Table 2.
Summary of SNP–trait associations related to sweet cherry fruit quality.
| Traits/reference genome | Chromosome | Physical position (bp) | Significance (P value) | Model | R 2a | Allele b /effect c |
|---|---|---|---|---|---|---|
| Fruit stem end cracking (SE) | ||||||
| Sweet cherry ‘Regina’ | 7 | 21 757 494 | 1.13e−10 | MLMM | 5.9 | A/G |
| 7 | 26 772 180 | 4.88e−07 | FarmCPU | 3.9 | A/C (0.01) | |
| Sweet cherry ‘Satonishiki’ | 4 | 4 381 656 | 1.13e−10 | MLMM | 30.9 | A/G |
| 1 | 26 464 729 | 2.00e−07 | FarmCPU | 20.9 | C/A (0.01) | |
| 4 | 4 381 656 | 1.38e−14 | 30.9 | A/G (−0.07) | ||
| 7 | 17 821 793 | 2.98e−07 | 9.6 | C/G (0.008) | ||
| 8 | 6 129 863 | 4.13e−07 | 16.0 | C/T (0.01) | ||
| Peach ‘PLov2-2n’ | 1 | 18 149 428 | 1.13e−10 | MLMM | 4.8 | A/T |
| 1 | 29 966 902 | 2.12e−09 | FarmCPU | 5.5 | A/G (0.009) | |
| 8 | 11 366 089 | 4.82e−09 | 6.0 | G/C (0.03) | ||
| Fruit pistillar end cracking | ||||||
| Sweet cherry ‘Regina’ | 4 | 6 606 690 | 1.38e−09 | MLMM | 8.9 | T/C |
| 1 | 759 551 | 1.64e−09 | FarmCPU | 11.4 | A/G (−0.01) | |
| 6 | 22 196 234 | 6.48e−09 | 7.7 | A/G (−0.009) | ||
| 6 | 31 626 357 | 1.10e−07 | 3.2 | G/A (−0.02) | ||
| 7 | 16 540 822 | 1.77e−07 | <0.1 | C/T (0.007) | ||
| 7 | 24 643 127 | 6.15e−09 | 6.9 | A/G (0.01) | ||
| Peach ‘PLov2-2n’ | 1 | 38 293 536 | 2.40e−09 | MLMM | 0.6 | A/C |
| 4 | 13 790 367 | 9.98e−15 | 9.0 | T/A | ||
| 1 | 13 745 047 | 1.74e−07 | FarmCPU | 2.8 | T/C (−0.01) | |
| 4 | 13 790 367 | 6.80e−16 | 9.0 | T/A (−0.06) | ||
| 5 | 1 152 140 | 1.39e−08 | 7.4 | A/G (−0.02) | ||
| 7 | 7 874 904 | 7.49e−11 | 4.9 | A/G (−0.03) | ||
| Fruit weight (FW) | ||||||
| Sweet cherry ‘Regina’ | 1 | 11 561 777 | 4.11e−13 | FarmCPU | 5.1 | T/G (0.82) |
| 1 | 38 707 331 | 1.08e−09 | 2.5 | A/T (0.44) | ||
| 1 | 50 388 238 | 5.52e−10 | 18.8 | G/A (−0.57) | ||
| 2 | 4 882 204 | 7.96e−08 | 5.8 | A/G (−0.31) | ||
| 3 | 15 787 719 | 1.34e−07 | 2.5 | T/C (0.45) | ||
| 3 | 26 866 585 | 4.78e−08 | 1.6 | T/C (−0.47) | ||
| 4 | 12 024 925 | 2.12e−07 | 17.2 | A/G (−0.42) | ||
| 4 | 21 277 766 | 4.42e−09 | 1.9 | A/G (0.54) | ||
| 6 | 11 112 467 | 1.59e−08 | <0.1 | T/C (0.51) | ||
| Peach ‘PLov2-2n’ | 2 | 28 325 332 | 8.87e−08 | FarmCPU | 7.3 | G/A (0.36) |
| 3 | 21 433 100 | 6.06e−09 | <0.1 | A/C (−0.45) | ||
| Fruit width | ||||||
| Sweet cherry ‘Regina’ | 1 | 50 388 238 | 8.60e−08 | FarmCPU | 15.0 | G/A (−0.79) |
| 3 | 27 845 320 | 2.41e−09 | <0.1 | A/T (−0.61) | ||
| 7 | 18 276 189 | 4.17e−11 | 8.0 | G/A (−0.70) | ||
| Peach ‘PLov2-2n’ | 1 | 8 612 931 | 1.48e−07 | FarmCPU | <0.1 | C/T (−0.69) |
| Fruit thickness | ||||||
| Sweet cherry ‘Regina’ | 1 | 50 388 238 | 3.38e−10 | FarmCPU | 17.3 | G/A (−1.00) |
| 2 | 4 882 204 | 3.23e−10 | 7.2 | A/G (−0.68) | ||
| 2 | 7 007 862 | 4.33e−11 | <0.1 | A/C (−1.00) | ||
| 6 | 23 191 731 | 2.25e−07 | 3.1 | T/C (0.79) | ||
| 7 | 18 276 189 | 2.98e−08 | 7.5 | G/A (−0.60) | ||
| 7 | 22 298 828 | 1.51e−07 | <0.1 | A/C (−0.58) | ||
| Peach ‘PLov2-2n’ | 1 | 34 857 341 | 1.13e−07 | FarmCPU | 6.9 | C/T (0.68) |
| 2 | 9 537 634 | 1.06e−10 | 8.6 | T/C (0.82) | ||
| 3 | 21 433 100 | 3.25e−09 | <0.1 | A/C (−0.60) | ||
| 4 | 20 079 115 | 3.96e−07 | 12.6 | A/G (0.45) | ||
| Stone width | ||||||
| Sweet cherry ‘Regina’ | 2 | 2 834 950 | 6.79e−09 | FarmCPU | 18.8 | T/G (0.20) |
| 3 | 1 281 929 | 1.32e−08 | 14.3 | T/C (0.21) | ||
| 4 | 9 562 013 | 9.05e−09 | 11.1 | T/C (−0.18) | ||
| 6 | 3 901 121 | 6.49e−10 | 7.4 | T/C (0.28) | ||
| Peach ‘PLov2-2n’ | 3 | 4 481 012 | 1.40e−08 | FarmCPU | 13.3 | C/T (−0.30) |
| 4 | 4 708 404 | 4.81e−09 | 0.4 | A/G (−0.22) | ||
| 4 | 11 571 511 | 1.36e−07 | 1.2 | A/C (−0.16) | ||
| Stone thickness | ||||||
| Sweet cherry ‘Regina’ | 8 | 21 099 455 | 1.75e−07 | FarmCPU | 4.4 | A/C (−0.25) |
| Sweet cherry ‘Satonishiki’ | 2 | 13 099 549 | 7.32e−15 | FarmCPU | 27.3 | A/G (−0.41) |
| 3 | 12 470 834 | 3.69e−07 | 10.9 | T/C (0.16) | ||
| 4 | 11 934 189 | 4.51e−10 | 14.8 | T/A (−0.19) | ||
| 4 | 17 172 922 | 1.35e−07 | 3.9 | T/A (−0.23) | ||
| 7 | 10 879 301 | 4.57e−07 | <0.1 | C/T (0.14) | ||
| Peach ‘PLov2-2n’ | 5 | 986 062 | 8.36e−08 | FarmCPU | 6.3 | A/G (−0.37) |
| 8 | 12 886 531 | 2.10e−07 | 12.2 | C/T (0.18) | ||
| Stone shape in central view | ||||||
| Peach ‘PLov2-2n’ | 2 | 11 962 528 | 5.52e−12 | FarmCPU | 19.7 | G/C (0.08) |
| 3 | 20 497 027 | 8.12e−09 | 3.3 | A/C (−0.10) | ||
| 3 | 23 321 947 | 3.98e−13 | 1.8 | C/G (−0.10) | ||
Allelic effect not available for the MLMM model.
Physical positions in italics indicate identical marker–trait associations between GWAS models.
Physical positions in bold indicate identical marker–trait associations between traits.
a
R 2 is the percentage of variance explained corrected for genome-wide background.
b
The first allele mentioned is the minor allele.
c
The allelic effect is the difference in mean of BLUPs between genotypes with one or other allele (sign: minor allele).