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Tree Genetics and Molecular Breeding 2014, Vol.4, No.2, 1
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1.2 QTL mapping
A total of 120 genome-wide SSR markers were used
to construct genetic linkage maps for ‘Fuji’ and
‘Maypole’. The ‘Fuji’ map consisted of 103 markers
ordered in 17 linkage groups. The map defined 932.3
cM of total map distance and was characterized by an
average distance between adjacent markers of 9.1 cM.
The ‘Maypole’ map was based on 97 markers on 17
linkage groups. The map defined 894.9 cM of total
map distance, with an average distance between
adjacent markers of 9.2 cM.
A major QTL [logarism of odds (LOD) = 17.13] for
fruit juice browning was detected on the upper part of
LG 16 in ‘Fuji’ (Figure 2). This QTL explained
57.5 % of the phenotypic variance in the Fj × Mp
population. Two minor QTLs were detected in other
linkage groups: one in the middle part of LG 17 in
‘Fuji’ (LOD=3.70; explained phenotypic variance =
9.4 %) and one in the middle part of LG 10 in
‘Maypole’ (LOD=3.49; explained phenotypic variance
=10.9 %). A major QTL (LOD=13.50) for fruit acidity,
presumably the
Ma
locus, was detected on the upper
part of LG 16 in ‘Fuji’ (Figure 2). This QTL explained
49.7 % of the phenotypic variance. In addition, a
minor QTL was detected on the lower part of LG 16
in ‘Maypole’ (LOD=2.81; explained phenotypic
variance = 15.6 %). From those results, we attempted
to perform QTL analysis using the phenotypic value
for each year from 2011 to 2013.
Figure 2 Linkage group 16 of ‘Fuji’ anchoring to physical map
of chromosome 16 and LOD profiles of the QTL for fruit juice
browning (solid line) and fruit acidity (dashed line)
Although the phenotypic variance fluctuated [36.0%
to 62.5% in fruit juice browning, 35.0% to 54.6% in
fruit acidity], the significant QTLs tested by the 1000
permutation test at 5% level of significance were also
detected on the upper part of LG16 in each year,
indicating that those QTLs seems to be stable over 3
successive years.
The two major QTLs for fruit juice browning and fruit
acidity were co-localized on LG 16 of ‘Fuji’ and were
tightly linked. They were located in the vicinity of the
SSR marker NH026a (Figure 2) and flanked by markers
CH02a03 and CH05c06. When genotype-phenotype
associations for fruit juice browning and fruit acidity
were analyzed, the NH026a genotype derived from
‘Fuji’ was clearly associated with both traits in the Fj
× Mp population (Figure 3). Progeny possessing the
Figure 3 Genotype-phenotype associations for fruit juice
browning and fruit acidity in F
1
populations of‘Fuji’בMaypole’
Note: Relationships of an allele of NH026a derived from
‘Fuji’with fruit juice browning (a) and fruit acidity (b). The
value of each individual represents the mean of up to 3
successive fruiting years from 2011 to 2013