Supporting Information Figs S1–S5, Tables S2–S4, S8 & S9 and Methods S1.
Methods S1 Estimating genetic gains from selection for RCN, XG, and TDM.
First generation gains were predicted for RCN, XG, or TDM individually and for a linear
combination of all three traits in CCLONES. The across-site additive genetic trait values
were estimated by adding the population mean to the across-site additive genetic
deviations for each individual (i.e. the vector ‘a’ in the across-site model). Percent change
in the population mean from selective breeding was predicted by comparing the mean
genetic values of all individuals that were sampled for resin canal traits in CCLONES to
the mean of individuals in the 95th percentile. The Box-Cox transformed oleoresin dry
mass (TDM) data were transformed back into the original units (g) to estimate gains in
oleoresin dry mass (Westbrook et al., 2013).
Westbrook JW, Resende MFR, Munoz P, Walker AR, Wegrzyn JL, Nelson CD, Neale DB,
Kirst M, Huber DA, Gezan SA et al. 2013. Association genetics of oleoresin flow in
loblolly pine: discovering genes and predicting phenotype for improved resistance to bark
beetles and bioenergy potential. New Phytologist 199: 89–100.
Table S2 Genetic distances between mapped genes in CCLONES and BC1
LG
1
2
3
4
5
6
7
8
9
10
11
12
Average
Total
All
All
ALL
CCLONES CCLONES CCLONES BC1
BC1
BC1
N genes avg. dist. max dist. N genes
avg. dist.
max dist.
N genes avg. dist. max dist.
259
0.575
3.672
107
1.308
6.346
53
2.275
9.911
309
0.500
6.826
118
1.252
23.732
55
2.634
32.538
245
0.642
8.061
110
1.142
7.625
65
1.843
12.917
267
0.571
3.610
100
1.367
6.944
56
2.422
16.615
344
0.413
4.006
135
1.057
9.763
75
1.831
11.853
292
0.434
5.211
115
1.055
7.269
52
2.044
8.549
296
0.510
2.686
125
1.140
5.572
54
2.152
22.866
284
0.665
16.769
118
1.270
8.036
64
1.757
16.370
273
0.550
9.323
118
1.183
7.533
66
1.907
14.404
287
0.611
8.000
112
1.314
7.585
59
2.028
15.897
240
0.507
2.676
99
1.118
11.202
58
1.467
10.363
256
0.465
3.568
116
1.001
8.016
64
1.827
10.879
279
0.533
6.201
114
1.180
9.169
60
1.998
15.263
3352
1373
721
N, number of mapped genes; avg. dist., mean distance between adjacent genes; max dist., maximum distance between adjacent genes; LG, linkage
group. Columns with ‘All’ represent the total set of mapped genes, while ‘CCLONES’ and ‘BC1’ columns represent the mapped genes that are
polymorphic within these populations.
Table S3 Identity-by-descent (IBD) proportions for pairs of individuals in CCLONES
that were sampled for resin canal traits
IBD proportion
0
0.0625
0.125
0.1875
0.25
0.3125
0.375
0.5
N relations
99,868
6,118
8168
812
16,276
616
240
3,362
% relations
73.7%
4.5%
6.0%
0.6%
12%
0.5%
0.2%
2.5%
Relationship type
Unrelated
Half first cousin
First cousin
Half sib
Full sib
Identity-by-descent proportions between all pairs of 520 individuals that were sampled resin canal traits
were obtained from the pedigree additive genetic relationship matrix. N relations, number of pairs of
individuals within a IBD proportion class; % relations, percent of pair wise relationships.
Table S4 Additional genetic correlations between RCN and TDM
RCN
site/yr
A6+7
C6+7
N6+7
N6
P6+7
TDM
site/yr
A7
C7
N7
N7
P7
rg ± SE
LLfull
LLnull
P
0.1825 ± 0.0991
0.1781 ± 0.1407
0.2606 ± 0.1378
0.1229 ± 0.1531
0.1256 ± 0.1473
3104.52
-2213.54
-2217.37
-1673.46
-2483.51
3102.99
-2214.30
-2219.00
-1673.76
-2483.81
0.08
0.48
0.07
0.43
0.43
A, across sites; C, Cuthbert; N, Nassau; P, Palatka; 6, age six; 7, age seven; 6+7, ages six and seven; LLfull,
log-likelihood of full model where rg is estimated; LLnull, log-likelihood of the null model where rg is fixed
to zero; P, P-value of likelihood ratio test.
Table S8 Number of significant xylem growth marker–trait associations shared between
field sites and ages in the P. taeda CCLONES population
Avg. #
shared
A6+7
5.36
A6
3.91
26
A7
3
3.09
25
C6+7
7
2
3.09
38
C6
6
1
12
2.18
24
C7
1
3
8
2
1.82
17
N6+7
5
6
0
0
1
4.18
45
N6
4
1
0
0
0
12
2.91
27
N7
3
7
0
0
1
13
4
3.27
28
P6+7
0
0
0
0
0
0
1
1
1.18
10
P6
1
1
0
0
0
0
3
2
9
2.36
32
P7
0
2
0
0
0
1
1
0
2
5
1.18
31
2.88
Avg. # shared among all analyses
A, across sites; C, Cuthbert; N, Nassau; P, Palatka; 6, age six; 7, age seven; 6+7, sum of ages six and seven.
A6+7
38
13
8
5
3
4
8
6
5
0
5
2
A6
A7
C6+7
C6
C7
N6+7
N6
N7
P6+7
P6
P7
Table S9 Tests for whether the number unidirectional associations shared between RCN,
XG, and TDM exceeded random expectation
Trait combination
RCN & XG
RCN & TDM
XG & TDM
RCN, XG, & TDM
Observed N
Max N random P
unidirectional unidirectional
associations
associations
49
17
0
19
18
0
16
17 0.00002
7
4
0
Random samples of SNPs equal in size to the observed number of loci associated with resin canal number
(RCN, 251), xylem growth (XG, 220), and transformed oleoresin dry mass (TDM, 231) were selected
50,000 times from the set of 4854 SNPs used for association analysis. A positive or negative effect was
randomly assigned to each SNP and the number SNPs that had unidirectional effect on combinations of two
or three traits were tallied. The probability observing the number of unidirectional associations for all trait
combinations by chance was calculated as one minus the quantile of the observed number unidirectional
associations within the random distributions of shared associations.
Fig. S1 Example CT image (resolution 10 m pixel-1) of wood cores used for resin
canal number (numbers) and xylem growth (brackets) phenotyping. Three 2 mm  15 mm
wood cores were sampled from each tree and phenotypes were averaged prior to
quantitative genetic analysis.
Fig. S2 Phenotypic distributions of resin canal traits, xylem growth, and oleoresin dry
mass from the Pinus taeda CCLONES population at three field sites. RCN, resin canal
number (ages six and seven); XG, xylem growth (ages six and seven); RCD, resin canal
density (average of ages six and seven); RCLWP, resin canal latewood proportion
(average of ages six and seven); MRCA, mean resin canal area (average of ages six and
seven); RDM, oleoresin dry mass (age seven).
Fig. S3 Decay of linkage disequilibrium (R2) with genetic map distance in BC1 and CCLONES. In BC1, pairwise R2 was
estimated among 721 mapped genes containing SNPs segregating in 345 individuals. In CCLONES, pairwise R2 was estimated
among 1373 mapped genes containing SNPs segregating in 520 individuals. Estimates of R2 were obtained with the R package
‘LDcorSV’. Kernal regression of R2 vs genetic distance was performed in R with the ‘ksmooth’ function using a bandwidth of
10 cM.
Fig. S4 All pair wise genetic and phenotypic correlations between resin canal number
(RCN), transformed oleoresin drymass (TDM), xylem growth (XG), resin canal density
(RCD), and resin canal latewood proportion (RCLWP) within and across sites in the P.
taeda CCLONES population. Significant deviation from zero correlation was assessed
with likelihood ratio tests: ns, not significant; *, P < 0.05; **, P < 0.01; ***, P < 0.001.
Fig. S5 Contrasts of resin canal number and xylem growth family means at age five
among parental half sibs and full sibs in the BC1 population. Pt1, half sib progeny of the
P. taeda grandparent from the first generation of selective breeding; Pe1, half sib progeny
from the P. elliottii grandparent from first generation selections, Pe3 – half sib progeny of
the P. elliottii parent from third generation selections, and BC1– pseudo-backcross ({Pt1
 Pe1}  Pe3) full sibs. Family means were contrasted with Tukey tests. Different letters
indicate significant differences at P < 0.05.