Am. J. Potato Res.

(2015) 92:518535
DOI 10.1007/s12230-015-9466-4

Influence of Mating Structure on Agronomic Performance, Chip

Fry Color, and Genetic Distance Among Biparental Tetraploid
Families
Kyle Rak 1 & Jiwan P. Palta 1

Published online: 20 June 2015

# The Potato Association of America 2015

Abstract The impact of mating structure on progeny performance is not routinely analyzed in potato breeding programs,
despite the importance of choosing parental lines. Varying
degrees of assortative and disassortative mating can have a
significant effect on the agronomic performance and cold
chipping ability of potato breeding clones. A disassortative
mating strategy of crossing parents from different market
types can incorporate commercially relevant traits into a market class which lacked that trait. Here we report the effect of
mating structure in three breeding families created from parental lines from different market classes, within the same
market class, and from self-pollination. Disassortative mating
structure produced clones with increased yield and tuber size
while assortative mating produced clones with improved coldstorage chipping ability. Inbreeding depression was observed
for yield, tuber traits, and chip color in the selfed progeny.
Chip color in a russet type clone was improved through crossing with an elite chipping parent, demonstrating a viable method for improving russet processing quality. Mating structure
explained a significant proportion of phenotypic variance for
yield, tuber, and chipping traits across the three families. Discriminant analysis of principal components and genetic distance based on SNP markers from the SolCAP project were
able to discriminate among family types and were informative
about the relative diversity generated from each particular
Electronic supplementary material The online version of this article
(doi:10.1007/s12230-015-9466-4) contains supplementary material,
which is available to authorized users.
* Kyle Rak
krak@wisc.edu
1

Department of Horticulture, University of Wisconsin-Madison, 1575

Linden Drive, Madison, WI 53706, USA

cross. A number of promising genotypes from both the russet

chipper family and the chipper chipper families were
identified which outperformed parental varieties for chip color
and tuber size.
Resumen El impacto en la estructura de apareamiento en el
comportamiento de la progenie no se analiza de rutina en los
programas de mejoramiento de papa, a pesar de la importancia
de la seleccin de las lneas parentales. La variabilidad de
grados de cruzamiento al azar y no al azar puede tener un
efecto significativo en el comportamiento agronmico y en
la habilidad de fredo en fro de los clones de papa. Una
estrategia de cruzas no al azar de los progenitores de diferentes
tipos de mercado puede incorporar comercialmente caracteres
relevantes en una clase de mercado que careca de tal
caracterstica. Aqu reportamos el efecto de estructura de
cruzas en tres familias de mejoramiento creadas de lneas
parentales de diferentes clases de mercado, dentro de la misma
clase, y de autopolinizacin. La estructura de apareamiento no
agrupada produjo clones con aumento en el rendimiento y
tamao de tubrculo, mientras que el cruzamiento agrupado
no al azar produjo clones con habilidad mejorada de fredo en
almacenamiento en fro. Se observ depresin endogmica
para rendimiento, caractersticas de tubrculo y color de fredo
en la progenie de autocruzas. Se mejor el color del fredo en
un clon tipo russet mediante el cruzamiento con un progenitor
lite de fredo, con lo que se demuestra un mtodo viable para
mejorar la calidad de procesamiento en tipo russet. La
estructura de los cruzamientos explicaron una proporcin
significativa de varianza fenotpica para caracteres de
rendimiento, tubrculo y fredo a lo largo de las tres familias.
El anlisis discriminativo de los componentes principales y de
distancia gentica con base en marcadores SNP del proyecto
SolCAP fue capaz de diferenciar entre los tipos de familia y
fueron informativos acerca de la diversidad relativa generada

Am. J. Potato Res. (2015) 92:518535

por cada cruza en particular. Se identific un nmero de

genotipos prometedores tanto de la familia de piel rugosa
procesamiento (russet chipper) como de la de procesamiento
procesamiento (chipper chipper) que superaron a las
variedades de los progenitores para color de la hojuela y
tamao de tubrculo.
Keywords Solanum tuberosum . Inbreeding .
Heterozygosity . Genetic distance . SNP genotyping .
Assortative mating . Russet processing quality . Biparental
families

Introduction
The process of potato variety development begins with hybridization between tetraploid potato varieties or elite clones
to create biparental families, followed by subsequent evaluation and advancement of individual clones. As with any crop,
the genetic background and pedigree of these families has a
key impact on the performance of individuals for traits of
commercial importance
Virtually all potato breeding programs follow a pedigree
breeding scheme in which biparental crosses are made between clones with complementary features, and parents are
chosen primarily on the basis of their phenotypic characteristics (Ross 1986; Bradshaw and Mackay 1994). Following the
creation of biparental families, evaluation is done across all
material at the clone level and families are not generally considered as a unit of selection (Bradshaw and Mackay 1994).
As a result, advantages or disadvantages of particular parents
or crossing combinations are generally overlooked within
standard breeding programs.
Breeding programs in North America typically focus on
making selections for particular market classes including fresh
market, processing russets, and round-white processing chippers (Douches et al. 1996). Potato breeding programs typically make hybridizations within clones of a particular market
class, and crossing between market classes is generally rare
(Hamilton et al. 2011). This has led to a divergence in trait
characteristics and evidence suggesting genetic divergence
among market classes has been presented (Hamilton et al.
2011; Hirsch et al. 2013).
Traditional traits of importance for chip processing varieties include high dry matter, low sugars and freedom from
defects (Dale and Mackay 1994). Cold-induced sweetening
(CIS) resistance, or the ability of a variety to produce lightcolored chips directly from cold (46 C) storage, has become
a key area of importance in potato breeding programs (Love
et al. 1998; Lynch et al. 2003). Substantial improvement for
this trait in the chip processing market class has been made
(Love et al. 1998). Since that study, a considerable number of
new cold chipping cultivars, including NorValley, White

519

Pearl, Dakota Pearl, Dakota Diamond, Tundra, Nicolet, and

Lelah have been released (Novy et al. 1998; Thompson et al.
2005, 2008; Groza et al. 2006; Jansky et al. 2011; Navarro
et al. 2012a, b, 2013). Although this trait is also desirable for
the processing russet market class, less progress has been
made within the russet type in terms of new clones released.
Over that time period, a limited number of russet varieties
have been released which describe substantial CIS resistance
(Premier Russet, Clearwater Russet, and Palisade Russet)
(Novy et al. 2008, 2010, 2011). A possible strategy to improve
CIS resistance in russet types may be to make hybridizations
between improved chip-processors and russet types to impart
improved processing traits to a russet-type potato.
In our work we focus on describing the variation within
and among families for cold-chipping quality and agronomic
traits across three bi-parental families, including crosses between chip and russet types and between two chip types.
Using these families we compare the effects of assortative
and disassortative mating on key commercially relevant traits.
Due to their highly heterozygous polyploid genomes, tetraploid bi-parental populations typically exhibit high levels of
variation for many traits of commercial importance (Bradshaw
et al. 1995, 2008; Zorrilla et al. 2014). Several studies have
documented variation among families, and characterized general and specific combining abilities (GCA, SCA) for parental
lines (Brown and Caligari 1989; Bradshaw et al. 1995; Gopal
et al. 2008). While many families are routinely generated in a
typical breeding program, with approximately 100,000 seedlings in the first cycle, the vast majority of clones (8598 %)
are eliminated by the first year of field evaluation, often based
solely on the breeders visual preference in the field
(Bradshaw and Mackay 1994). This practice precludes the
opportunity for unbiased study of commercially important
traits on a within- or among-family basis. Evidence shows that
pedigree testing on larger bi-parental families before selection
allows for the analysis of quantitative trait segregation and
better determination of parental breeding value (Brown et al.
1988; Brown and Caligari 1989). This approach, when families are sufficiently large, also produces material which is well
suited to genetic studies based on family structure, such as
linkage mapping. Recently, bi-parental tetraploid families
from highly heterozygous parents have been used for a number of linkage mapping and trait segregation studies (McCord
et al. 2011a, b; Hackett et al. 2013; Zorrilla et al. 2014).
The relationship between inbreeding, heterozygosity and
agronomic performance has been studied across other potato
populations. For example, Bonierbale et al. (1993) identified
significant differences in performance and relative
homozygosity between families of adapted S. tuberosum
germplasm, an unadapted S. tuberosum family, and an
interspecific S. phureja x S. tuberosum family, specifically
observing higher levels of inbreeding in adapted
S. tuberosum germplasm. Loiselle et al. (1991) identified

520

significant negative relationships between inbreeding coefficient based on pedigree and both yield and tuber number
across 25 adapted S. tuberosum families. Bradshaw et al.
(2000) observed significant inbreeding depression in selfed
versus outcrossed tetraploid families for agronomic traits.
The Bradshaw et al. (2000) study utilized a limited set of
restriction fragment length polymorphism (RFLP) markers.
However, current SNP based molecular marker platforms allow a much greater depth of information to investigate genetic
distance and family structure. In addition, these previous studies have focused primarily on yield and agronomic performance, which while important, are just a part of the complete
package of traits needed in a successful variety. In our study,
we expand the use of molecular tools to investigate relationships within and among populations, and expand the focus of
traits evaluated to include cold-chipping and long-term
chipping ability.
Our study utilized the advancements in potato genotyping
made by the Solanaeae Coordinated Agricultural Project
(SolCAP). The project developed an 8303 single nucleotide
polymorphism (SNP) marker array using SNPs chosen after a
full genome sequencing effort towards SNP discovery in highly adapted cultivars Atlantic, Premier Russet, and Snowden
(Hamilton et al. 2011). This array can now be used to efficiently genotype hundreds of individuals for a common set of
genome-wide SNPs. One of the efforts in our study was to
leverage this resource to understand the population structure
of our breeding material on a deeper genetic level.
The main objective of our study was to examine the differences in segregation for commercial potato traits within and
among families of considerable size. We examined the effect
of trait segregation based on crosses which exhibit assortative
versus disassortative mating. We aimed to identify any relationship between inbreeding, heterozygosity, and parental relatedness with traits of commercial importance across these
three families. These families, now substantially characterized, can serve as a germplasm resource as a number of individuals have consistently outperformed current commercial
Fig. 1 Pedigree diagram
showing parental information the
W9817, W10010rus, and
TundraS1 families. Pedigree
information obtained from the
Potato Bedigree Database (van
Berloo et al. 2007)

Am. J. Potato Res. (2015) 92:518535

checks. The phenotyping and genotyping efforts performed

on these families also set the stage for linkage mapping and
genome wide association studies.

Materials and Methods

Plant Material
Two bi-parental tetraploid F1 populations as well as a selfed S1
population were evaluated in this study. The F1 populations
consisted of a cross between a chip processing cultivar
(Liberator) and an elite chip processing breeding clone
(W4013-1), as well as a cross between a dual-purpose
processing/fresh market russet (Bannock Russet) and a chip
processing cultivar (Tundra). The S1 population was created
through self-pollination of Tundra. Pedigrees of the three families and tuber types for the parental lines are presented in
Figures 1 and 2. Parents were selected based on a combination
of their pedigree, traits of interest, and their relatedness to the
other parent (Fig. 1, Table 1). The crosses were made in 2009
and 2010 and genotypes were maintained in the field as
breeders seed at the Rhinelander Agricultural Research Station (RARS) of the University of Wisconsin-Madison from
2010 to 2013. The number of genotypes evaluated each year
varied according to the amount of seed available (Table 2).
Field Trial Design
Field trials were conducted at the Hancock Agricultural Research Station (HARS) and RARS between 2011 and 2014
(Table 2). The trials were managed under standard production
practices for irrigation, nutrient applications, and pest and disease control during the growing season. All trials were planted
in fields which followed a crop rotation scheme where potatoes were planted every fourth year. The experimental designs
used varied depending on the seed availability each year as
well as the priorities of the years trial. In 2011 and 2012 a

Am. J. Potato Res. (2015) 92:518535

521

Fig. 2 Tuber samples from the

parental genotypes of families
W9817 (a, b), W10010rus (c, d),
and TundraS1 (d)

randomized incomplete block design (IBD) was used

(Cochran and Cox 1992). This allowed control for heterogeneity across the field through the use of replicated
checks within each block. Each block included 28 genotypes, including two check varieties. A randomized
complete block design (RCBD) was adopted in 2013
after determining that the heterogeneity among blocks
did not significantly affect the traits of interest. This
design allowed a smaller set of check materials to be
evaluated. A modified augmented design II was used in
2014 (Lin and Poushinsky 1985). This allowed for the
evaluation of the greatest number of genotypes based on
seed availability. Fourteen genotypes were grouped into
a block with one check variety replicated within each
block and two additional checks randomly scattered
throughout the field. Experimental units consisted of
one row of 5 plants per genotype in 2011, one row of
8 plants in 2012 and 2013, and one row of 20 plants in

Table 1

2014. A summary of the experimental field design by

year and location is presented in Table 2.
Field Trait Evaluations
Traits measured directly following harvest included tuber
yield (TY), specific gravity (SG), tubers per plant (NT), tuber
weight (WT), tuber width (WD), and tuber length (LG) as
listed in Table 3. In 2011 and 2012, TY was measured as the
total weight of all tubers per plot. In 2013 and 2014 TY, NT,
WT, WD, and LG were measured using the AgRay X-ray
grader/sizer/sorter (AgRay Sizer Manual 2013). For this purpose, all tubers from each plot were fed individually into the
AgRays X-Ray optical scanner. This scanner images each
tuber and calculates its size and weight (AgRay Sizer Manual
2013). Plot TY and NT were calculated as the sum of weights
and observations per plot, and plot WT, WD, and LG were
calculated as the average for each trait within a plot. SG was

Parents, population size, relatedness and inbreeding coefficient for three bi-parental tetraploid potato families

Family

Male parent

Female parent

Number of progeny

Parental relatednessa

Coefficient of inbreeding (F)b

W9817

Liberator

W4013-1

110

0.903

0.13

W10010rus
TundraS1

Bannock Russet
Tundra

Tundra
Tundra

87
60

0.844
1.0

0.04
0.52

1-Modified Rogers Distance (Rogers 1972); estimated using 3712 biallelic SNP calls across the SolCAP diversity panel

Based on pedigree data from van Berloo et al. 2007

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Table 2

Am. J. Potato Res. (2015) 92:518535

Information on the genotypes evaluated, locations, and season information for three experimental families
Hancock
2011

Totala

Rhinelander
2012

2013

2014

2011

2012

2013

Four yearsb

Three yearsc

Number of lines evaluated by family

W9817

82

96

97

110

82

96

110

73

98

W10010rus
TundraS1

26
20

63
32

54
31

81
47

86
60

12
6

50
25

Experimental design
Design
IBD
Plot size

5 hills

Replicates
2
Season information
Planting
Harvestd

Apr23
Sep 2

IBD

RCBD

MAD2

RCBD

RCBD

8 hills

8 hills

20 hills

8 hills

8 hills

8 hills

2 or 3

May18
Aug 31

May 6
Aug26

May 9
Aug 3

May29
Oct 3

May23
Oct 3

Jun 4
Sep 27

RCBD randomized complete block design, IBD incomplete randomized block design, MAD2 modified augmented design 2, 5 hill 5 tuber seed pieces
separated by 30.5 cm, 8 hill 8 tuber pieces separated by 30.5 cm, 20 hill 20 tuber pieces separated by 30.5 cm
a

Total number of genotypes evaluated in all trials

Genotypes evaluated in all years

Genotypes evaluated in 3 years

Vines killed 10 days before harvest

calculated by weighing a basket containing between 1 and

2 kg of tubers in the air and then weighing while submerged
in water and using the following formula:
SG Weightair =Weightair Weightwater :

Storage Trial Design

Potato storage trials were conducted from 2011 to 2013. All
storage trials were conducted at the University of Wisconsin
Potato and Vegetable Storage Research Facility in Hancock,
Table 3 Traits and the abbreviations used for the traits evaluated across
the three tetraploid breeding families from 2011 to 2014
Trait (units)

Abbreviation Year of evaluation

1

Total tuber yield (t ha )

Specific Gravity (g g1)
Tubers per plant
Mean tuber weight (g)
Mean tuber width (cm)
Mean tuber length (cm)
Mean tuber length to width ratio
Chip lightness (Hunter L units)
Chip redness (Hunter a units)
Chip yellowness
(Hunter b units)

TY
SG
NT
WT
WD
LG
LW
L
a
b

2011, 2012, 2013, 2014

2014
2013, 2014
2013, 2014
2014
2014
2014
2011, 2012, 2013
2011, 2012, 2013
2011, 2012, 2013

WI. After harvest and grading of tubers each year, samples for
measuring potato chip fry color were moved into controlled
storage lockers set at 12.8 C and 98 % relative humidity
(RH). Storage temperature was held constant for 2135 days
while tuber suberization occurred. Following suberization,
sprout inhibitor isopropyl N-(3-chlorophenyl) carbamate
(CIPC) was applied by fog. Seven to 10 days following CIPC
fogging, storage locker temperatures were ramped down by
0.25 C per day until final set temperature was reached. Final
set temperature was 7.2 C in 2011 and 2012, and 5.5 C in
2013. Following 3, 6, and 9 months in storage, a sample of 8
to 10 tubers from each plot was used for the evaluation of
potato chip fry color.
Chip Color Evaluations
Following a given storage period, 810 tubers were taken for
chip fry color evaluation. For this purpose the tubers were
longitudinally sliced in two halves and two 1-mm slices were
taken from the middle for frying. Slices were fried in cotton
seed oil at 175 C for 2 min and 10 s. The overall color of the
1620 chips from each sample was evaluated together and this
was considered as the experimental unit for chip color.
Chip color was measured using a Hunter Lab D25L colorimeter (Hunter Associates Laboratory, Inc., Virginia USA).
The Hunter Lab D25LT measures color values according to
the Hunter scale, which is based on the opponent-color scale.
The opponent-color scale is based on three independent variables as the basis of color vision which consist of color pairs

Am. J. Potato Res. (2015) 92:518535

exhibiting unique sensory properties (Hurvich and Jameson

1957). These color pairs include black-white, blue-yellow,
and green-red, which correspond to the L, a, and b values
generated by the Hunter Lab D25LT. In the Hunter scale, the
L value measures lightness, which varies from 0 for complete
black to 100 for complete white. Chromaticity, which refers to
the lightness-independent aspects of hue and chroma, is measured by Hunter a & b values. Hunter a value measures redness when positive, grayness when zero and greenness when
negative; Hunter b measures yellowness when positive, grayness when zero, and blueness when negative (D25LT Users
Manual Version 2.1).
For chip color measurements, chip samples were crushed
to create an even distribution of the sample across the sample
viewer. Samples were read in triplicate and the means for L, a,
and b calculated for each plot.
SNP Genotyping
Two hundred thirty eight potato individuals, including the
progeny and parents of the three populations were genotyped
for 8303 SNPs using the SolCAP Potato genotyping array
(Hamilton et al. 2011). The array was processed at the Michigan State University SNP Genotyping Facility in East Lansing, MI on an Illumina iScan system using an Illumina
Infinium platform. Marker genotype calls for one of the five
possible biallelic dosages (AAAA, AAAB, AABB, ABBB,
BBBB) were made for each locus using the GenomeStudio
software version 2011.1 (Illumina) and the SolCAP Infinium
SNP Chip 5 Cluster Boundary Positions (Hirsch et al. 2013).
Of the original 8303 SNPs, 5031 were assigned allele dosages.
Marker data from the SolCAP diversity panel of 222 tetraploid
clones was obtained from the SolCAP database and included
in the analysis (Hirsch et al. 2013). Within that group, 3712
SNPs were assigned allele dosages. The SolCAP diversity
panel dataset and our marker dataset of biparental families
were combined for further population structure analysis. From
the combined group, a set of 3091 SNPs were selected, with
the selection criteria being less than 10 % missing marker calls
across the combined set.
Statistical Analysis
Linear fixed effects models were used for the phenotypic trait
data and analysis of variance was performed to test the significance of the main effects for each trait. The assumptions of
normality and homogeneity of variances were tested by observing the Q-Q and residuals versus fitted plots. Influential
observations were tested and removed using the outlierTest
function in the car package in R version 3.1.1 (R Development Core Team 2011). Linear mixed effects models and restricted maximum likelihood (REML), treating genotype as a
random effect, was used to estimate variance components

523

using R package lme4 (Corbeil and Searle 1976; Bates et al.

2014). From the mixed models, best linear unbiased predictions (BLUP) were generated to estimate the overall performance of genotypes for each trait (Henderson 1974). The
models used were:
A: y Gi j Y k GY ik i jk
B: y Gi j Y k Ll GY ik i jl
C: y Gi j Y k Dm GY ik ijkm
Where is the population mean, G is the effect of genotype i, is the effect of block j, Y is the effect of year k, L
is the effect of location l, D is the effect of storage duration m, GY is genotype i by year k interaction, and is the
residual error. Model A was used for yield and tuber traits
which were evaluated across multiple years. Model B
was used when evaluating population W9817 separately,
as it was evaluated in two locations. Model C was used
for evaluating chip color traits, as storage duration can
significantly affect chip color. For analysis within single
years, factors Y and GY were omitted. To estimate the
contribution of family to the variance, a main family effect F was added to the above models and G was nested
within F. An additional interaction term FY was included
along with GY.
Broad-sense heritability of traits was calculated on an
entry-mean basis using the variance components from REML
and the formula H 2

2G
2G

2
2
GY e
ry
y

from Fehr (Fehr 1987), where

H2is the broad-sense heritability, 2G is the genotypic variance,

2GY is the genotype by year variance, 2e is the residual variance, y is the number of years and r is the number of replicates
within year. To test for significant differences among families,
Tukeys test for honest significant difference was calculated
with the R package agricolae (Mendiburu 2014).
Population Structure Analysis
Family pedigrees are presented in Fig. 1. Pedigree information
was obtained from the Wageningen University Online Potato
Pedigree Database (van Berloo et al. 2007). A pedigree diagram starting with the three families and branching back to
include 249 total varieties was assembled using the Pedigraph
software (Garbe and Da 2008). Inbreeding coefficient F for
each family was estimated based on the available pedigree
data according to the Wright equation (Wright 1922).
Relatedness among the three families, as well as across the
diversity panel of 222 tetraploid varieties from the SolCAP
project, was estimated using Rogers and Neis measures of
genetic distance using 3091 SNP markers (Rogers 1972; Nei

524

1987; Hirsch et al. 2013). Homozygosity index was calculated

as the percent of loci with only one allele within each individual. Observed heterozygosity was calculated as the percent of
loci with two alleles present within each family or group. Kmeans and discriminant analysis of principal components
(DAPC) was performed with the R package adegenet to visualize groupings across the families and the diversity panel
(Jombart and Ahmed 2011). R package ggplot2 was used to
generate several of the figures in this study (Wickham 2009).

Results
Clustering Analysis

Am. J. Potato Res. (2015) 92:518535

Heterozygosity Within Families

SNP genotyping revealed essentially equivalent levels of observed genomic heterozygosity (Ho) between the two biparental F1 populations, with a mean Ho per locus of 0.64
for each population. This was comparable to the Ho levels in
the SolCAP diversity panel russet and chip groups of 0.62 and
0.64 (Table 4). In contrast, the S1 population TundraS1 had a
lower mean Ho of 0.5 (Table 4). While average heterozygosity
per locus was similar among the F1 families and diversity
panel groups, the proportion of homozygous loci within each
group differed drastically (Table 4). Out of 3091 total loci the
SolCAP russet and chip groups had only 51 and 12 homozygous loci respectively for every individual within the group.
The F1 population W10010rus had 305, and W9817 had 515
completely homozygous loci within the same marker set,
whereas within the TundraS1 population, 1194 of the 3091
markers were completely homozygous (Table 4).

Bayesian information criterion (BIC) on the DAPC of the

combined biparental families and SolCAP diversity panel
genotypes revealed the optimum number of groups to be
seven. The clustering analysis grouped all individuals
from each family into a respective group and split the
SolCAP diversity panel genotypes into four groups based
on the markers labeled Div1-Div4 (Fig. 3). These four
groups corresponded to potato market classes, with Div 1
representing russet types, Div 2 representing plant introductions (PI) and exotic germplasm, Div 3 representing
chipping types, and Div 4 representing pigmented and
legacy varieties. The parental genotypes of the three biparental families were also included in the SolCAP diversity panel, though with DAPC clustering, each parental line was assigned to the cluster of its progeny rather
than the diversity panel cluster of its respective market
class (Fig. 3).

The levels of homozygosity observed in the marker data was

in agreement with the estimation of inbreeding based on pedigree information (Tables 1 and 4). Using a pedigree set of 249
individuals branching back from the three biparental populations, the inbreeding coefficient (F) was estimated to be 0.52
for the TundraS1 family, 0.13 for the W9817 family, and 0.04
for the W10010rus family (Table 1). The differences in inbreeding between the two F1 populations is represented in
the pedigree diagram (Fig. 1), as the parents of W10010rus,
Bannock Russet and Tundra have no shared ancestors within
recent generations, while the ancestry of W9817 consists of

Fig. 3 Scatterplot of individuals on (a) first two, and (b) second and third
principal components of discriminant analysis of principal components
(DAPC) on 3081 SNP markers. Retained principal component and
discriminant analysis eigenvalues are displayed in inset a. Populations
are shaded according to their group assignment from the find.clusters

option, and groups are labeled according to their makeup of either a

biparental family or members from the SolCAP diversity panel. Here
the SolCAP diversity groups are labeled according to market type Div
1: russet types; Div 2: plant introductions and exotic germplasm; Div 3:
chipping types; and Div 4: pigmented and legacy varieties

Inbreeding

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525

Table 4 Count of fixed loci, population means of homozygosity index,

observed heterozygosity per locus (Ho) and Rogers genetic distance
between any two individuals within a population based on 3091
biallelic SNP markers
Population

Fixed Loci Homozygosity Ho

index

Rogers distancea

W9817

515

0.360.02b

0.64 0.0650.008b

W10010rus

305

0.350.02b

0.64 0.0700.009c

TundraS1
1194
SolCAP russets 51

0.490.03a
0.360.02b

0.50 0.0500.006a
0.62 0.1070.012d

SolCAP chips

0.340.37b

0.64 0.1100.012d

12

SolCAP Russets consist of 36 cultivated russet varieties and SolCAP

Chips consist of 83 cultivated chip processing varieties from the SolCAP
diversity panel (Hirsch et al. 2013) grouped by DAPC clustering
a

Means in same column with the same letter are not significantly different
at the p<0.05 level, using Tukeys HSD

multiple contributions from the varieties Norchip and Lenape.

While the coefficient of inbreeding was higher in W9817 than
W10010rus, there was not a significant difference in mean
homozygosity index between the two populations (Table 4).
There were however, 65 % more fixed loci within the W9817
population than W10010rus (Table 4). In the S1 population,
39 % of the SNPs were fixed in the population, and the mean
homozygosity index was 0.49. Tundras homozygosity index
is 0.38, so one generation of selfing increased homozygosity
by 29 %.

Genetic Distance
Rogers and Neis estimates of genetic distance were calculated between each family at a population level. The TundraS1
and W10010rus families were the closest of the three families
by both metrics (Table 5). However, TundraS1 was the
most distant from W9817 as well as from the SolCAP
russet and chip groups (Table 5). W10010rus had the
shortest distance from the SolCAP russet group (Div 1)
while W9817 had the shortest distance from the SolCAP
chip groups (Div 3) (Table 5, Fig. 3). Rogers and Neis
measures of genetic distance between families had a
Pearsons correlation coefficient of 0.993. Rogers distance calculated within families was in agreement with
expectation as TundraS1 had the shortest average distance among individuals within the family (0.05) while
W10010rus had the greatest distance (0.07) (Table 4). In
this analysis, the SolCAP chip and russet groups had
significantly greater genetic distance between any two
individuals than in any of our biparental populations,
even though the homozygosity index within the chips,
russets, and F1 populations was essentially equivalent
for the 3091 markers analyzed (Table 4).

Table 5 Rogers (1972) and Nei (1987) genetic distances between

populations based on 3091 biallelic SNP markers
Population A

Population B

Rogers distance

Neis distance

W9817

W10010rus

0.168

0.073

W9817

TundraS1

0.203

0.100

W10010rus
W9817

TundraS1
SolCAP Russets

0.128
0.154

0.040
0.062

W10010rus

SolCAP Russets

0.124

0.040

TundraS1
W9817

SolCAP Russets
SolCAP Chips

0.208
0.117

0.099
0.037

W10010rus
TundraS1

SolCAP Chips
SolCAP Chips

0.122
0.170

0.038
0.066

SolCAP Russets

SolCAP Chips

0.095

0.023

SolCAP Russets consist of 36 cultivated russet varieties and SolCAP

Chips consist of 83 cultivated chip processing varieties from the SolCAP
diversity panel (Hirsch et al. 2013) grouped by discriminant analysis of
principal components (DAPC) clustering

Yield and Tuber Traits

Yield and tuber trait mean values and standard errors were
estimated for each family (Table 6). Significant differences
among families were observed for all agronomic and tuber
traits evaluated, including tuber yield, specific gravity, and
tubers per plant, as well as tuber weight, length, width, and
tuber length to width ratio (Table 6). On average, the
W10010rus population significantly out yielded the other
two populations in all 3 years, producing a population mean
of 49.3, 42.9, and 50.9 metric tons per hectare (t/ha) for 2012
2014 years respectively. This population mean was below the
average yields of commercial checks Atlantic and Snowden,
which produced an average of 65.7, 55.1, and 79.4 t/ha respectively for 2012, 2013, and 2014 years in the same trial
(Table 6). However, certain clones from the W10010rus family outperformed Atlantic and Snowden for yield and other
traits (Table 7).
BLUPs were generated for each individual for performance
across all years of evaluation and plotted against BLUPs for
parental performance (Fig. 4). In the TundraS1 population,
none of the S1 individuals had a higher overall yield BLUP
than Tundra. A substantial number of W10010rus F1 lines
produced higher yields than the parents. In this regard, 33 %
of F1 clones had a higher overall yield BLUP than both parents, 28 % outperformed both parents in 2013, and 29 %
outperformed both parents in 2012. The W9817 family had
the greatest difference in yield performance between the two
parents. Liberator had an overall BLUP for yield of 57.3 t/ha
while W4013-1 was 26.6 t/ha (Fig. 4a). Liberator had a higher
yield BLUP than all but 5 % of the F1 progeny, while 66 % of
the F1 progeny outperformed the breeding clone W4013-1 for
tuber yield.

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Table 6 Mean and standard error

of yield and tuber traits for two
biparental F1 families W9817 and
W10010rus, and a self-pollinated
S1 family (TundraS1) along with
two commercial checks

Traita

TYd

SG
NT
WTe
WDf
LGf
LW

Trialb

Family meansc (SE)

Check means (SE)

W9817

W10010rus

TundraS1

Atlantic

Snowden

2012

40.3b (1.0)

49.3a (2.1)

35.7b (1.8)

65.8 (3.6)

2013

36.0b (0.8)

42.9a (1.7)

27.5c (1.4)

55.1 (11.2)

65.1 (7.9)

2014
2014

45.5b (1.4)
1.081a (0.001)

50.9a (1.8)
1.077b (0.001)

36.9c (1.8)
1.082a (0.001)

79.4 (1.4)
1.093 (0.001)

81.3 (1.3)
1.087 (0.001)

2013
2014
2013

9.4a (0.2)
10.7a (0.3)
108.2b (1.8)

8.2b (0.3)
8.7b (0.4)
149.9a (4.0)

7.6b (0.3)
8.7b (0.4)
107.0b (5.5)

11.6 (1.1)
12.4 (0.2)
131.3 (15.0)

15.7 (1.9)
12.4 (0.3)
115.6 (0.3)

2014
2014
2014

121.6b (3.2)
6.1b (0.1)
6.6b (0.1)

171.4a (5.0)
6.7a (0.1)
8.0a (0.1)

121.2b (5.9)
6.1b (0.1)
6.6b (0.1)

179.0 (3.5)
7.0 (0.5)
7.3 (0.1)

183.1 (2.7)
7.1 (0.1)
7.4 (0.1)

2014

1.2b (0.01)

1.3a (0.01)

1.2b (0.01)

1.1 (0.01)

1.1 (0.01)

SE standard error
a

For trait abbreviations see Table 3

Trials listed performed at Hancock Agricultural Research Station

Family means in the same row with the same letter are not significantly different at the p<0.05 level, using
Tukeys HSD

Tuber yield in metric tons per hectare

Tuber weight in grams

Tuber width and length in centimeters

Among the three families, W9817 produced significantly

more tubers per plant than the other two families in 2013 and
2014, averaging 9.4 and 10.7 (Table 6). Mean tuber weight
was significantly higher in the W10010rus family than
W9817 and TundraS1, while the S1 population had essentially
equivalent mean tuber weight to the W9817 family (Table 6).
Tuber length and length to width ratio was significantly higher
in the W10010rus population, the only family evaluated with
a russet genetic background. Even without any russet pedigree
contribution, some individuals from the W9817 and TundraS1
families exhibited oblong tuber phenotypes (Fig. 4).
Variance components and heritabilities of tuber traits
are presented in Table 8. Each trait evaluated across

multiple years had a significant year and genotype year

effect, but variance due to genotype alone explained the
majority of the variance for all tuber and yield traits
(Table 8). The tuber and yield traits evaluated exhibited
high heritability, ranging from 0.74 for tubers per plant
to 0.89 for mean tuber weight (Table 8). When genotypic
variance was parsed into family effect and clone within
family effect, clone-in-family consistently contributed to
a greater proportion of the variance, although both effects were significant (Table 9). Tubers per plant and
tuber length were the traits with highest family effect,
while tuber weight and specific gravity had relatively
low variance explained by family (Table 8).

Table 7 Best linear unbiased predictions (BLUPs) for yield, tuber, and chipping traits for 6 promising clones and two check varieties across 3 years of
evaluation at Hancock Agricultural Research Station
Family

W9817

Clone ID

MPa

Yield (t/ha)
Tubers/plant
Tuber weight (g)
Specific gravity
L3 months
L6 months
L9 months

49.0
10.3
137.9
1.087
60.8
56.1
50.7

MP mid-parent value

W10010rus
10
61.9
11.2
159.7
1.076
60.2
58.2
54.7

16
56.1
11.5
143.0
1.110
60.6
56.2
53.5

102
55.7
12.7
125.7
1.091
60.2
59.6
56.7

MP
49.8
7.5
153.5
1.077
55.5
56.1
48.6

Checks
29
48.2
8.8
164.4
1.089
61.4
60.6
47.3

49
69.8
13.5
150.6
1.074
57.6
56.3
44.7

155
43.7
7.9
163.1
1.085
58.6
59.8
43.1

Atlantic
64.4
11.6
159.2
1.092
56.6
55.9
43.5

Snowden
67.8
12.9
154.3
1.088
57.5
58.9
48.8

Am. J. Potato Res. (2015) 92:518535

527

Fig. 4 Boxplots of best linear unbiased predictions (BLUPs) for (a) tuber
yield (metric tons/hectare), (b) specific gravity, (c) tubers per plant, (d)
tuber weight (grams), (e) tuber length (cm), (f) tuber length to width ratio
for 260 potato breeding clones across three segregating populations

measured across three growing seasons at Hancock, WI. Overall

BLUPs for the parent lines (Liberator, W4013-1, Bannock Russet and
Tundra) are indicated by the symbols on the right of each plot, with each
color corresponding to the population(s) of which it is a parent

Chip Fry Color

color, while an L-value over 55 is very good, and an L-value

over 60 is exceptional. Hunter b-value was highly correlated
with L-value (r2 =0.85) while a-value had a high negative
correlation with L (r2 =0.80).
Chip color was highly influenced by environmental conditions, with storage duration explaining 48.6 % of the phenotypic variance across 3 years of chipping trials (Table 10). An
additional 12 % of the variance was explained by genotype x
storage interaction, which was parsed into 7 % from family x
storage and 5 % from clone within family x storage. Finally,
7.4 % was explained by year to year variation. As with the
yield and tuber traits, clone-in-family effect was greater than
family effect, but with chip color, family had a higher relative
importance in relation to clone within family.
The distribution of the 2013 chip color scores, the year of
the most complete comparisons, is displayed in Fig. 5. Across
all three populations, the distribution of chip color scores increased as the length of storage increased, while the mean chip
color score decreased (Fig. 5). The TundraS1 family exhibited
the narrowest distribution in chip color after early and middle
duration storage, while W10010rus exhibited the widest
(Fig. 5). The distribution of L-value resembled a normal
distribution for all three populations after short duration
chipping, and as storage length increased the distributions became more negatively skewed with long left
tails (Fig. 5).

Chip color was assessed with the Hunter D25LT colorimeter.

Generally, a Hunter L-value over 50 is an acceptable chip
Table 8 Variance components and broad sense heritability (H2) for
yield and tuber traits evaluated in multiple years
Traitsa Trialb Main effects

TY

NT

TW

2012
2013
2014
All
2013
2014
Both
2013
2014
Both

Variance components

GY B

***
***
***
***
***
***
***
***
***
***

***

***

***

***

**

.
**

2G

ns
170.40
*
162.40
*
220.65
*** 117.65
ns
6.19
ns
7.02
ns
5.59
ns 1187.7
ns 1420.0
ns 1401.49

2GY

2e

40.90

58.32

23.25
60.11 52.42

3.29

1.69
0.99
2.96

271.6

366.0
81.35 268.22

H2
0.89
0.85
0.90
0.85
0.79
0.81
0.74
0.89
0.78
0.89

G genotype, Y year, GY genotype year, B block, e error. Significance is

indicated by the following symbols: p<0.1 (.), p<0.05 (*), p<0.01 (**),
p<0.001 (***), p>0.1 (ns)
a

For trait abbreviations and units see Table 3

Trials grown at Hancock Agricultural Research Station, Hancock WI

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Am. J. Potato Res. (2015) 92:518535

Table 9 Percent variance explained by main and interaction effects for potato yield and tuber traits across three families evaluated in 13 years at
Hancock WI
Factor

Percent variance explaineda

Traitb
TY

SG

NT

WT

WD

LG

LW

Family

15.2***

1.4**

20.6***

8.1***

13.1***

25.9***

13.3***

Clone in family
Year

46.2***
9.0***

95.8**

42.3***
2.2***

54.2***
15.8***

78.6***

67.6***

82.4***

Family Year

0.3***

0.5 ns

7.8***

Clone Year
Residuals

10.5**
18.7

2.8

8.9**
25.5

2.0*
12.0

8.3

6.5

4.3

Significant effects indicated as (* p<0.05; ** p<0.01; *** p<0.001)

a

Percent variance explained obtained from linear random effect model

For trait abbreviations and years evaluated see Table 3

Group means for chip color values were calculated for each
family across different years and storage regimes (Table 11).
Tukeys HSD identified significant differences among families within storage durations and within families among storage durations (Table 11). Among the three families, W9817
exhibited the best mean chip color score following storage in
each year. W10010rus generally had the worst mean performance overall, though when BLUPs of individual clone performance for each storage duration were generated, it was not
significantly worse than TundraS1 (Fig. 6). Most clones in the
TundraS1 family exhibited darker mean chip color than its
parent Tundra across all three storage durations (Fig. 6). Mean
Table 10 Percent variance explained by main and interaction effects
for potato chip color (Hunter values L, a, and b) across three families
evaluated after three storage durations in 3 years at Hancock WI
Factor

Percent variance explaineda

Traitbc

Family
Clone in family
Duration
Family Duration
Clone Duration
Year
Family Year
Clone Year
Residuals

5.3
10.3
48.6
7.0
5.0
7.4
1.6
4.1
10.7

9.6
13.6
22.0
12.5
4.9
10.0
5.0
3.5
18.9

5.5
6.1
57.7
4.1
9.8
0.3
0.6
3.9
11.8

chip color score of the W10010rus population was close to the

mid-parent value after both early and middle duration storage,
but fell below the mid-parent value after long duration storage.
The W9817 population showed chip color score similar to its
mid-parent value after short and middle duration storage, but
after long duration storage, it exhibited mid-parent Heterosis
(Fig. 6). Of the four parental lines, W4013-1 had the lightest
chip color and the most stable performance, producing acceptable chips even from the lowest temperature (5.5 C) and
longest duration (9 months). Tundra performed well in most
storage regimes, while Liberator only chipped well after
3 months of storage. Bannock Russet exhibited the worst chip
color scores among all the parents in all storage regimes.
According to overall BLUPs estimated for chip color
across all durations and years, 44 % of the W10010rus clones
outperformed the mid-parent value for L-value, though only
3 % of clones outperformed both parents. In the W9817 population, 53 % of the clones outperformed the mid-parent Lvalue and 42 % outperformed both parents for overall L-value
BLUP, while 55 % of clones outperformed both parents for
long storage L-value BLUP. None of the TundraS1 progeny
outperformed parent Tundra for overall hunter L-value. Although 69 % of the progeny had a higher L-value BLUP after
short duration storage, by the time of the long storage evaluations, only 1 individual from the TundraS1 still outperformed
Tundra for L-value.

Discussion
Parental Line Selection

All main effects and interactions were significant at the p<0.001 level
a

Percent variance explained obtained from linear random effect model

For trait abbreviations and years evaluated see Table 3

For relationship between Hunter value and visual rating see Fig. 6

Highly adapted parental lines were chosen to maximize the

application of the study to varietal breeding. The first family,
W9817, is the result of a cross between the variety Liberator

Am. J. Potato Res. (2015) 92:518535

529

Fig. 5 Distribution of chip color

L-value for three families across
three storage durations during the
2013 storage season. Samples
were evaluated 3 months after
harvest from 12.8 C (Early),
6 months from 5.5 C (Mid), and
9 months from 5.5 C (Late).
Family means at each duration are
indicated by dashed vertical lines
and mean parent performance at
each duration is indicated by
symbols at the top of each
distribution

Table 11 Mean of Hunter chip color values for two biparental F1 families W9817 and W10010rus and a self-pollinated S1 family, TundraS1 following
cold storage
Hunter valuea

Family

Storage durationbc

2011

2012

2013

2011

2012

2013

2011

2012

2013

W9817d

Early
Mid
Late
Early
Mid
Late
Early
Mid

57.6bcf
53.9d
57.9abc
54.7 cd
45.4e
60.7a
61.6ab

55.2ab
51.6c
54.0b

56.6a

60.7a
56.5b
51.5d
56.0bc
53.9c
40.9e
56.5b
55.3bc

3.1bc
2.4c
0.8d
4.3b
6.4a
1.4e
0.4de

4.0a
2.7b
4.3a

2.5b

0.4f
3.3 cd
4.4b
3.7c
3.6c
5.8a
2.5de
2.1e

23.3a
20.3c
21.5b
20.7bc
19.1d
21.3bc
20.4bc

23.1a
20.5c
22.3b

22.5ab

23.2a
22.4bc
20.3d
23.2a
22.0c
16.8e
23.1ab
22.2bc

Late

51.6d

42.0e

3.5bc

5.3a

20.8bc

W10010rus

TundraS1

17.4e

Trials were grown, stored, and processed at Hancock Agricultural Research Station (HARS) unless otherwise indicated
a

Relationship between chip visual rating and Hunter Value displayed in Fig. 6

Number of individuals evaluated each year indicated in Table 2

Storage conditions in 20112012: Early fry from storage at 12.8 C, Mid and Late from 7.2 C; 2013: Early fry from 12.8 C, Mid and Late from 5.5 C

W9817 grown at Rhinelander Agricultural Research Station in 2011 and moved to HARS for storage and processing

Storage Duration: Early 34 months; Mid 67 months; Late 89 months

Means in the same column with the same letter are not significantly different at the p<0.05 level, using Tukeys HSD

530

Am. J. Potato Res. (2015) 92:518535

Fig. 6 Box and whisker plots depicting BLUPs for Hunter L-value (chip
color) for potato chip samples from individual clones within three
biparental families, evaluated across three storage regimes (Early 3
4 months after harvest, storage temperature 8.912.8 C; Mid 6
7 months, 5.57.2 C; Late 89 months, 5.57.2 C) and three growing
seasons (20112013). Letters across the top indicate Family x Storage

combinations with significantly different means for L-value (p<0.05)

from Tukeys HSD. BLUPs of the parent lines for each family within
storage regimes are indicated by arrows and the first letter in the parent
name (B- Bannock Russet, L- Liberator, T- Tundra, W- W4013-1). On the
Hunter L scale, 0 is completely black, and 100 is completely white

and breeding clone W4013-1. Liberator was selected because

it is a vigorous variety with high yields, good specific gravity
and resistance to scab, although it does not have elite performance for cold-chipping ability (Douches et al. 2001).
W4013-1 is the result of a cross between NorValley and
W2504-9. W4013-1 has a number of key cold-chipping progenitors in its pedigree including Lenape, S438, and
NorValley, which have previously been used as parents in a
number of successful cold-chipping lines (Fig. 1) (Akeley
et al. 1968; Douches et al. 1996; Novy et al. 1998). W40131 was also found to have the best cold-chipping ability in the
Wisconsin breeding program in an analysis of all chipping
clones evaluated from 2001 to 2005 (Table S1). The second
family, W10010rus, is the result of a cross between the varieties Bannock Russet and Tundra. Tundra was used as a parent
because it is an elite cold-chipping variety which can store
well at 8 C for long durations. It has elite cold chipping
progenitor S440 in its pedigree (Fig. 1) (Navarro et al.
2012b). Bannock Russet was selected because it represented
a divergence from the narrow germplasm pool which is typically used as parents in chip-processors, and the aim was to
bring in allelic diversity to the chip stock family. Bannock
Russet is a high yielding variety with high solids, and higher
processing merit than its market class standard, Russet Burbank (Novy et al. 2002). Bannock Russet is also a progenitor
of recent CIS resistant russet varieties, Premier Russet and
Clearwater Russet (Novy et al. 2008, 2010). Bannock Russet
has rough russeted skin and an oblong tuber shape, which
distinguishes it from chip processing types (Fig. 2).

Clustering and Marker Metrics Distinguish

among Families and Market Types
Clustering by DAPC of marker data for individuals from the
three families along with the SolCAP diversity panel discriminated well among families and potato market types. Plotting
by principal components 1 and 2 revealed separation among
the three families, while the four SolCAP groups clustered
within a small window (Fig. 3a). While the Rogers & Neis
genetic distance indices indicated a close genetic relationship
between the biparental populations and the SolCAP diversity
panel (Table 5), plotting of PC 1 and PC2 revealed greater
separation between the families and SolCAP panel (Fig. 3).
The tight clustering of the 4 SolCAP groups on the first two
principal components is likely due to those PCs explaining a
large amount of variance due to loss of variation in the biparental families relative to the germplasm panels (Table 4).
Principal component 3 was able to better parse the SolCAP
groups, and appeared to be explaining more of the genetic
variation associated with market class, as the four SolCAP
groups segregated along the PC3 axis (Fig. 3b). SolCAP Russets group (Div 1) and the W10010rus family had similar
values on the PC3 axis, as did the SolCAP chips group (Div
3) and the W9817 family (Fig. 3b).
The number of groups identified and group memberships
within the SolCAP panel was similar to the clustering analysis
by Hirsch et al. (2013). In that analysis the cultivated tetraploids were parsed into seven total groups: three distinct chip
processing groups, a russet group, a yellow-flesh and round-

Am. J. Potato Res. (2015) 92:518535

white group, a pigmented group, and a wild species and

genetic stock group. Our single chip processing group
encompassed the three identified by Hirsch et al. (2013) and
our pigmented and legacy varieties included the groups of
yellow, round-white, and pigmented varieties. It is likely the
SolCAP panel was not further parsed in our analysis because
we included three biparental families which greatly shifted the
structure of genotypic variability of germplasm panel.
Both Rogers and Neis genetic distance metrics identified
the W10010rus family as the closest of the three families to
the SolCAP russet group (Table 4). This is intuitive because
50 % of its pedigree comes from russet lineage. The same two
metrics identified W9817 as the closest to the SolCAP chips
group, although in this case the W10010rus group was only
slightly more distant (Table 4). The TundraS1 family clustered
further from the SolCAP groups with larger genetic distances
away, which is may be due to the shift in relative heterozygosity and major fixation of loci which segregated in both F1
families as well as in the SolCAP groups.
The shift in calculated homozygosity due to selfing was
pronounced, as the TundraS1 had an average homozygosity
index just below 50 %, while the other families and SolCAP
chips and russets were close to 35 % (Table 4). Observed
heterozygosity per locus in the biparental F1 populations
was 0.64, while after one generation of selfing, the TundraS1
population was at 0.50 (Table 4). This observation is in exact
accordance with the theoretical rate of decline in heterozygosity from selfing in autotetraploids with random chromatid segregation of 0.78 per generation (Fisher 1947; Gallais 2003). It
was also expected that a significant difference in homozygosity index and observed heterozygosity would be detected between the W9817 and W10010rus due to the increased level
of inbreeding in the W9817 pedigree (Fig. 1). However, significant differences for these metrics were not detected between the two families, despite substantial differences in the
number of fixed loci across the families (Table 4). Family
structure did however impact the average genetic distance
within groups. Rogers distance revealed significantly greater
average distance between any two individuals within the
SolCAP panels than between any two progeny in the F1 families (Table 4). Among biparental families, significant differences in the average distance between individuals was found,
with the wide cross W10010rus corresponding to a greater
genetic distance, the narrow cross W9817 a shorter distance,
and the self-hybridization the shortest average distance of all
between full sibs (Table 4). These ranks correspond to the
expectation of population structure based on the pedigree data. These results suggest an index of Rogers
distance based on dense marker array data among individuals within a population is a more descriptive metric
than homozygosity index or observed heterozygosity
when comparing allelic diversity among different
families.

531

Heterosis and Pedigree Effects Detected for Yield

and Tuber Traits
Both family and clone-in-family effects significantly contributed to variance for the yield and tuber traits measured across
the three families (Table 9). For each trait, the clone-in-family
effect was much greater than the family effect, ranging from
explaining twice the percent of total variance for number of
tubers, to 68-fold more for specific gravity (Table 9). The
comparisons between these two effects are somewhat confounded by the large numbers of clones evaluated compared
to the number of families, but the results indicate that there can
be substantial variation both within and among biparental
families for yield, specific gravity, tubers per plant, tuber
weight, tuber length, and tuber length : width ratio (Fig. 4).
The phenotypic segregation patterns observed in the families agree with studies on other biparental tetraploid populations including families of 12601ab1 Stirling, Atlantic x
B1829-5, and Atlantic x Superior, which all noted substantial
within-family variation for most quantitative agronomic traits
measured (Bradshaw et al. 2008; McCord et al. 2011b;
Zorrilla et al. 2014). The high heritabilities for yield, tuber
weight, and number are within the same range as estimated
by other studies (Bradshaw et al. 2008; Bisognin et al. 2012;
Zorrilla et al. 2014) (Table 8). In both the Zorrilla et al. (2014)
and Bradshaw et al. (2008) studies, progeny means were either intermediate between the two parents (specific gravity) or
close to the worst parent (tuber yield, size and shape). The
families from Zorrilla et al. (2014) and Bradshaw et al.
(2008) consisted of crosses within the same market type
(round-white). The same phenomenon was observed within
the chip x chip family W9817 in the present study (Fig. 4).
However, in the russet x chip family W10010rus, the progeny
mean performed either above or close to the best parent (tuber
size, number, shape), or near the mid-parent value (tuber yield,
specific gravity, and tuber weight) (Fig. 4). The general improvement for the W10010rus familys performance versus
the parents could be attributed to the increase of allelic diversity due to a cross between market types. This would be in
agreement with the theory that maximum heterozygosity leads
to maximum heterosis in autopolyploids (Bingham 1980).
Similar observations on the positive relationship between heterozygosity and yield traits in adapted germplasm were made
by Bonierbale et al. (1993). That study used restriction fragment length polymorphic (RFLP) markers which have the
advantage that tri- and tetra-allelic loci can be detected. We
used codominat SNP markers, which limit the number of detectable alleles per locus to two. However, the vast increase in
marker density in this study compensated for this factor and
allowed for a genome-wide characterization of allelic diversity
within and among clones.
The maximum heterozygosity theory is further supported
by the performance of the TundraS1 family for agronomic

532

performance. By all metrics, TundraS1 was more homozygous and displayed less within-family allelic diversity than
both F1 families (Table 4). Likewise, its performance for tuber
yield was significantly lower than the other two families
(Table 6). While its yield was significantly lower, TundraS1
was not significantly different than one or both of the F1 families for specific gravity, tubers per plant, tuber weight, and
tuber shape (Table 6). Further generations of selfing may be
necessary to cause inbreeding depression for these traits, as
the rate of increase in homozygosity per generation of selfing
in autotetraploids is low (Wright 1922).
Storage Environment remains the Primary Factor
Affecting Chip Color
While there appears to be evidence for heterosis and family
structure effects for yield and tuber traits, the effects on
chipping performance are more nuanced. One key difference
between agronomic and chipping traits is the additional effect
of storage environment on the chip color phenotype. Numerous studies have described the general negative effect of cold
storage as well as the occurrence of certain genotype x storage
environment interactions (Shallenberger et al. 1959; Coffin
et al. 1987; Loiselle et al. 1990; Tai and Coleman 1999; Rak
et al. 2013). Our evaluations once again confirm a strong
effect of storage duration on chip color. In addition our study
identifies family x duration and clone-in-family x duration
interaction effects on potato chip color (Table 10). Whereas
the clone and family effects explained the most variance for
yield and tuber traits, those effects for chip color were dwarfed
by the duration effect (Table 10). Nonetheless, clone and family contributed significantly to the variance observed for chip
color L, a, and b values.
The steady increase in the chip color score distribution with
increasing storage duration is consistent with our previous
evaluations of breeding program germplasm (Rak et al.
2013) (Fig. 5). An unfortunate interpretation of this is that elite
chipping clones are most effectively identified after long storage durations, a factor that slows the advancement decision
process. Since potato chip color declines over the storage season, a clone that has good chip color after a long duration can
be expected to also perform well after a shorter storage period.
This means that a possible labor saving strategy could be to
evaluate chip color only after long durations, as long as the
researcher can tolerate high selection intensity.
Assortative Mating Produces Elite Chipping Progeny
Unlike for yield and tuber traits, a wider cross did not lead to a
progeny with lighter chip color. The W9817 population, despite having an inbreeding coefficient of F=0.13, had significantly better chip color than W10010rus in both early and late
duration evaluations. The W9817 family also outperformed

Am. J. Potato Res. (2015) 92:518535

the TundraS1 family for chip color in those same regimes. A

likely reason for the elite chipping performance of the W9817
population is the extensive contribution of Lenape in its pedigree (Fig. 1). The performance of W9817 compared to the
other families supports the hypothesis that Lenape is a major
contributor of cold-chipping alleles (Love et al. 1998). It also
supports previous findings in diallel type progeny tests that
crossing between like individuals produces the best results for
sugars and fry color (Dale and Mackay 1994; Bradshaw et al.
2000). A promising aspect of the W9817 family is how well it
performs compared to the parents. The mean of W9817 chip
color BLUPs are near the mid-parent value after early and
mid-duration storage and above the high parent value after
long duration storage (Fig. 6). After long duration, 55 % of
the progeny was outperforming the parent W4013-1, which is
substantial considering W4013-1 had the best cold chipping
performance across all chipping clones evaluated in the Wisconsin breeding program from 2001 to 2005 and among the
best of the SolCAP diversity panel evaluated by Hirsch et al.
(2013, Table S1). This result suggests there is still considerable room for improvement, even in elite cold chipping backgrounds, and that W4013-1 is an optimal parental choice for
imparting elite cold-chipping alleles.
The chipping performance of the TundraS1 family seems
to indicate that assortative mating is only advantageous to a
certain degree. The TundraS1 family, while originating from
an elite cold-chipping parent, primarily produced darker chips
than parent Tundra, especially after long duration (Fig. 6). The
effect of inbreeding depression in the population is evident,
which is contrary to observations of selfed progeny by
Bradshaw et al. (2000) which observed slightly improved
chipping performance in selfed progenies over their parents.
The hypothesis of Dale and Mackay (1994) that cold-chipping
alleles tend to be recessive may not be universally true. However, the largest decline in progeny performance occurred after
long storage duration, which may indicate that loci tied to
other processes such as senescent sweetening may have resistance alleles acting in a dominant manner.
Disassortative Mating can Improve Chip Color in Russet
Types
Potato breeding programs typically make hybridizations within clones of a particular market class, and crossing between
two market classes is generally rare (Hamilton et al. 2011).
Our study provides evidence that this trait in russets may be
improved by the introgression of chipping alleles from elite
chip clones. For example, the performance of W10010rus
progeny for chip color after early and mid-duration storage
shows a substantial improvement over the russet type parent
(Fig. 6). A majority of individual progeny were improved for
chip color and specific gravity over Bannock Russet (Fig. 6).
Still, within the W10010rus population, it was rare to identify

Am. J. Potato Res. (2015) 92:518535

533

Fig. 7 Tuber images of select clones from family (a) W9817 and (b) W10010rus. Phenotypic trait estimates for these clones are listed in Table 11

genotypes which exhibited both the desirable russet characteristics such as long shape and skin type, along with improved
chip color and dry matter content. However, these traits appear
to assort independently as no significant correlations were
found between shape, skin type, dry matter, or chip color.
Nonetheless, even with a relatively small family size, a number of improved individuals were identified exhibiting the
desired characteristics (Table 7).
Future Directions and Promising Genotypes
The information we have collected in this study lends itself
well to further analysis, and in an upcoming paper we will
report linkage and association mapping using these families
and processing traits. In the current study, a number of promising clones were identified which warrant further evaluation
or use as parental stocks. Of particular interest are clones
W9817-10, W9817-16, W9817-102, W10010-29, W1001049, and W10010-155. Tubers of the promising clones are
shown in Fig. 7. The main breeding goals in these evaluations
were to identify elite cold chipping germplasm with strong
yield performance and tuber traits within the W9817 population. Within the W10010rus population, we aimed to identify
clones which combined russet characteristics with improved
processing/storage ability. The most promising clones were
identified in the W9817 population. The selected W9817
clones consistently outperformed the mid-parent value for agronomic traits and were at least equivalent for chip color
(Table 7). The selected W10010 clones displayed equal or

better agronomics and short-mid duration chip color than the

mid-parent value (Table 7). Only a limited number of clones in
W10010rus exhibited the favorable traits of both parents. No
exceptionally promising clones were identified in the TundraS1 population although a number of the progeny were
not substantially worse than Tundra overall.
From these evaluations, it appears that both yield and tuber
traits can be improved by making wide crosses, but when
particular market class traits are desired, a narrow cross can
produce greater gain. A more conventional type of mating
design such as a diallel will be needed to draw hard conclusions about the effect of heterozygosity and wide versus narrow crosses for the improvement of commercial traits via biparental mating. The findings reached in this study are a valid
but admittedly incomplete assessment of heterosis and inbreeding depression in tetraploid potato. While this study
has not utilized a conventional mating design, it serves as an
example of ways to incorporate molecular information into a
mating study, and offers conclusions which are informative to
biparental crossing decisions.

Acknowledgments This research was completed by Kyle Rak as a part

of his PhD dissertation. He was supported by fellowships from Monsanto
Company and the Wisconsin Potato and Vegetable Growers Association.
This work was supported in part by a grant from USDA-NIFA and the
University of Wisconsin-Madison College of Agriculture and Life
Sciences.

534

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