Chickpea ascochyta - is the pathogen changing and what are the implications for management

Author: Kevin Moore(1), Kristy Hobson(1), Prabhakaran Sambasivam(2), Rebecca Ford(2,3), Steve Harden(1), Paul Nash1, Gail Chiplin1 and Sean Bithell1 | Date: 24 Feb 2015

1Department Primary Industries NSW, 2University of Melbourne VIC, 3Griffith University, QLD

Take home message

Ascochyta blight occurred in more chickpea crops (62 of 332 crop inspections) in 2014 than in 2012 and 2013 combined. Most infected crops were PBA HatTrick but PBA HatTrick was also the most commonly grown variety.

Inoculum for the 2014 Ascochyta infections resulted from dry summer (2012/2013 and 2013/14) conditions contributing to slow stubble breakdown and infection of volunteers.

Work to determine if the unexpected number of 2014 infections, especially on PBA HatTrick, is related to the changes in the Ascochyta fungus has started.  Initial results show that the population varies both in ability to cause disease (pathogenicity) and time to develop fruiting bodies (latent period).  

Localities where Ascochyta was found on any variety in 2014 are considered high risk for 2015 crops and growers are advised to apply a preventative fungicide before the first post-emergent rain event to all varieties with less resistance than PBA HatTrick, PBA HatTrick will also need to be sprayed. 

The 2014 GRDC Northern Region chickpea season

Although all parts of north central NSW, northern NSW and southern QLD experienced a very wet March, the 2014 winter crop season in the GRDC Northern region was a mixed bag depending on where you were.  Overall, southern areas (north central NSW) were wetter than the northern ones (northern NSW/southern QLD), especially early in the season with above average rain in June and July.  However, from about mid-August onwards things started to get tough, with rainfall well below average throughout the region; some centres recording single digit falls in September and/or October.  In those areas, many chickpea crops were harvested before the end of October.  So how dry was it?

  • At Trangie, from June to November, 137 mm fell on 16 days with 6 days >1.0mm, compared with a long-term average of 225 mm on 41 days (28 days >1.0mm). 
  • At Dubbo, for the same period, 167 mm fell on 37 days with 20 days >1.0mm, compared with a long-term average of 277 mm on 46 days (32 days >1.0mm). 
  • Moree had 129 mm on 20 days with 12 days >1.0mm, compared with a long-term average of 258 mm on 36 days (26 days >1.0mm). 
  • Goondiwindi had 101 mm on 21 days with 15 days >1.0mm, compared with a long-term average of 254 mm on 35 days (26 days >1.0mm). 

The season also had some unusual temperature events.  June was milder than normal which encouraged rapid growth and many crops sown mid-May had 10-15 nodes by the end of June.  In most areas, July and August had considerable extremes in daily temperatures with warm days and cold nights and some severe frosts.  The cool weather continued with frosts and low temperatures common well into spring.  The average daily temperature in all districts fluctuated above and below 15°C until several times from early September to mid-October and did not stay above 15°C until the 3rd week in October.  These milder conditions led to intermittent flower and pod abortion from August to mid-October, which, coupled with the lack of decent spring rain, resulted in missing pods, ghost pods and pods with single seed.  Many growers were disappointed in that crops looked better than they were.  In most areas, yields were restricted to 800 to 1500kg/ha; however, in more favourable areas yields reached 2t/ha and higher.  Hail storms on 25 Oct and 5 Nov caused some losses in a strip from east of Gilgandra to west of Armatree.

These seasonal conditions did not favour diseases and across the region they were uncommon and generally had no or little impact on yield.  Most chickpea crops in northern NSW west of the Newell highway did not receive a single fungicide spray.  However, two diseases did occur in 2014 that warrant discussion because they highlight some basic elements of epidemiology. One disease also raises the question of "has the pathogen changed ie has resistance broken down"?

There were two noteworthy cases of Phytophthora root rot (PRR) both illustrating the key drivers of PRR.  At Gilgandra, PBA HatTrick had been direct drilled with a tyne planter on 19 May into a paddock with a history of PRR (although no chickpeas had been grown in the paddock for 10 years).  From the end of May till 14 Jun, there were 6 rain events totaling 60mm.  When inspected on 25 Jun, the planter furrows in low spots had 5-10mm water.  Seedlings in these spots were chlorotic, wilting and dying; laboratory work confirmed PRR.  The second crop, at North Star, had been sown into a paddock that had never had chickpeas but prior to wheat in 2012 and 2013, had been grass pasture with clover and medic.  On 23 May, it was sown 25mm deep with a tyne and leveling bar; 13mm rain fell that night.  When first inspected on 8 July, there was no sign of PRR; but when re-inspected on 1 September, there were several foci of chlorotic, wilting PBA HatTrick plants (early flowering) but only where water had sat in the contours.  Following a call from the concerned grower, a 3rd inspection was done on 12 October (crop turning).   Scattered throughout most of the paddock were small circular patches of 2 – 10 dead or dying plants with black rotted roots.  Laboratory work confirmed PRR.  The problem was absent from the lighter areas of the paddock and the grower noted that medics were far less prevalent in those areas. 

By far the most striking chickpea disease in the region in 2014 was Ascochyta.

Ascochyta in 2014 chickpea crops

Ascochyta Blight (AB) was first found in the GRDC Northern Region at North Star on 2 July as a small (2-5 plants) focus in a crop of Flipper.  By the end of September, AB had been detected in 62 of 332 crop inspections (18.7%), considerably more than was found in 2013 (5/280 crops, 1.8%) and 2012 (11/213 crops, 5.2%).  Most of the 2014 cases were in NSW but four were confirmed in QLD, including one crop of PBA Boundary at Toobeah, west of Goondiwindi.  The NSW cases covered an area from Yallaroi in the east, west to Mungindi, Nevertire and Tullamore and south to Forbes.

Four cases of AB were found in July, with the majority detected in August (25) or September (33) with none in October. 

Two cases involved Flipper, two PBA Boundary, one PBA Slasher, one Yorker (that the grower believed was PBA HatTrick) and the rest were PBA HatTrick. This distribution of cases by variety reflects the fact that in 2014, PBA HatTrick was by far the predominant variety grown in north central NSW, northern NSW and southern QLD.

Infected crops had typical symptoms of AB including ghosting leaf lesions, mature leaf lesions and stem lesions.  In most cases, the disease was limited to isolated areas in the paddock but in several crops the infection was widespread with foci being detected every 10-30 seconds.  In these crops, stem breakage was common.  In spite of the incidence of AB infection and severity of symptoms, all growers were able to manage the disease with judicious use of chlorothalonil fungicides (up to four applications in the worst cases), further, all believed the disease had little if any impact on yield although it did impact on production costs. 

Why was there more Ascochyta in 2014 than in the previous two seasons?

Although total winter crop rainfall was well below average across the region, June and July were above average in southern parts (57.4mm & 34mm respectively at Trangie; 57.6mm and 55.6mm at Dubbo).  At Moree and Goondiwindi, Jun/Jul rain was 23.8/5.0mm and 29.2/15.4mm, respectively.  The AB fungus requires the impact energy of raindrops to disperse its conidia so it has to rain for the disease to establish ie dews alone will not produce the initial infection.  However, the pathogen only needs 3-6 hours leaf wetness to infect; a few mm of rain falling late on a winter’s day or at night will satisfy that requirement.  Although Moree Airport only recorded 23.8/5mm in Jun/Jul, the AWS at Kindee (north east of Moree) recorded 44.0/11.4mm for the same period with 5/2 days >1.0mm respectively.  Kindee is only a few km from a local epidemic of AB in several PBA HatTrick crops.  That the disease did occur over such a broad geographical is evidence that sufficient rain fell to initiate and spread infections.  As well as favourable weather conditions, another explanation for the amount of AB in 2014 is varietal impurity ie not every plant in a paddock of PBA HatTrick was actually a PBA HatTrick plant.  Varietal purity is a concern in the GRDC Northern Region and the presence of plants of susceptible varieties in a crop of PBA HatTrick would increase disease pressure on bona fide PBA HatTrick plants.

Where did the inoculum come from?

The AB pathogen, Phoma rabiei (previously called Ascochyta rabiei) survives on volunteer chickpeas, on chickpea residue and on seed.  Volunteers with AB were reported in fallows and nearby wheat crops.  We tested some of the seed used to plant the crops in the above-mention local epidemic.  Five thousand seeds (untreated) were surface sterilised and plated to detect any seed borne infections – none were found.  This does not exclude seed as a source of primary inoculum, but together with the absence of any lesions on pods of 2012 and 2013 crops, presents a robust case against seed as the main source of inoculum for the 2014 infections.

We believe the main source of inoculum was infected chickpea residue from 2012 and 2013 crops.  We propose the dry summers of 2012/13 & 2013/14 slowed residue breakdown both in situ and in the following years chickpea paddocks and that this provided inoculum for summer volunteers and the 2014 crop.

Has the Ascochyta pathogen changed?

The short answer is we don’t yet know.  Why?  Because we have limited data on pathogenic variability in the pathogen population.  However, as a population of living individuals (isolates), we should expect it to change.  The little research that has been done shows that there are differences in pathogenicity among isolates.  Table 1 classifies 35 isolates of Phoma rabiei collected from northern NSW chickpea crops in 2013.  Isolates were rated low, medium or high based on their ability to cause disease on ICC3996 (R), GenesisTM 090 (R) and PBA HatTrick (MR).  We conclude from Table 1 that none of the isolates caused severe disease on the two resistant genotypes and that most did likewise on PBA HatTrick.  Three caused severe, and three caused moderate, disease on PBA HatTrick.  This establishes that the pathogen varies in pathogenicity.

 Table 1. Pathogenicity ranking of 35 isolates of Phoma rabiei collected in 2013 (location and host shown) on three chickpea genotypes, ICC3996, GenesisTM 090 and PBA HatTrick

Location

Variety

ICC3996

GenesisTM 090

PBA HatTrick

Overall Pathogenic Rank

North Star

Flipper

Low

Low

Low

Low

North Star

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

High

High

Tooraweenah

PBA HatTrick

Low

Low

High

High

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Medium

Medium

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Medium

Medium

Tooraweenah

PBA HatTrick

Low

Low

High

High

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Medium

Medium

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Tooraweenah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

High

High

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Garah

PBA HatTrick

Low

Low

Low

Low

Another way of assessing pathogenic variability in the AB pathogen populations is to determine the latent period for individual isolates.  The latent period is the time from infection to the development of pycnidia, the small dark fruiting bodies that develop in the leaf and stem lesions.  Six isolates representing a sub-set of the pathogen population in Eastern Australia were evaluated in a growth cabinet (20°C/15°C 12h day/12h night) on four chickpea genotypes ICC3996 (rated R, coded ICC), GenesisTM 090 (rated R, coded GEN), PBA HatTrick (rated MR, coded HAT) and Kyabra (rated S, coded KYB).  There were eight replicates (pots) for each of the 24 genotype by isolate combinations. The latent period was estimated by survival analysis with the status of a pot being whether pycnidia had or had not developed. For each pot, the data is the latent period or the day of last observation if pycnidia had not developed. Details of the isolates are:

  • T12437 – 2010, Darling Downs, QLD, highly pathogenic on PBA HatTrick and ICC3996, moderate on GenesisTM 090 (glasshouse)
  • 10TEM005 – 2010, Temora, NSW, highly pathogenic on PBA HatTrick and ICC3996, moderate on GenesisTM 090 (glasshouse)
  • 13MUR002 – 2013, Murtoa, VIC, highly pathogenic on GenesisTM 090 (field and glasshouse)
  • 13DON002 – 2013, Donald, VIC, highly pathogenic on GenesisTM 090 (field and glasshouse)
  • TR6415 – 2014, Yallaroi, NSW, highly pathogenic on PBA HatTrick (field)
  • 10MEL001– 2010, Melton, SA, extremely low pathogenicity

Latent Period (LP) varied with isolate and genotype (Table 2). All isolates had the shortest LP on the most susceptible entry, KYB and the longest LP on the most resistant entry, ICC.  The isolate from Yallaroi (TR6415) had the shortest LPs on all genotypes and we interpret this as meaning that isolate was the most aggressive in the experiment.  This LP experiment complements the pathogenicity work and confirms variability does exist in the pathogen population.  However, it does not prove that it has changed in response to the widespread cultivation of PBA HatTrick

Table 2.  Mean Latent period (days) of six P. rabiei isolates on six  isolates of P. rabiei on four chickpea genotypes, ICC3996 (ICC), GenesisTM 090 (GEN), PBA HatTrick (HAT) and Kyabra (KYB).

Genotype Isolate Latent Period SE (mean)
GEN T12437 7.13 0.117
HAT T12437 6.75 0.153
ICC T12437 7.75 0.153
KYB T12437 6 0
GEN 10TEM005 7.25 0.153
HAT 10TEM005 7 0
ICC 10TEM005 7.88 0.117
KYB 10TEM005 6 0
GEN 13MUR002 7.38 0.303
HAT 13MUR002 6.88 0.212
ICC 13MUR002 8 0
KYB 13MUR002 6 0
GEN 13DON002 6.13 0.117
HAT 13DON002 6.38 0.171
ICC 13DON002 7.25 0.153
KYB 13DON002 6 0
GEN TR6415 6 0
HAT TR6415 6 0
ICC TR6415 7.13 0.117
KYB TR6415 6 0
GEN 10MEL001 7 0.25
HAT 10MEL001 6.88 0.117
ICC 10MEL001 7.88 0.117
KYB 10MEL001 6 0

Management of Ascochyta in 2015 chickpea crops

The following strategy should reduce losses from Ascochyta in 2015:

  • Spray all varieties with less Ascochyta resistance than PBA HatTrick with a registered Ascochyta fungicide prior to the first rain event after crop emergence, three weeks after emergence, or at the 3 branch stage of crop development, whichever occurs first.
  • For localities where Ascochyta WAS found on any variety in 2014 inoculum will be present in 2015 and the Ascochyta risk is high.  Apply a registered Ascochyta fungicide prior to the first rain event after crop emergence to all varieties with less resistance than PBA HatTrick, PBA HatTrick will also need to be sprayed.  Monitor the crop 2 weeks after rain and if Ascochyta is detected, consider a second fungicide spray.
  • Localities where Ascochyta was NOT found in 2014 are considered low risk. PBA HatTrick or PBA Boundary and most GenesisTM varieties should not require their first Ascochyta spray until the disease is detected.  Monitor these crops 2-3 weeks after each rain event from emergence onwards and spray if Ascochyta is detected in the crop or is found in the district on any variety.
  • Ground application of fungicides is preferred. Select a nozzle such as a DG TwinJet® or Turbo TwinJet® that will produce no smaller than medium droplets (ASAE) and deliver the equivalent of 80–100 litres water/hectare at the desired speed.
  • Where aerial application is the only option (e.g. wet weather delays) ensure the aircraft is set up properly and that contractors have had their spray patterns tested.

Further information

Further information on chickpea disease management can be found at the Pulse Australia website www.pulseaus.com.au and in the NSW DPI 2015 Winter Crop Variety Sowing Guide eg:

Acknowledgements

This research would not be possible without the considerable and ongoing support from growers and the GRDC for which we are most grateful. Thanks also to agronomists for help with the crop inspections and submitting specimens.

Contact details

Kevin Moore
Department of Primary Industries, Tamworth, NSW 2340
Ph: 02 6763 1133
Mob: 0488 251 866
Fx: 02 6763 1100
Email: kevin.moore@dpi.nsw.gov.au

GRDC Project code: DAN00176, UM00052, DAN00151