Figures (5)  Tables (4)

    • Figure 1. 

      Map of seed orchards and natural stand locations sampled for this study. (a) Scots pine, (b) Norway spruce.

    • Figure 2. 

      Comparison of genetic diversity in Norway spruce and Scots pine seed orchard crops and natural stands. (a) Variation in observed heterozygosity HO, (b) expected heterozygosity HE, (c) inbreeding coefficient FIS in orchard crops and natural stands, and (d) the general least squares (gls) comparison between species and seed source within species in diversity estimates. Bar length indicates 95% confidence interval (CI).

    • Figure 3. 

      PCA plots of genetic variation of each orchard crop(s) and parents in comparison to natural stands. Left panels depict the pine orchards while the right panels depict the spruce orchards. Where arrows are depicted, they point to a group of offspring, which the particular parent has contributed to. In Klocke, parent BD2120 and BD1234 each has six and five offspring from self-pollination, shown as dots around each parent.

    • Figure 4. 

      Parental contribution to each orchard crop. Parent IDs are on the x-axis.

    • Figure 5. 

      Variation in parental contribution among orchard crops. (a) The cumulative sums of orchard parents' contribution to each crop. (b) The variation in parents' contribution among orchards crops. Numbers above bars indicate the number of identified parents (and rootstock for Västerhus) within the orchard that contributed to the crop.

    • Orchard & stand nameType of
      material      		LatitudeLongitudeYear orchard
      established      		Orchard
      size
      (ha)      		Orchard
      age of the
      crop      		Orchard
      crop size
      (kg/ha)      		No.
      parents
      in orchard      		No.
      parents
      genotyped      		No.
      seedlings
      genotyped
      Scots pine
      Lilla Istad orchardCrop 200756°57' N16°48' E198221254.44039314
      Klocke orchardCrop 198562°56' N18°21' E197016150.866163215
      Klocke orchardCrop 1996262.8293
      Klocke orchardCrop 2008381.1301
      Västerhus orchardCrop 201463°18′ N18°33′ E199113.7235.42828299
      Västerhus orchardRootstock67
      SkillingarydNatural stand57°43' N14°02' E50
      KuttainenNatural stand68°22' N22°48' E50
      LillbergetNatural stand64°17' N19°33' E50
      Total1971,572
      Norway spruce
      Lillpite orchardCrop 198365°21' N21°10' E1963102038.03635231
      Bredinge orchardCrop 200056°28' N16°25' E198312174.42042146431
      Maglehem orchardCrop 199355°46' N14°10' E195753621.03632137
      Maglehem orchardCrop 20004344.032330304
      ÄlmebodaNatural stand56°38' N15°15' E27
      EmmabodaNatural stand56°37' N15°31' E39
      FullsbornNatural stand61°25' N15°42' E17
      LjungaverkNatural stand62°31' N15°48' E26
      LångseleNatural stand63°10' N17°4' E36
      NätrafjälletNatural stand63°10' N18°14' E11
      DegerlidenNatural stand65°04' N20°51' E29
      Total2431,288
      1 Six genotypes were planted with 1 or 2 ramets at establishment, some of them were lost at later age.
      2 Genetic thinning in Bredinge during 2012−2013 removed a section containing 58 parents.
      3 Genetic thinning in Maglehem in 1994 reduced the number of genotypes and changed ramet frequency among remaining genotypes.

      Table 1. 

      Summary of samples included in this study.

    • Orchard crop,
      natural stand      		Sample
      size*      		HO (± SE)HE (± SE)FIS (95% CI)Both parents assignedBPCSelfingNot
      assigned      		NepNep2
      Scots pine
      Lilla Istad 2007314 (261)0.351 ± 0.0010.288 ± 0.0006−0.134 (−0.189−0.083)169 (53.9%)136 (43.3%)5 (1.6%)926.646.1
      Klocke 1985215 (199)0.333 ± 0.00120.287 ± 0.0008−0.088 (−0.145−0.034)24 (11.2%)186 (86.5%)6 (2.8%)529.8122.0
      Klocke 1996293 (212)0.308 ± 0.00110.274 ± 0.0007−0.058 (−0.113−0.007)251 (85.7%)35 (11.9%)17 (5.8%)751.559.5
      Klocke 2008301 (276)0.296 ± 0.00090.285 ± 0.00050.032 (−0.031−0.092)152 (50.5%)145 (48.2%)16 (5.3%)436.768.7
      Västerhus 2014299 (277)0.340 ± 0.00090.286 ± 0.0005−0.112 (−0.166−0.061)202 (67.6%)93 (31.1%)9 (3.0%)416.824.0
      Skillingaryd50 (45)0.341 ± 0.00570.284 ± 0.0035−0.121 (−0.181−0.064)
      Kuttainen50 (47)0.352 ± 0.00570.294 ± 0.0033−0.115 (−0.181−0.051)
      Lillberget50 (49)0.363 ± 0.00550.294 ± 0.0031−0.148 (−0.210−0.088)
      Sum1,572 (1,366)7985955329
      Norway spruce
      Lillpite1983231 (160)0.233 ± 0.00120.243 ± 0.0010.070 (0.018−0.121)209 (90.5%)20 (8.7%)7 (3.0%)223.626.0
      Bredinge 2000431 (347)0.272 ± 0.00060.255 ± 0.0004−0.010 (−0.060−0.036)313 (72.6%)116 (26.9%)11 (2.6%)265.089.7
      Maglehem1993137 (127)0.254 ± 0.00170.239 ± 0.0013−0.008 (−0.066−0.048)130 (94.9%)5 (3.6%)5 (3.6%)225.126.2
      Maglehem 2000304 (259)0.231 ± 0.00080.224 ± 0.00060.008 (−0.041−0.055)277 (91.1%)20 (6.6%)7 (2.3%)720.922.4
      Älmeboda27 (22)0.273 ± 0.00980.263 ± 0.0072−0.004 (−0.069−0.059)
      Emmaboda39 (36)0.282 ± 0.00580.267 ± 0.0042−0.014 (−0.073−0.043)
      Fullsborn17 (17)0.260 ± 0.01270.263 ± 0.00990.029 (−0.042−0.102)
      Ljungaverk26 (26)0.259 ± 0.0080.263 ± 0.00630.038 (−0.027−0.103)
      Långsele36 (34)0.277 ± 0.00630.265 ± 0.0047−0.010 (−0.072−0.052)
      Nätrafjället11 (10)0.269 ± 0.0240.261 ± 0.0183−0.014 (−0.095−0.07)
      Degerliden29 (24)0.275 ± 0.00920.267 ± 0.00690.001 (−0.067−0.069)
      Sum1,288 (1,062)9291613013
      BPC – Background pollen contamination. Nep – effective no. of parents from orchard. Nep2 – effective no. of parents including external pollen donors. Selfing belongs to the category 'Both parents assigned'
      * Sample size within parenthesis are the number of samples with high breadth of coverage (≥ 80% of the total number of SNPs) used for heterozygosity and FIS estimates

      Table 2. 

      Results of genetic diversity and parentage analyses. Genetic diversity in orchard crops and natural stands were measured by observed HO and expected HE heterozygosity and inbreeding coefficient FIS.

    • HOHEFISBPCSelfingNepNep2AgeCensus no. parents
      HE0.94***
      FIS−0.88**−0.66
      BPC0.68*0.74*−0.47
      Selfing−0.010.190.27−0.13
      Nep00.090.110.010.34
      Nep20.390.48− 0.20.78*0.090.57
      Age−0.41−0.420.34−0.440.25−0.31−0.53
      Census no. parents0.050.140.070.130.180.93***0.61−0.36
      Var(logit(Psuc))−0.05−0.12−0.05−0.14−0.40−0.53−0.470.00−0.28
      Significance level * p < 0.05, ** p < 0.01, *** p < 0.0001
      HO – observed heterozygosity; HE – expected heterozygosity; FIS – inbreeding coefficient; BPC – background pollen contamination; Nep – effective no. of parents from orchard; Nep2 – effective no. of parents including external pollen donors; Psuc – relative reproductive success

      Table 3. 

      Spearman´s rank correlation between diversity and mating system parameters across orchard crops for both species. Significant ρ are in bold.

    • OrchardPlantval Under the observed BPC
      Exp. gainBPC CropBPCGain
      Norway spruce
      Lillpite10%0% Lillpite19838.7%9.1%
      Bredinge15%0% Bredinge 200026.9%11.0%
      Maglehem10%0% Maglehem 19933.6%9.6%
      Maglehem 20006.6%9.3%
      Scots pine
      Klocke5%40% Klocke 198586.5%1.1%
      Västerhus19%40% Klocke 199611.9%7.3%
      Lilla istad11%40% Klocke 200848.2%4.3%
      Västerhus 201431.1%21.8%
      Lilla Istad 200743.3%10.4%

      Table 4. 

      Impact of background pollen contamination (BPC) on expected breeding gain.