Figures (5)  Tables (3)

    • Figure 1. 

      Histograms of architectural/vigor traits collected in 2020 and 2021. TCA: trunk cross-sectional area.

    • Figure 2. 

      Pearson’s correlations of 2020 and 2021 architectural/vigor traits. All coefficients are at significance levels of p < 1 × 10−4.

    • Figure 3. 

      Detection of quantitative trait loci associated with architectural/vigor traits on (a) chromosome 5, and (b) chromosome 15 of 'H4'. Solid-filled horizontal bars denote quantitative trait loci detected at 1.5-logarithm of odds (LOD) support. Genetic positions of haploblocks on chromosomes 5 and 15 are highlighted in magenta. TCA: trunk cross-sectional area.

    • Figure 4. 

      Haplotype effects of architectural/vigor traits on chromosome 5 and 15 loci. All within-chromosome haplotypes were statistically significant at p ≤ 1 × 10−3. Dwarfing and vigorous haplotypes were denoted as A and B, respectively. Ch: chromosome; TCA: trunk cross-sectional area; 1r: chromosome 15 rootstock haploblock; 2r: chromosome 15 rootstock haploblock.

    • Figure 5. 

      Combined haplotype effects of architectural/vigor traits on chromosome 5 and 15 loci. Different mean separation letters were determined using Tukey’s Honest Significant Difference (p < 0.05). Dwarfing and vigorous haplotypes were denoted as A and B, respectively. The numbers of individuals for each haplotype combination, from left to right, are: 36, 33, 22, and 45. For rootstock TCA plot, the numbers of individuals for each haplotype combination, from left to right, are: 37, 32, 24, and 44. Ch: chromosome; TCA: trunk cross-sectional area; 1r: chromosome 15 rootstock haploblock; 2r: chromosome 15 rootstock haploblock.

    • TraitLODGWCh.Highest LOD
      marker      		Position
      (cM)      		LODPVE (%)Ch.Highest LOD
      marker      		Position
      (cM)      		LODPVE (%)
      Height_20203.25AX-17237593984.77.416.415AX-1718637844.25.611.5
      Height_20213.15AX-17237593984.79.820.815AX-1718637844.28.216.9
      CL_AG_20203.15AX-17237593984.77.316.515AX-1718637844.25.912.5
      CL_AG_20213.05AX-17237593984.77.515.915AX-1718637844.27.517.4
      TS_AG_20202.95AX-17237593984.73.910.215AX-1718637844.23.68.6
      TS_AG_20212.85AX-17237593984.76.715.815AX-1718637844.25.010.6
      TCA_R10_20203.05AX-17237593984.74.611.015AX-17198221019.56.318.0
      TCA_R10_20213.15AX-17237593984.78.520.615AX-17198221019.57.619.6
      TCA_S20_20203.15AX-17237593984.74.711.715AX-1718637844.23.57.6
      TCA_S20_20213.15AX-17237593984.77.917.415AX-1718637844.26.713.9
      LODGW: Genome-wide logarithm of odds significance threshold (α = 0.05); Ch.: chromosome; LOD: logarithm of odds; PVE: phenotypic variance explained; Height: tree height; CL_AG: central leader annual growth; TS_AG: total scion annual growth; TCA_R10: rootstock trunk cross-sectional area at 10 cm below union; TCA_S20: scion trunk-sectional area at 20 cm above union.

      Table 1. 

      QTL results (on 'H4' map) for vigor traits phenotyped in two years.

    • TraitModel: y ~ Q1 + Q2Model: y ~ Q1 + Q2 + Q1 : Q2
      QTLch5 (%)QTLch15 (%)Total (%)QTLch5 (%)QTLch15 (%)Interaction (%)Total (%)
      Height_2020 16.4 11.5 27.9 25.8 20.8 9.3 44.2
      Height_2021 20.8 16.9 37.6 30.6 26.7 9.8 56.8
      CL_AG_2020 16.5 12.5 28.9 26.4 22.3 9.9 46.0
      CL_AG_2021 15.9 17.4 33.2 23.4 24.9 7.5 49.1
      TS_AG_2020 10.2 8.6 18.8 20.8 19.2 10.6 33.7
      TS_AG_2021 15.8 10.6 26.4 26.9 21.7 11.1 44.0
      TCA_R10_2020 11.0 18.0 28.9 19.1 26.1 8.1 43.0
      TCA_R10_2021 20.6 19.6 40.2 30.7 29.6 10.1 57.7
      TCA_S20_2020 11.7 7.6 19.3 20.2 16.2 8.5 32.6
      TCA_S20_2021 17.4 13.9 31.3 26.3 22.8 8.9 48.0
      y: variance/effects; Q: quantitative trait locus (QTL); ch: chromosome; Height: tree height; CL_AG: central leader annual growth; TS_AG: total scion annual growth; TCA_R10: rootstock trunk cross-sectional area at 10 cm below union; TCA_S20: scion trunk-sectional area at 20 cm above union.

      Table 2. 

      QTL effects estimated with two models on 'H4' chromosome 5 and 15 haplotypes.

    • TraitChromosome 5 haplotype from 'H4'pChromosome 15 haplotype from 'H4'p
      Dwarfing (n)Vigorous (n)Dwarfing (n)Vigorous (n)
      Height_20205A635B629.5E-0815_1A5715_1B788.0E-06
      Height_20215A635B624.8E-1015_1A5715_1B782.1E-08
      CL_AG_20205A635B621.1E-0715_1A5715_1B785.1E-06
      CL_AG_20215A635B627.5E-0815_1A5715_1B789.4E-09
      TS_AG_20205A635B624.8E-0515_1A5715_1B782.8E-04
      TS_AG_20215A635B629.7E-0815_1A5715_1B786.0E-06
      TCA_R10_20205A635B624.1E-0515_2A6215_2B768.3E-08
      TCA_R10_20215A635B626.5E-0915_2A6215_2B761.3E-08
      TCA_S20_20205A635B621.0E-0515_1A5715_1B786.7E-04
      TCA_S20_20215A635B621.1E-0815_1A5715_1B786.2E-07
      n: number of seedlings with the haplotype; Height: tree height; CL_AG: central leader annual growth; TS_AG: total scion annual growth; TCA_R10: rootstock trunk cross-sectional area at 10 cm below union; TCA_S20: scion trunk-sectional area at 20 cm above union.

      Table 3. 

      One-way analysis of variance (ANOVA) for dwarfing versus vigorous haplotype on chromosomes 5 and 15 of 'H4'.