blotch and spot blotch in barley, and the mycosphaerella/ascochyta complex in pulses;
• Delaying seeding until soil temperatures are warmer (15-25^oC) may increase the risk for some pathogen species, e.g. Fusarium graminearum;
• Seed treatments can help to limit risk from seed- and soil-borne pathogens;
• Use good application technology to ensure even seed coverage and choose seed treatments that are effective against the disease(s) you are dealing with;
• Consider a small test of seed germination and emergence in soil collected from the field(s) in which you plan to plant a given crop;
• Use treated and untreated seed from the same lot, in the same soil;
• Note seed testing companies may also provide testing of treated and untreated seed and may actually do the treating of the seed you send in and with the treatment of your choice;
• Seed treatments may not compensate for very high levels of seed-borne disease and it may be beneficial to look at a different seed lot;
• Seed treatments may be of limited benefit if seed germination and vigour problems are due to non-disease issues;
• Seed shallow if moisture conditions permit and ensure balanced soil fertility levels, limit seed-placed fertilizer, especially for nitrogen, and ensure good seed and fertilizer separation at the time of seeding;
• Preharvest application of products like glyphosate may comprise subsequent seed germination and vigour, especially for pulses when applied too early.

 

A few key links to aid in the management to seed and seedling diseases include: 

Saskatchewan Ministry of Agriculture: 

1. Put your best crop forward by knowing your seed-borne disease risk. (M. Hladun; released March 2024; URL retrieved 2024May29). 

2. Seed quality and seed-borne diseases of cereal crops. (URL retrieved 2024May29).  

Saskatchewan Pulse Growers: 

3. Link opens sub-directory then search key word of "seeding"  (URL retrieved 2024May31). 

Canola Council of Canada: 

4. Seedling disease management to improve canola plant establishment. (Canola Research Hub; released May 13, 2022; URL retrieved 2024May29). 

5. Seedling disease complex. (Canola Encyclopedia; released 2020; URL retrieved 2024May29).  

Manitoba Crop Alliance: 

6. Seed treatments in wheat, barley and flax: What they are, how they work and when they should be used. (URL retrieved 2024May29).  

Manitoba Pulse and Soybean Growers: 

7. Minimizing air seeder damage to field peas. (Laura Schmidt, released 2022; URL retrieved 2024May29).   

8. Soybean seed treatments: Assessing your risk. (No author cited; Updated 2022; URL retrieved 2024May29).   

Crop Protection Network:

9. An overview of soybean seedling diseases. (published 2020Mar01; doi.org/10.31274/cpn-20190620-023; URL retrieved 2024May29). 

10. Scouting for soybean seed diseases. (published 2016Nov07; doi.org/10.31274/cpn-20190620-018; URL retrieved 2024May29).   

Montana State University: 

11. Small grain seed treatment guide. (A. Dryer, J. Johnston, C. Tharp, U. Mckelvy, T., Lane, J. Fullbright, J. Rupp; updated May 2022; URL retrieved 2024May29).  

Agriculture and Horticulture Development Board AHDB (note this is a UK site, but some concepts and recommendations are relevant for Prairie cereal crops): 

12. Seedborne diseases of cereals: Tests and thresholds. (No author cited; Publication date not available; URL retrieved 2024May29).  

Examples of disease related seed and seedling issues:

Examples of non-disease related seed and seedling issues:

Compiled by T.K. Turkington (AAFC Lacombe), Mike Harding (AAI Brooks), Alireza Akhavan (Sask. Ag.), David Kaminski (Manitoba Ag.), Syama Chatterton (AAFC Lethbridge), Michelle Hubbard (AAFC Swift Current), and Sabine Banniza (U of Saskatchewan).

2024 Cereal Rust Risk Report (May 20-26, 2024)

The third weekly Prairie wind trajectory cereal rust risk report for 2024 is available for download now at the following link: May 20-26, 2024 report.  

As of the week of May 20-26, 2024, the overall Prairie cereal rust risk assessment and need for in-crop scouting is as follows:

Pacific Northwest – There were low numbers of reverse wind trajectories that passed over the PNW region and into the Prairies, while stripe rust development is continuing in the PNW.  Prairie winter wheat crops are progressing into the tillering and stem elongation stages, while much of the spring wheat crop has now been seeded or will be seeded soon.  Overall, as of May 26, 2024, the risk of stripe rust appearance from the PNW is relatively low and scouting for this disease in the Prairie region is generally not urgent.

Texas-Oklahoma corridor – There was only one reverse wind trajectory that passed over the TX/OK region and into the Prairies from May 20-26, 2024, while stripe and leaf rust development are continuing, although levels appear to be generally low, especially in commercial winter wheat fields in the TX/OK region.  As Texas and Kansas winter wheat crops move towards maturity and harvest, they will no longer represent a source of rust inoculum for the Prairie region.  Prairie winter wheat crops are progressing into the tillering and stem elongation stages, while much of the spring wheat crop has now been seeded or will be soon.  Overall, as of May 26, 2024, the risk of stem, leaf, stripe, and crown rust appearance from the Texas-Oklahoma corridor is relatively low and scouting for these diseases in the Prairie region is not urgent.

 

Kansas-Nebraska corridor – There was a small number of reverse wind trajectories that passed over the KS/NE region and into the Prairies from May 20-26, 2024, while stripe and leaf rust (Kansas) development are continuing in commercial winter wheat fields in this region.  Prairie winter wheat crops are moving into the tillering to stem elongation stages, while much of the spring wheat crop has now been seeded or will be soon.  Overall, as of May 26, 2024, the risk of stem, leaf, stripe, and crown rust appearance from the Kansas-Nebraska corridor is relatively low and scouting for these diseases in the Prairies is not urgent.

The early and widespread appearance of stripe rust in the PNW, TX/OK and KS/NE regions is still concerning, while the recent stripe rust observations from South Dakota and Wisconsin bring the stripe rust issue ever closer to the Prairies, especially the central to eastern region.  Over the next 2-4 weeks if favourable weather conditions (especially more rainfall) occur in these source US regions, further rust development could occur.  This would result in more rust spores being available to be blown into the Prairie region, as well as more northerly rust development into the Dakotas and Minnesota/Wisconsin.  Currently, Prairie winter wheat fields are most at risk, but fortunately most current winter wheat varieties have intermediate to high levels of resistance, although AC Radiant, CDC Buteo, AAC Elevate, Broadview, and CDC Falcon are rated as susceptible (https://www.seed.ab.ca/variety-data/cereals/; https://saskseed.ca/wp-content/uploads/2020/12/2024-Varieties-of-Grain-Crops.pdf; https://www.seedmb.ca/pdf-editions-and-separate-section-pdfs/).  In terms of spring wheat (various classes) and durum the following varieties are either an S or MS: 5700PR, AAC Cameron, AAC Iceberg, AAC Tisdale, AAC Tomkins, AAC Warman, AAC Whitefox, AC Foremost , Cardale, CDC Abound, CDC Adamant, CDC Flare, CDC Pilar, Faller, Prosper, SY Natron, SY Rorke, SY Torach, and Unity.  If you are growing a stripe rust susceptible variety, it will be important to keep an eye on your crops and follow further PCDMN cereal risk updates (https://prairiecropdisease.blogspot.com/).  

Prairie Crop Disease Monitoring Network Quick Disease Reporter Tool (PCDMN QDRT): Please contribute your Prairie field crop disease observations in 2024!

The spring of 2024 started dry in some Prairie regions, but recent rains have resulted in improved moisture conditions for crop establishment and subsequent development.  Most of the Prairies have 30 day rainfall amounts were normal to above normal (Figure 1). Cumulative rainfall has been greatest along the Alberta-Saskatchewan border and across southern regions of Manitoba, Saskatchewan and Alberta. Total rainfall (mm) over the past 30 days was 64 mm and was 233% of climate normal values. So far, rainfall amounts in 2024 are much greater than last year. In 2023, rain for April 20 to May 19 was 48% of normal. This is good news for farmers, but moist conditions can elevate disease risk.  Moisture can increase the risk of seed and seedling disease issues, early season root infections, and facilitate pathogen fruiting body and spore development.  As we move into June this moisture can increase the risk of subsequent canopy disease development, and thus the potential need for fungicide application for foliar disease management in cereals and pulses.  Staying on top of rapidly emerging disease issues such as leaf spots and rusts can be challenging during a very busy growing season.  

Figure 1.  Percent of average precipitation on the Prairies over the past 30 days as of May 22, 2024.

To help facilitate awareness of developing plant disease issues on a regional- and prairie-wide basis, the Prairie Crop Disease Monitoring Network (PCDMN) and the three Prairie provincial pathologists have worked with colleagues from the Agriculture and Agri-Food Canada (AAFC) Geomatics Group since summer 2021.  The result of this collaboration is the development and deployment of the Prairie Crop Disease Monitoring Network Quick Disease Reporter Tool (PCDMN QDRT).  

The PCDMN QDRT can be used to make quick general reports of diseases in common crops over the Prairie region as part of the Prairie Crop Disease Monitoring Network.  These reports will be used to prepare PCDMN QDRT disease update maps.  Initially our target is to provide bi-weekly map updates.  The maps will be shared via the PCDMN Blog and PCDMN Twitter feed as well as via provincial government or producer group crop/disease updates during the summer.  PCDMN QDRT reports will aid in identifying regions where disease outbreaks are starting to occur.  This information provides a timely heads-up for producers and crop consultants indicating where further in-crop scouting and risk assessment are needed, especially when a fungicide application is being considered for foliar disease management.  Please note the success of the PCDMN QDRT is dependent on farmer, consultant/agronomist, researcher and producer group/provincial extension staff participation.  The greater the number of reports, the better able we are to inform individuals and organizations regarding emerging disease issues so they can take appropriate and timely actions.

A tutorial for the installation and use of the PCDMN QDRT can be found here: PCDMN QDRT tutorial (Spring 2023 version).

Please consider installing the PCDMN QDRT app (used in conjunction with the Survey 123 app) on your smartphone and contributing your field crop disease observations as we move into June and July.  The PCDMN respects individual farmer's and consultant's privacy concerns.  All QDRT submissions are made on a municipality basis for each Province without having to provide specific field location information.

Associated with the use of the PCDMN QDRT is the need to take digital photographs of symptoms when scouting crops.  In addition, farmers and crop consultants may share these images with consultants, provincial plant disease specialists, plant pathology researchers, producer group extension coordinators, and industry representatives to request a digital diagnosis.  In July 2023, the PCDMN posted a tutorial on digital diagnosis, which highlighted some of the more common mistakes that can be made when taking pictures of disease symptoms. Included in the PCDMN blog article are tips to improve your plant disease photos, which will help facilitate the ability to digitally diagnose issues during the growing season.  The blog article can be accessed here: Say cheese: digital photos and effective plant health diagnostics! 

2024 Cereal Rust Risk Report (May 14-20, 2024)

The second weekly Prairie wind trajectory cereal rust risk report for 2024 is available for download now at the following link: May 14-20, 2024 report.  

As of the week of May 14-20, 2024, the overall Prairie cereal rust risk assessment and need for in-crop scouting is as follows:

Pacific Northwest – There were relatively low numbers of reverse wind trajectories that passed over the PNW region and into the Prairies, while stripe rust development is continuing, although levels are generally low, especially in commercial winter wheat fields in the PNW.  Prairie winter wheat crops are progressing into the tillering stage, while much of the spring wheat crop has just been seeded or will be seeded over the next two weeks.  Overall, as of May 20, 2024 the risk of stripe rust appearance from the PNW is limited and scouting for this disease in the Prairie region is generally not urgent.

Texas-Oklahoma corridor – There were no reverse wind trajectories that passed over the TX/OK region and into the Prairies from May 14-20, 2024, while stripe and leaf rust development are continuing, although levels are generally low, especially in commercial winter wheat fields in the PNW.  Prairie winter wheat crops are progressing into the tillering stage, while much of the spring wheat crop has just been seeded or will be seeded over the next two weeks.  Overall, as of May 20, 2024 the risk of stem, leaf, stripe, and crown rust appearance from the Texas-Oklahoma corridor is relatively low and scouting for these diseases in the Prairie region is not urgent.

Kansas-Nebraska corridor – There were no reverse wind trajectories that passed over the KS/NE region and into the Prairies from May 14-20, 2024, while stripe and leaf rust development are continuing, albeit levels are generally low, especially in commercial winter wheat fields in this region.  However, elevated stripe rust levels have been observed in central regions of Kansas.  Prairie winter wheat crops are moving into the tillering stage, while much of the spring wheat crop has just been seeded or will be seeded over the next two weeks.  Overall, as of May 20, 2024 the risk of stem, leaf, stripe, and crown rust appearance from the Kansas-Nebraska corridor is relatively low and scouting for these diseases in the Prairies is not urgent.

The early and widespread appearance of stripe rust in the PNW, TX/OK and KS/NE regions is still concerning.  Over the next 2-4 weeks if favourable weather conditions (especially more rainfall) occur in these source US regions, further rust development could occur.  This would result in more rust spores being available to be blown into the Prairie region, as well as more northerly rust development into the Dakotas and Minnesota/Wisconsin.  Currently, Prairie winter wheat fields are most at risk, but fortunately most current winter wheat varieties have intermediate to high levels of resistance, although AC Radiant, CDC Buteo, AAC Elevate, Broadview, and CDC Falcon are rated as susceptible (https://www.seed.ab.ca/variety-data/cereals/; https://saskseed.ca/wp-content/uploads/2020/12/2024-Varieties-of-Grain-Crops.pdf; https://www.seedmb.ca/pdf-editions-and-separate-section-pdfs/).  If you are growing a stripe rust susceptible variety, it will be important to keep an eye on your crops and follow further PCDMN cereal risk updates (https://prairiecropdisease.blogspot.com/).