Molecular Breeding of Potato in the Postgenomic Era - The Potato: Botany, Production and Uses - page 293

coverage, demonstrating the possibilities for
QTL analysis, genome-wide association stud-
ies, and map-based gene cloning (Felcher et
al ., 2012).
Ortega and Lopez-Vizcon (2012) discuss
the current state of marker-assisted selection in
potato breeding from the practical perspective of
application in a commercial breeding program.
Among the reasons they present for the limited
impact of marker-assisted selection in potato
breeding to date are the paucity of markers in
adapted tetraploid germplasm, the high cost of
screening a large population of seedlings, and
the poor adaptation of clones in which markers
have been developed. The availability of new re-
sources should help to facilitate the adoption of
marker-assisted selection.

A bioinformatics in silico approach was used to
identify 217 cumulative abiotic stress genes from
multiple microarrays (Barozai and Wahid, 2012).
Transcriptome analysis of potato cultivar Kennebec
exposed to various stress treatments including salt
and drought provided an array of candidate genes
for investigation of abiotic stress response (Rensink
et al ., 2005a,b) and the possibility of introducing
these genes transgenically into potato cultivars.
Genes regulated by day length and light quality
were identified by Rutitzky et al . (2009), who found
conserved as well as species-specific photoperiodi-
cally regulated genes between potato and tobacco.
A potato microarray dedicated to food safety, with
emphasis on nutrient-related pathways, basal
physiology, and stress-related metabolic pathways,
was designed to assess the relative importance of
the cultivar or environment on the transcriptomics
of two cultivars grown under two different fertil-
izer regimes and two different plant protection re-
gimes; genetic differences between the two culti-
vars were more pronounced than those due to
different cultural practices (van Dijk et al ., 2009,
2010). In a subsequent study of a single cultivar
grown under organic and conventional agricul-
tural practices, van Dijk et al . (2012) used the
microarray to identify differing expression patterns
of genes and pathways under the different envir-
onmental conditions.
Microarray analysis of a transgenic potato
cultivar carrying the trehalose- 6- phosphate syn-
thase 1 gene of yeast to improve stress tolerance re-
vealed the concomitant up- and downregulation
of 74 and 25 native genes (Kondrák et al ., 2011).
Stushnoff et al . (2010) examined pigmented and
non-pigmented tuber tissues from potato clones
with differential expression of anthocyanins with a
microarray to identify 27 genes likely to have af-
fected anthocyanin accumulation. D'Ippólito et al .
(2010) used a macroarray to demonstrate the up-
regulation of several hundred cDNA clones result-
ing from the inoculation of potato with Fusarium
solani f. sp. eumartii , the cause of dry rot in potato.
Ballvora et al . (2007) used microarrays and
real-time reverse transcriptase polymerase chain
reaction (RT-PCR) on a wild relative of cultivated
potato and an advanced tetraploid clone to study
gene expression induced by inoculation with
P. infestans ; they found some unique genes in the
defense pathway for each genotype, or that the
same genes were activated at different times during
disease development.

17. 3 Transcriptomics

The age of transcriptomics in potato began with
the sequencing of EST libraries from various
tissues of the plant (Crookshanks et al ., 2001;
Ronning et al ., 2003; Armstrong et al ., 2005;
Nielsen et al ., 2005) during its interaction with a
pathogen, such as Phytophthora infestans (Birch
et al ., 2003; Evers et al ., 2004), or subjected to
abiotic stress (Rensink et al ., 2005b; Rotter et al .,
2007). Comparative analysis of solanaceous
species revealed some 23% of ESTs unique to
potato compared to 55- 81% of ESTs with sig-
nificant similarity among six of the species
examined (Rensink et al ., 2005c). Transciptomic
analysis of an isogenic series of potato differing
by ploidy demonstrated only subtle expression
changes related to ploidy differences among 1 x ,
2 x , and 4 x lines (Stupar et al ., 2007).
Once sufficient EST data had been generated,
Kloosterman et al . (2008) developed a 44K 60- mer
oligo array (the Potato Oligo Chip Initiative) that al-
lowed facile identification of differentially ex-
pressed genes among tissues or stress challenges,
thereby facilitating functional annotation of po-
tato genes. This breakthrough was subsequently
implemented to describe differential gene expres-
sion patterns as potato was subjected to drought
(Watkinson et al ., 2006; Mane et al ., 2008; Evers
et al ., 2010), cold (Oufir et al ., 2008; Evers et al .,
2012), salinity (Legay et al ., 2009; Evers et al .,
2012), and heat stress (Ginzberg et al ., 2009).