Landscape genetics of Persian walnut (Juglans regia L.) across its Asian range
Tree Genetics and Genomes
Paola Pollegioni, Keith E. Woeste, Francesca Chiocchini, Irene Olimpieri, Virginia Tortolano, Jo Clark,
Gabriel E. Hemery, Sergio Mapelli, Maria E. Malvolti
C.N.R. Institute of Agro-environmental and Forest Biology, viale Marconi 2, 05010, Porano, Terni, Italy.
paola.pollegioni@ibaf.cnr.it
ESM_3. Genetic diversity of SSR loci.
All fourteen SSR loci used in the present study were highly polymorphic in the sampled
populations (see below Table 1). A total of 182 alleles were amplified in the 926 genotyped trees of J.
regia. The number of alleles per locus varied from five at locus WAG27 and WGA331 to 34 at locus
WGA32, with an average of 13. Similarly, the effective number of alleles (Ae) ranged from a minimum of
1.558 (WGA27) to a maximum of 8.119 (WGA32) and 9.401 (WGA276) with a mean value of 4.351 (SE
= 2.294). Except WGA27 (0.331), all markers were highly informative (PIC > 0.50). Observed
heterozygosity and gene diversity greatly varied across the fourteen SSR loci. The average observed (HO)
and expected (HE) heterozygosity over all loci were 0.550 (SE = 0.139) and 0.711 (SE = 0.140),
respectively. In addition, a significant positive within-population inbreeding coefficient FIS was detected at
eleven loci. In this study, analysis using FreeNa indicated that none of the 14 SSR loci displayed a
conclusive evidence of null alleles (estimated null allele frequency for each SSR ranged from 0.1 to 0.3 in
less than 30% of populations). Furthermore, population genetic differentiation was significant (P < 0.001)
for each SSR locus, with a relatively high average multilocus estimate of FST (0.1582). After ENA
correction, values of FST(null) for each locus and over all loci were only slightly lower than FST values, with
a mean value of 0.1530 (Table 1). In addition, the mean actual differentiation (Dest) calculated across all
populations was 0.2620. The hierarchical locus-by-locus AMOVA revealed that the majority of molecular
variance (76.94%) was partitioned within individuals, while 15.82% was distributed among populations,
and the remaining 7.23% among individuals within populations.
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Table. 1 Genetic characterization of 14 microsatellite loci for 39 Persian walnut populations: shown are
for each locus total number of alleles (A), the effective number of alleles (Ae), observed (Ho) and
expected heterozygosity (HE), polymorphic information content (PIC), and the unbiased estimate of
Wright’s fixation indices, within-population inbreeding coefficient f (FIS), total-population inbreeding
coefficient F (FIT) and among-population genetic differentiation coefficient  (FST), among-population
genetic differentiation coefficient calculated on allele frequencies adjusted for null allele estimates FST (null)
and the estimator of actual differentiation Dest, (Jost, 2008).
Size
range
(bp)
A
WGA1
WGA4
WGA9
WGA27
WGA32
WGA69
WGA72
WGA79
WGA89
WGA118
WGA202
WGA276
WGA321
WGA331
176-194
231-252
231-251
203-212
157-229
157-193
126-184
198-216
209-225
183-293
198-295
140-197
224-249
270-278
10
7
10
5
34
12
10
9
8
13
22
25
12
5
Mean
(SE)
-
Locus
PIC
0.764
0.653
0.694
0.331
0.865
0.795
0.510
0.653
0.554
0.639
0.834
0.885
0.642
0.592
Ae
4.862
3.305
3.839
1.558
8.119
5.537
2.390
3.439
2.587
3.127
6.640
9.401
3.180
2.926
HO
HE
f (FIS) a
F (FIT) a
FST) a
0.605
0.587
0.681
0.239
0.661
0.533
0.404
0.606
0.496
0.574
0.653
0.773
0.523
0.367
0.795
0.698
0.740
0.358
0.877
0.819
0.582
0.709
0.614
0.681
0.849
0.894
0.686
0.659
0.1230**
0.0394*
-0.0138
0.1967**
0.1117**
0.2190**
0.0909*
0.0223
0.0718**
0.0447*
0.0882**
0.0225
0.1036**
0.1652**
0.2424**
0.1599**
0.0818**
0.3377**
0.2504**
0.3529**
0.3113**
0.1497**
0.1959**
0.1591**
0.2351**
0.1384**
0.2417**
0.4484**
0.1361**
0.1254**
0.0943**
0.1765**
0.1561**
0.1713**
0.2425**
0.1304**
0.1337**
0.1197**
0.1612**
0.1186**
0.1540**
0.3393**
FST
(null)
0.1314
0.1247
0.0933
0.1738
0.1521
0.1596
0.2416
0.1290
0.1335
0.1155
0.1579
0.1149
0.1459
0.3167
Dest
0.3459
0.2163
0.2142
0.0793
0.5410
0.4482
0.2525
0.2570
0.1850
0.1938
0.5040
0.5163
0.2626
0.4134
13
0.672 4.351 0.550 0.711 0.0859** 0.2306** 0.1582** 0.1530 0.2620
(8.320) (0.151) (2.294) (0.139) (0.140)
Level of significance of unbiased estimate of Wright’s fixation indices were tested using a non-parametric approach
described in Excoffier et al., (1992) with 1000 permutations : * = p < 0.05, ** = p < 0.001
a
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