Table Of ContentGenetic Evaluation Models and Strategies
for Potato Variety Selection
A thesis
submitted in partial fulfilment
of the requirements for the Degree
of
Doctor of Philosophy
in the
University of Canterbury
Mark F. Paget
University of Canterbury
2014
Abstract
A series of studies are presented on the genetic evaluation of cultivated potato (Solanum
tuberosum L.) to improve the accuracy and efficiency of selection at various stages of a
breeding programme. The central theme was the use of correlated data, such as relationship
information and spatial and across-trial correlations, within a linear mixed modelling
framework to enhance the evaluation of candidate genotypes and to improve the genetic
response to selection. Analyses focused on several social and economically-important traits
for the enhancement of the nutritional value, disease resistance and yield of potato tubers.
At the formative stages of a breeding scheme, devising a breeding strategy requires an
improved understanding of the genetic control of target traits for selection. To guide a
strategy that aims to enhance the micronutrient content of potato tubers (biofortification),
univariate and multivariate Bayesian models were developed to estimate genetic parameters
for micronutrient tuber content from a breeding population generated from crosses between
Andean landrace cultivars. The importance of the additive genetic components and extent of
the narrow-sense heritability estimates indicated that genotypic ‘individual’ recurrent
selection based on empirical breeding values rather than family-based selection is likely to
be the most effective strategy in this breeding population. The magnitude of genetic
correlations also indicated that simultaneous increases in important tuber minerals, iron and
zinc, could be achieved.
Optimising selection efficiency is an important ambition of plant breeding programmes.
Reducing the level of candidate replication in field trials may, under certain circumstances,
contribute to this aim. Empirical field data and computer simulations inferred that improved
rates of genetic gain with p-rep (partially replicated) testing could be obtained compared
with testing in fully replicated trials at the early selection stages, particularly when testing
over two locations. P-rep testing was able to increase the intensity of selection and the
distribution of candidate entries across locations to account for G×E effects was possible at
an earlier stage than is currently practised. On the basis of these results, it was
recommended that the full replication of trials (at the first opportunity, when enough
planting material is available) at a single location in the early stages of selection should be
replaced with the partial replication of selection candidates that are distributed over two
locations.
Genetic evaluation aims to identify genotypes with high empirical breeding values
(EBVs) for selection as parents. Using mixed models, spatial parameters to target greater
i
control of localised field heterogeneity were estimated and variance models to account for
across-trial genetic heterogeneity were tested for the evaluation of soil-borne powdery scab
disease and tuber yield traits at the early stages of a selection programme. When spatial
effects improved model fit, spatial correlations for rows and columns were mostly small for
powdery scab, and often small and negative for marketable and total tuber yield suggesting
the presence of interplot competition in some years for tuber yield traits. For the evaluation
of powdery scab, genetic variance structures were tested using data from 12 years of long-
term potato breeding METs (multi-environment trials). A simple homogeneous correlation
model for the genetic effects was preferred over a more complex factor analytic (FA)
model. Similarly, for the MET evaluation of tuber yield at the early stages, there was little
benefit in using more complex FA models, with simple correlation structures generally the
most favourable models fitted. The use of less complex models will be more straightforward
for routine implementation of potato genetic evaluations in breeding programmes.
Evaluations for (marketable) tuber yield were extended to multi-location MET data to
characterise both genotypes and environments, allowing a re-evaluation of New Zealand
MET selection strategies aimed at broad adaptation. Using a factor analytic mixed model,
results indicated that the programme’s two main trial locations in the North and the South
Islands optimised differentiation between genotypes in terms of G×E effects. There was
reasonable performance stability of genotypes across test locations and evidence was
presented for some, but limited, genetic progress of cultivars and advanced clonal selections
for tuber marketable yield in New Zealand over recent years.
The models and selection strategies investigated and developed in this thesis will allow
an improved and more systematic application of genetic evaluations in potato selection
schemes. This will provide the basis for well informed decisions to be made on selection
candidates for the genetic improvement of potato in breeding programmes.
ii
Deputy Vice-Chancellor’s Office
Postgraduate Office
Co-Authorship Form
This form is to accompany the submission of any thesis that contains research reported in
co-authored work that has been published, accepted for publication, or submitted for
publication. A copy of this form should be included for each co-authored work that is
included in the thesis. Completed forms should be included at the front (after the thesis
abstract) of each copy of the thesis submitted for examination and library deposit.
Please indicate the chapter/section/pages of this thesis that are extracted from co-
authored work and provide details of the publication or submission from the extract
comes:
Chapter 2. Genetic evaluation of micronutrient traits in diploid potato from a base population of
Andean landrace cultivars. M. Paget, W. Amoros, E. Salas, R. Eyzaguirre, P. Alspach, L. Apiolaza,
A. Noble, M. Bonierbale. Crop Science (in press). doi: 10.2135/cropsci2013.12.0809
Please detail the nature and extent (%) of contribution by the candidate:
90% data analysis. 90% writing of the manuscript.
Certification by Co-authors:
If there is more than one co-author then a single co-author can sign on behalf of all
The undersigned certifys that:
The above statement correctly reflects the nature and extent of the PhD candidate’s
contribution to this co-authored work
In cases where the candidate was the lead author of the co-authored work he or she
wrote the text
Name: Luis Apiolaza Signature: Date: 27th March 2014
iii
Deputy Vice-Chancellor’s Office
Postgraduate Office
Co-Authorship Form
This form is to accompany the submission of any thesis that contains research reported in
co-authored work that has been published, accepted for publication, or submitted for
publication. A copy of this form should be included for each co-authored work that is
included in the thesis. Completed forms should be included at the front (after the thesis
abstract) of each copy of the thesis submitted for examination and library deposit.
Please indicate the chapter/section/pages of this thesis that are extracted from co-
authored work and provide details of the publication or submission from the extract
comes:
Chapter 4. Genetic variance models for the evaluation of resistance to powdery scab (Spongospora
subterranea f. sp. subterranea) from long-term potato breeding trials. M. Paget, P. Alspach, R.
Genet, L. Apiolaza. Euphytica 197(3): 369-385 (2014). doi: 10.1007/s10681-014-1073-9
Please detail the nature and extent (%) of contribution by the candidate:
90% data analysis. 90% writing of the manuscript.
Certification by Co-authors:
If there is more than one co-author then a single co-author can sign on behalf of all
The undersigned certifys that:
The above statement correctly reflects the nature and extent of the PhD candidate’s
contribution to this co-authored work
In cases where the candidate was the lead author of the co-authored work he or she
wrote the text
Name: Luis Apiolaza Signature: Date: 27th March 2014
iv
Acknowledgements
Thesis work is a prolonged endeavour and there are numerous people that have provided me
with the support, instruction and inspiration to help me complete this venture. These people
deserve special mention.
I would therefore like to take this opportunity to express my gratitude to my senior
supervisor Luis Apiolaza, whose support and guidance has always been helpful and
willingly offered. Likewise, Peter Alspach, colleague and co-supervisor, deserves special
thanks as an enthusiastic source of advice, insight and encouragement throughout. My
appreciation must also go to Russell Genet whose knowledge of potato breeding has been
acquired over many years. This was a great resource when I needed a better understanding
of the practical implications of potato breeding research.
Merideth Bonierbale, Walter Amoros and Elisa Salas, at the International Potato Center
(CIP) in Lima, Peru, were very generous in their hospitality and also provided a wealth of
knowledge with regard to potato breeding and genetics. I am sincerely grateful to them for
allowing me access to and exploration of their data.
Jeanette Allen of the School of Forestry at the University of Canterbury provided
thorough guidance and clarification on all administrative requirements, for which I am
grateful. I would also like to extend my gratitude to a number of staff members who mostly
reside at The New Zealand Institute of Plant & Food Research Limited: to John Anderson
and Fred Braam for their help in organising and managing field trials and collecting data at
Pukekohe and Lincoln; to Russell and John once again for providing their many years of
New Zealand trial data; to Alasdair Noble and Raul Eyzaguirre (CIP) for their advice on
using Bayesian methods and Ruth Butler for her guidance on field trial design in general
and the use of trial design software in particular; to Donna Gibson and Robert Lamberts for
photographs; to Naomi Shaw for locating elusive articles and books, and for help with
formatting the bibliography; and to Ron Beatson, Richard Falloon, Anne Gunson, Steve
Lewthwaite, Carolyn Lister, Sathiyamoorthy ‘Mei’ Meiyalaghan, Gail Timmerman-
Vaughan and Richard Volz for their miscellaneous advice on various aspects of this study.
I gratefully acknowledge the generous financial support from the Potatoes NZ Charitable
Trust. My appreciation also goes to The New Zealand Institute of Plant & Food Research
Limited and, in particular, Bill Griffin and Tony Conner for providing me with the
opportunity and privilege to study towards this degree.
v
To Frances, James, Heather and Samuel
vi
Declaration
I declare that the material presented in this thesis is my own work, with the following
exceptions:
i. Alasdair Noble provided the R code for analysis using the package ‘rjags’ in
Chapter 2, (p. 42).
ii. Peter Alspach helped to develop the method and R code for the bootstrap resampling
procedure outlined in Chapter 3, (p. 52).
iii. Luis Apiolaza and Peter Alspach provided miscellaneous pieces of R code that were
used throughout the thesis.
iv. Trial data was collected by staff at the International Potato Centre (CIP) in Chapter 2
and The New Zealand Institute for Plant & Food Research in Chapters 3, 4, 5 and 6.
Material presented in Chapter 2 has previously been published (online, to date) in Paget, M.
et al. (2014) Genetic evaluation of micronutrient traits in diploid potato from a base
population of Andean landrace cultivars. Crop Science (in press). doi:
10.2135/cropsci2013.12.0809
Material presented in Chapter 4 has previously been published in Paget, M. et al. (2014)
Genetic variance models for the evaluation of resistance to powdery scab (Spongospora
subterranea f. sp. subterranea) from long-term potato breeding trials. Euphytica 197(3):
369-385. doi: 10.1007/s10681-014-1073-9
vii
Contents
Abstract................................................................................................................................. i
Acknowledgements ............................................................................................................. v
Declaration ........................................................................................................................ vii
List of Figures..................................................................................................................... xi
List of Tables .................................................................................................................... xiv
List of Abbreviations ....................................................................................................... xvii
1 General Introduction .................................................................................................... 1
1.1 The potato: a world food staple ............................................................................... 1
1.2 The origin of modern cultivars ................................................................................ 1
1.3 Breeding objectives and selection criteria ............................................................... 3
Tuber yield as an ongoing target for selection ................................................................ 4
Quality characteristics for processing and table markets ............................................... 6
Abiotic and biotic considerations .................................................................................... 7
Enhancing the nutritional value of potato tubers ............................................................ 8
1.4 Breeding strategies for cultivar development ........................................................ 10
The challenge of developing new cultivars ................................................................... 10
Selection methods .......................................................................................................... 10
Molecular strategies ...................................................................................................... 13
1.5 Potato genetic evaluation and selection ................................................................. 14
Estimation (prediction) of genetic and breeding values ............................................... 15
Variance component estimation .................................................................................... 17
Spatial models ............................................................................................................... 18
Evaluation of multi-environment (MET) trials .............................................................. 19
Field trials for early stage testing ................................................................................. 22
1.6 Study motivation and aims .................................................................................... 24
2 Genetic parameter estimation of micronutrient traits in diploid potato from
a base population of Andean landrace cultivars and the implications for breeding ..... 26
2.1 Summary ............................................................................................................... 26
2.2 Introduction ........................................................................................................... 26
2.3 Materials and Methods .......................................................................................... 29
Plant material ................................................................................................................ 29
Data analysis ................................................................................................................. 30
2.4 Results ................................................................................................................... 33
2.5 Discussion ............................................................................................................. 37
Genetic variation and heritabilities .............................................................................. 37
Genetic correlations ...................................................................................................... 40
viii
Bayesian analysis of genetic parameters ...................................................................... 42
2.6 Conclusions ........................................................................................................... 43
3 Empirical and simulation studies of partially replicated (p-rep) field trials
for early-stage selection in a potato breeding programme .............................................. 44
3.1 Summary ............................................................................................................... 44
3.2 Introduction ........................................................................................................... 44
3.3 Materials and Methods .......................................................................................... 46
Trial data ....................................................................................................................... 46
Statistical analysis ......................................................................................................... 49
Simulation of genetic response: parameter-based simulation ...................................... 50
Simulation of genetic response: bootstrap resampling using historic empirical data .. 52
3.4 Results ................................................................................................................... 54
Field trials ..................................................................................................................... 54
Parameter and empirical-based simulations ................................................................ 55
3.5 Discussion ............................................................................................................. 59
Empirical and simulated data ....................................................................................... 60
Early-stage testing in multiple locations ....................................................................... 62
Implications for selection .............................................................................................. 63
3.6 Conclusions ........................................................................................................... 65
4 Genetic variance models for the evaluation of resistance to powdery scab
(Spongospora subterranea f. sp. subterranea) from long-term potato breeding
trials ...................................................................................................................................... 66
4.1 Summary ............................................................................................................... 66
4.2 Introduction ........................................................................................................... 66
4.3 Materials and Methods .......................................................................................... 70
Data ............................................................................................................................... 70
Model selection .............................................................................................................. 71
Prediction of breeding values ........................................................................................ 75
4.4 Results ................................................................................................................... 76
Data ............................................................................................................................... 76
Single trial analyses ...................................................................................................... 77
MET analyses ................................................................................................................ 78
4.5 Discussion ............................................................................................................. 83
4.6 Conclusions ........................................................................................................... 88
5 Selection for tuber yield in a potato improvement programme: trial
heterogeneity and genetic variance models in early stage evaluation ............................ 90
5.1 Summary ............................................................................................................... 90
5.2 Introduction ........................................................................................................... 90
5.3 Materials and Methods .......................................................................................... 93
ix
Description:for routine implementation of potato genetic evaluations in breeding . New Zealand trial data; to Alasdair Noble and Raul Eyzaguirre (CIP) for their
