Chickpea varietal purity and implications for disease management

Varieties displaying this symbol beside them are protected under the Plant Breeders Rights Act 1994.

 

GRDC code: DAN00143

Authors

Kevin Moore, Tamworth Agricultural Institute, NSWDPI, Tamworth NSW 2340, Australia

Kristy Hobson, Tamworth Agricultural Institute, NSWDPI, Tamworth NSW 2340, Australia

Ata-ur Rehman, EH Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW 2650, Australia

Jon Thelander, Seednet, Toowoomba, QLD 4350, Australia

Background

Australian chickpea varieties differ in their reaction to Ascochyta blight, caused by the fungus Phoma rabiei (syn Ascochyta rabiei).  Varieties released before 2005 e.g. Jimbour, are susceptible to Ascochyta and, in seasons conducive to disease, require intensive management with foliar fungicides.  Most cultivars released in 2005 and later e.g PBA HatTrick, have improved Ascochyta resistance and require fewer fungicide sprays.  Accurate identification of chickpea varieties is thus critical to Ascochyta management in commercial crops. 

Since 2011, several chickpea crops in the GRDC northern region have shown inconsistencies in their reactions to Ascochyta blight.  In all cases the variety was named as PBA HatTrick and the seed was grower retained.  PBA HatTrick, released in 2009, is rated Moderately Resistant (MR) to Ascochyta but the level of disease in these crops was more typical of varieties rated as Susceptible (S).  Possible explanations for these unexpected higher levels of disease include (i) a change in the pathogenicity of P. rabiei ie breakdown of varietal resistance, and (ii) authenticity and/or purity of the variety ie mix up in seed source or contamination.  Leo et al (2014), in a comprehensive study of the Australian population of P. rabiei, found the genetic diversity of isolates was low and there was little evidence for widespread changes in pathogenicity.  Simpfendorfer et al (2013) showed varietal contamination caused the higher than expected levels of stripe rust in the MR bread wheat variety Sunvale.  This posed the question: could contamination or a mix-up in source of planting seed account for the observed differences in Ascochyta levels in “HatTrick” crops grown from grower retained seed.  It also raised the larger issue of maintaining genetic purity in Australian chickpea varieties after their release.

Purity of chickpea varieties ex 2011 harvest

Thirty six seed-lots from commercial chickpea crops grown in the GRDC northern region in the 2011 season were assessed for seed purity using four simple sequence repeats (SSR, also called microsatellite) markers.  These four were a subset of 15 SSR markers that were shown to differentiate 24 Australian commercially released chickpea varieties and breeding lines.  These, and for the varieties, their year of release are listed in Table 1. 

For each seed lot, DNA was extracted from eight seedlings and each seedling was assayed using the four SSR markers.  Note:  this work has not yet been peer reviewed.

The seed weight for each seed lot was determined by weighing three random subsamples, each of 100 seeds, per lot.

Table 1. Australian chickpea varieties and breeding lines used to identify SSR markers that could discriminate among individual varieties

Variety/Genotype	Year of Release
Jimbour	2001
Moti	2003
Sonali	2004
Flipper	2005
Kyabra	2005
Yorker	2005
Almaz	2005
Genesis™ 090	2005
Genesis™ 425	2007
CICA0709	not released
CICA0912	not released
CICA1016	not released
PBA HatTrick	2009
PBA Slasher	2009
Genesis™ 079	2009
Genesis™ 114	2010
Genesis™ Kalkee	2011
PBA Pistol	2011
PBA Boundary	2011
PBA Striker (CICA0603)	2012
PBA Maiden (CICA0717)	2013
PBA Monarch (CICA0857)	2013
CICA1007	not released
04067-81-2-1-1	not released

Results

In only 15 of the 36 seed lots, were all eight seedlings deemed to be the same; the remaining 21 lots showed varying degrees of contamination by known and unknown genotypes.  Results for eight seed lots are in Table 2.

Table 2. Selected results from 36 chickpea seed lots ex 2011 harvest showing the variety declared at receival, 100 seed weight and identity of each of 8 seedlings as determined by four SSR markers based on DNA profiles

Declared	100 sdw g	DNA Identity (max 8)
Jimbour	21.8	Jimbour (1), Kyabra(6), Undetermined (1)
Jimbour	20.0	HatTrick(8)
Kyabra	21.8	Moti (7), Kyabra(1)
Kyabra	20.9	HatTrick(4), Kyabra(1), Undetermined (3)
Kyabra	18.3	Kyabra(1), Jimbour (2), Moti (4), Undetermined (1)
Howzat	17.2	Flipper(6), Undetermined (2)
HatTrick	21.2	HatTrick (8)
Amethyst	18.2	Jimbour (7), Undetermined (1)

The DNA assays for the 36 seed lots suggest that unintentional contamination, or mix up in planting seed, is the most plausible explanation for any differences among the eight seedlings.

The seed weight data support the findings of the DNA assays.  The 100 seed weights for Amethyst, Flipper, PBA HatTrick, Howzat, Jimbour, and Kyabra in field trials conducted in Southern QLD from 2005 – 2008, were 14, 18, 20, 21, 20 and 24 grams respectively.  Thus it is not surprising that the seed lot declared to be Amethyst in Table 2 was determined to be a variety with a 100 sdw greater than 14g.  Similarly the lot declared to be Howzat had seeds that were too small to be Howzat (100 sdw 21g) but that were similar to those of Flipper (100 sdw 18g).

For more information see the varieties of chickpeas.

How widespread is the purity problem?

We don’t know but the results of the 36 seed lots suggest it is a far bigger problem than the chickpea industry currently believes.  It’s not difficult to see how this can happen.  Assuming the multiplication rate for chickpea is 50 ie you plant one seed and get 50 back, a single seed of say Jimbour in a one hectare block of otherwise pure PBA HatTrick yields 50 Jimbour seeds at the end of season one.  Season two gives 2,500 Jimbour contaminants; season three 125,000 etc.  And that is just one hectare.  Whilst the problem first surfaced in 2011, it does appear to be getting worse.  In 2013, on a property near Moree, three paddocks had been planted with seed from three different sources, all grower retained and all believed to be PBA HatTrick.  When inspected on 8 & 9 August 2013, it was obvious that one of the paddocks was different from the other two and was clearly not PBA HatTrick (possibly Howzat).  A similar situation was observed, again in 2013, on another north western NSW property where the grower had sown one half of a paddock with grower retained seed and the other half with a different source of grower retained seed.  The seed from the two sources was believed to be PBA HatTrick but it was obvious when inspected that they were not the same variety and again one was not PBA HatTrick (possibly Yorker).

Does it really matter if a chickpea crop is a mixture of varieties?

Why is it important to know what you are growing and the level of contamination, if any?  Accurate identification of chickpea variety is essential for:

• Implementing appropriate disease management strategies
• Minimising the risk to resistance genes in MR varieties from increased inoculum generated on contaminant plants or “mix up” crops, of susceptible varieties
• Maximising marketing opportunities by producing pure seed of one variety
• Supporting grower’s legal rights eg if seed you purchased is not what you paid for
• Assessing compliance with plant breeder’s rights legislation thus ensuring breeding programs receive the appropriate royalties
• Prolonging the commercial life of new varieties
• Providing confidence in the chickpea seed industry
• Providing technical support to research programs eg knowing the genotype of a plant from which an Ascochyta isolate is obtained is critical to the current GRDC project on the variability of the Australian population of the chickpea Ascochyta pathogen
  
  

Cost of Ascochyta management – an example of a consequence of varietal impurity

In a season that is conducive to chickpea Ascochyta, Tamworth research has shown that a crop of pure PBA HatTrick will require two foliar fungicide sprays totalling $30/ha.  A crop of an Ascochyta susceptible variety eg Jimbour would need six sprays costing $90/ha. This equates to a difference of $30,000 for a 500ha planting. If you are unsure of the variety’s identity or it is a mixture, the crop must be treated as a susceptible variety.

Where to from here?

As mentioned earlier, the molecular work has not been peer reviewed and, due to staff changes, is currently on hold.  However, continuation of the variety identification work is being discussed with the University of Adelaide and that there is an opportunity to tap into existing genomic resources that have been funded by the Australian Federal Government through the Australia India Strategic Research Fund.

Conclusions

• DNA evidence has identified genetic contamination in commercial chickpea crops going back to at least 2011
• Crop inspections have revealed obvious differences among plantings believed by growers to be the one variety
• Minimise the risk of contamination of your 2014 planting seed by obtaining seed from a registered seed merchant
• When retaining your own seed, put in place a quality control system to avoid accidental contamination
  
  

Acknowledgements

Thanks to agronomists and growers for identifying paddocks and giving permission to inspect and sample crops.  Thanks to Paul Nash and Gail Chiplin for technical support.

References

Leo A, Ford R and Linde C (2014)  Evolution and dispersal of a recently introduced pathogen of chickpea, Ascochyta rabiei, to Australia.  Accepted by Biological Invasions

Simpfendorfer S, Martin A and Sutherland M (2013)  Use of SSR markers to determine the genetic purity of a popular Australian wheat variety and consequences for stripe rust reactions.  Seed Sci. & Technol., 41, 98-106

Contact details

Dr Kevin Moore

NSW Department Primary Industries, Tamworth
Ph: 02 6763 113302 6763 1133
Mb: 0488 251 8660488 251 866
Email: kevin.moore@dpi.nsw.gov.au

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