Skip to main content

Advertisement

SpringerLink
Log in

Genetic variance models for the evaluation of resistance to powdery scab (Spongospora subterranea f. sp. subterranea) from long-term potato breeding trials

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Breeding for resistance to soil-borne powdery scab in potato is an important component of the integrated management of this disease. Different genetic variance models within a mixed model framework were applied to data from long-term potato breeding trials, for the genetic evaluation of breeding lines. The multi-environment trial (MET) data came from 12 growing seasons (“years”, synonymous with environments) of New Zealand field trials screening for resistance to powdery scab on potato tubers. Pedigree information on a total of 1,031 genotypes was available. Additive components of the genetic effects were important with narrow-sense heritability estimates (and 95 % confidence intervals) from single-year analyses ranging from 0.26 (0.20, 0.44) to 0.57 (0.53, 0.85). Spatial components estimated from the residual plot effects were not important for most years and even when they were significant, estimates were small. In MET analyses, different variance structures for the genetic effects were tested; a homogeneous correlation model (CORH) gave a better fit to the data than a factor analytic FAk model of order (k), 1 and 2. The year-to-year genetic correlation estimate from CORH was 0.81 and compared with a range of 0.59–0.95 estimated from the FA1 model. There was no strong evidence of non-additive genetic effects with zero or boundary estimates for most years. Models which included the pedigree provided a better fit to the data than models that did not include this relationship information. There was no evidence for genetic improvement in resistance for powdery scab on tubers in the breeding population studied. This suggests that selection pressure for resistance in the past has been weak and greater consideration should be given to selecting parents on empirical breeding values to genetically improve breeding populations for resistance to powdery scab.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Baldwin SJ, Genet RA, Butler RC, Jacobs JME (2008) A greenhouse assay for powdery scab (Spongospora subterranea f. sp subterranea) resistance in potato. Potato Res 51:163–173. doi:10.1007/s11540-008-9100-7

    Article  Google Scholar 

  • Balzarini M (2001) Applications of mixed models in plant breeding. In: Kang MS (ed) Quantitative genetics, genomics and plant breeding. CABI Publishing, Wallingford, pp 353–363

    Chapter  Google Scholar 

  • Beeck CP, Cowling WA, Smith AB, Cullis BR (2010) Analysis of yield and oil from a series of canola breeding trials. Part I. Fitting factor analytic mixed models with pedigree information. Genome 53:992–1001. doi:10.1139/g10-051

    Article  CAS  PubMed  Google Scholar 

  • Bhattacharya SK, Sheo R, Dwivedi R (1985) Sources of resistance to powdery scab in potatoes. Indian Phytopathol 38:174–175

    Google Scholar 

  • Burgueño J, Crossa J, Cornelius PL, Trethowan R, McLaren G, Anitha K (2007) Modeling additive × environment and additive × additive × environment using genetic covariances of relatives of wheat genotypes. Crop Sci 47:311–320. doi:10.2135/cropsci2006.09.0564

    Article  Google Scholar 

  • Burgueño J, Crossa J, Cotes JM, San Vicente F, Das B (2011) Prediction assessment of linear mixed models for multi-environment trials. Crop Sci 51:944–954. doi:10.2135/cropsci2010.07.0403

    Article  Google Scholar 

  • Burgueño J, de los Campos G, Weigel K, Crossa J (2012) Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers. Crop Sci 52:707–719. doi:10.2135/cropsci2011.06.0299

    Article  Google Scholar 

  • Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2009) ASReml-R reference manual, VSN International, Hemel Hempstead, UK. http://www.vsni.co.uk/downloads/asreml/release3/asreml-R.pdf

  • Crossa J, Burgueño J, Cornelius PL, McLaren G, Trethowan R, Anitha K (2006) Modeling genotype × environment interaction using additive genetic covariances of relatives for predicting breeding values of wheat genotypes. Crop Sci 46:1722–1733. doi:10.2135/cropsci2005.11-0427

    Article  Google Scholar 

  • Cullis BR, Smith AB, Coombes NB (2006) On the design of early generation trials with correlated data. J Agric Biol Environ Stat 11:381–393

    Article  Google Scholar 

  • Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics. Longman Group Limited, Harlow

    Google Scholar 

  • Falloon RE (2008) Control of powdery scab of potato: towards integrated disease management. Am J Potato Res 85:253–260. doi:10.1007/s12230-008-9022-6

    Article  Google Scholar 

  • Falloon RE, Viljanenrollinson SLH, Coles GD, Poff JD (1995) Disease severity keys for powdery and downy mildews of pea, and powdery scab of potato. N Z J Crop Hortic Sci 23:31–37

    Article  Google Scholar 

  • Falloon RE, Genet RA, Wallace AR, Butler RC (2003) Susceptibility of potato (Solanum tuberosum) cultivars to powdery scab (caused by Spongospora subterranea f. sp subterranea), and relationships between tuber and root infection. Australas Plant Pathol 32:377–385. doi:10.1071/ap03040

    Article  Google Scholar 

  • Falloon R, Curtin D, Lister R, Butler R (2005) Root function and growth of potato plants reduced by Spongospora subterranea infection. Am J Potato Res 82:68

    Google Scholar 

  • Falloon RE, Merz U, Lister RA, Wallace AR, Hayes SP (2011) Morphological enumeration of resting spores in sporosori of the plant pathogen Spongospora subterranea. Acta Protozool 50:121–132

    Google Scholar 

  • Gau RD, Merz U, Falloon RE, Brunner PC (2013) Global genetics and invasion history of the potato powdery scab pathogen, Spongospora subterranea f.sp subterranea. PLoS ONE 8(6):e67944. doi:10.1371/journal.pone.0067944

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Genet RA, Falloon RE, Braam WF, Wallace AR, Jacobs JME, Baldwin SJ (2004) Resistance to powdery scab (Spongospora subterranea) in potatoes—a key component of integrated disease management. In: Nichols MA (ed) Proceedings of the First International Symposium on root and tuber crops: food down under. Palmerston North, New Zealand, pp 57–62

    Google Scholar 

  • Gilmour AR, Cullis BR, Verbyla AP, Gleeson AC (1997) Accounting for natural and extraneous variation in the analysis of field experiments. J Agric Biol Environ Stat 2:269–293

    Article  Google Scholar 

  • Gilmour AR, Gogel B, Cullis BR, Thompson R (2006) ASReml, user guide. Release 2.0. VSN International Ltd, Hemel Hempstead

    Google Scholar 

  • Gleeson AC (1997) Spatial analysis. In: Kempton RA, Fox PN (eds) Statistical methods for plant variety evaluation. Chapman & Hall, London, pp 69–85

    Google Scholar 

  • Hardner CM, Bally ISE, Wright CL (2012) Prediction of breeding values for average fruit weight in mango using a multivariate individual mixed model. Euphytica 186:463–477. doi:10.1007/s10681-012-0639-7

    Article  Google Scholar 

  • Harrison JG, Searle RJ, Williams NA (1997) Powdery scab disease of potato—a review. Plant Pathol 46:1–25. doi:10.1046/j.1365-3059.1997.d01-214.x

    Article  Google Scholar 

  • Hill WG, Goddard ME, Visscher PM (2008) Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet 4(2):e1000008. doi:10.1371/journal.pgen.1000008

    Article  PubMed Central  PubMed  Google Scholar 

  • Kelly AM, Smith AB, Eccleston JA, Cullis BR (2007) The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials. Crop Sci 47:1063–1070. doi:10.2135/cropsci2006.08.0540

    Article  Google Scholar 

  • Kelly AM, Cullis BR, Gilmour AR, Eccleston JA, Thompson R (2009) Estimation in a multiplicative mixed model involving a genetic relationship matrix. Genet Sel Evol 41(1):33. doi:10.1186/1297-9686-41-33

    Article  PubMed Central  PubMed  Google Scholar 

  • Kerr RJ, Li L, Tier B, Dutkowski GW, McRae TA (2012) Use of the numerator relationship matrix in genetic analysis of autopolyploid species. Theor Appl Genet 124:1271–1282

    Article  PubMed  Google Scholar 

  • Lister R, Falloon R, Curtin D, Butler R (2004) Spongospora subterranea reduces host (Solanum tuberosum) growth. Proceedings of the 3rd Australasian Soilborne Diseases Symposium. South Australian Research and Development Institute, Adelaide, pp 135–136

    Google Scholar 

  • Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates Inc., Sunderland

    Google Scholar 

  • Merz U (2008) Powdery scab of potato—occurrence, life cycle and epidemiology. Am J Potato Res 85:241–246. doi:10.1007/s12230-008-9019-1

    Article  Google Scholar 

  • Merz U, Falloon RE (2009) Review: powdery scab of potato—increased knowledge of pathogen biology and disease epidemiology for effective disease management. Potato Research 52:17–37. doi:10.1007/s11540-008-9105-2

    Article  Google Scholar 

  • Merz U, Lees AK, Sullivan L, Schwarzel R, Hebeisen T, Kirk HG, Bouchek-Mechiche K, Hofferbert HR (2012) Powdery scab resistance in Solanum tuberosum: an assessment of cultivar ×  environment effect. Plant Pathol 61:29–36. doi:10.1111/j.1365-3059.2011.02489.x

    Article  Google Scholar 

  • Meyer K (2009) Factor-analytic models for genotype × environment type problems and structured covariance matrices. Genet Sel Evol 41:21. doi:10.1186/1297-9686-41-21

    Article  PubMed Central  PubMed  Google Scholar 

  • Mrode RA (1996) Linear models for the prediction of animal breeding values. CAB International, Wallingford

    Google Scholar 

  • Oakey H, Verbyla A, Pitchford W, Cullis B, Kuchel H (2006) Joint modeling of additive and non-additive genetic line effects in single field trials. Theor Appl Genet 113:809–819. doi:10.1007/s00122-006-0333-z

    Article  PubMed  Google Scholar 

  • Oakey H, Verbyla AP, Cullis BR, Wei XM, Pitchford WS (2007) Joint modeling of additive and non-additive (genetic line) effects in multi-environment trials. Theor Appl Genet 114:1319–1332. doi:10.1007/s00122-007-0515-3

    Article  PubMed  Google Scholar 

  • Piepho HP (1997) Analyzing genotype-environment data by mixed models with multiplicative terms. Biometrics 53:761–767

    Article  Google Scholar 

  • Piepho HP (1998) Empirical best linear unbiased prediction in cultivar trials using factor-analytic variance-covariance structures. Theor Appl Genet 97:195–201

    Article  Google Scholar 

  • Piepho HP, Möhring J (2007) Computing heritability and selection response from unbalanced plant breeding trials. Genetics 177:1881–1888. doi:10.1534/genetics.107.074229

    Article  PubMed Central  PubMed  Google Scholar 

  • Piepho HP, Möhring J, Melchinger AE, Büchse A (2008a) BLUP for phenotypic selection in plant breeding and variety testing. Euphytica 161:209–228. doi:10.1007/s10681-007-9449-8

    Article  Google Scholar 

  • Piepho HP, Richter C, Williams E (2008b) Nearest neighbour adjustment and linear variance models in plant breeding trials. Biom J 50:164–189. doi:10.1002/bimj.200710414

    Article  PubMed  Google Scholar 

  • R Development Core Team (2012) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna

    Google Scholar 

  • Rv Berloo, Hutten RCB, Eck HJV, Visser RGF (2007) An online potato pedigree database resource. Potato Res 50:45–57

    Article  Google Scholar 

  • Shah FA, Falloon RE, Butler RC, Lister RA (2012) Low amounts of Spongospora subterranea sporosorus inoculum cause severe powdery scab, root galling and reduced water use in potato (Solanum tuberosum). Australas Plant Pathol 41:219–228. doi:10.1007/s13313-011-0110-6

    Article  Google Scholar 

  • Smith AB, Cullis BR, Thompson R (2001) Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57:1138–1147. doi:10.1111/j.0006-341X.2001.01138.x

    Article  CAS  PubMed  Google Scholar 

  • Smith AB, Cullis BR, Thompson R (2005) The analysis of crop cultivar breeding and evaluation trials: an overview of current mixed model approaches. J Agric Sci 143:449–462. doi:10.1017/s0021859605005587

    Article  Google Scholar 

  • So YS, Edwards J (2011) Predictive ability assessment of linear mixed models in multi-environment trials in corn. Crop Sci 51:542–552. doi:10.2135/cropsci2010.06.0338

    Article  Google Scholar 

  • Thompson R, Cullis B, Smith A, Gilmour A (2003) A sparse implementation of the average information algorithm for factor analytic and reduced rank variance models. Austral NZ J Stat 45:445–459. doi:10.1111/1467-842x.00297

    Article  Google Scholar 

  • van de Graaf P, Wale SJ, Lees AK (2007) Factors affecting the incidence and severity of Spongospora subterranea infection and galling in potato roots. Plant Pathol 56:1005–1013. doi:10.1111/j.1365-3059.2007.01686.x

    Article  Google Scholar 

  • Wastie RL (1991) Resistance to powdery scab of seedling progenies of Solanum tuberosum. Potato Res 34:249–252

    Article  Google Scholar 

Download references

Acknowledgments

We would like to thank Fred Braam for the management of the powdery scab screening trials and Alasdair Noble for discussions on the data. We thank Richard Falloon, Richard Volz and an anonymous reviewer for helpful suggestions that improved the manuscript. We also gratefully acknowledge the funding of this study by Potatoes NZ Charitable Trust.

Author information

Authors and Affiliations

  1. The New Zealand Institute for Plant & Food Research Limited, Lincoln, Christchurch, 8140, New Zealand

    M. F. Paget & R. A. Genet

  2. The New Zealand Institute for Plant & Food Research Limited, Motueka, 7198, New Zealand

    P. A. Alspach

  3. School of Forestry, University of Canterbury, Christchurch, New Zealand

    L. A. Apiolaza

Authors
  1. M. F. Paget
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. P. A. Alspach
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. A. Genet
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. A. Apiolaza
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. F. Paget.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Paget, M.F., Alspach, P.A., Genet, R.A. et al. Genetic variance models for the evaluation of resistance to powdery scab (Spongospora subterranea f. sp. subterranea) from long-term potato breeding trials. Euphytica 197, 369–385 (2014). https://doi.org/10.1007/s10681-014-1073-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-014-1073-9

Keywords

Search

Navigation