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. 2023 Jun 7;14:1182790. doi: 10.3389/fpls.2023.1182790

Table 2.

SNP-trait associations and candidate genes for blackberry firmness and RDR detected across 2019-2021.

Trait Chromosome Model Position Ref Alt LOD r2 (%) i Variant type Gene Annotation and Arabidopsis homologii
Fruit firmness Ra01 additive 4352940 T G 5.84 5.27 Intron variant Ra_g890 Pectinesterase/pectinesterase inhibitor PPE8B; At3g43270
additive 4422023 T G 5.77 5.36 67,850 bp dsiii Ra_g890 Pectinesterase/pectinesterase inhibitor PPE8B; At3g43270
Ra02 additive 6321370 C T 6.11 11.40 Silent Ra_g5252 Glucan endo-1,3-beta-glucosidase 7; At4g34480
additive 6321387 T C 5.48 10.48 Missense Ra_g5252 Glucan endo-1,3-beta-glucosidase 7; At4g34480
general 8025922 G T 5.55 12.70 NA
Ra03 general 3633404 G A 6.34 8.76 833,124 bp usiv Ra_g10675 Glucan endo-1,3-beta-D-glucosidase; At2g43670
Ra06 general 17273160 A G 7.21 11.47 Silent Ra_g27483 Probable polygalacturonase; At3g15720
RDR Ra02 1-dom-ref 5150596 G A 6.05 8.26 Missense Ra_g5108 Probable polygalacturonase; At3g15720
1-dom-ref 5150747 G T 5.63 7.66 Missense Ra_g5108 Probable polygalacturonase; At3g15720
1-dom-ref 6320015 C A 5.52 7.44 Missense Ra_g5252 Glucan endo-1,3-beta-glucosidase 7; At4g34480
general 13296902 v C A 7.00 11.13 Intron variant Ra_g5949 2-oxoglutarate-dependent dioxygenase; AT2G36690.2
1-dom-ref 21494838 C T 5.55 7.64 Missense Ra_g6621 Endo-1,3;1,4-beta-D-glucanase; At3g23600
1-dom-ref 21495058 A T 6.02 8.33 Missense Ra_g6621 Endo-1,3;1,4-beta-D-glucanase; At3g23600
1-dom-ref 24484457 T C 5.76 7.97 Missense Ra_g7012 Expansin-like A1; At3g45970
1-dom-ref 24485338 T C 5.38 7.41 Missense Ra_g7012 Expansin-like A1; At3g45970
1-dom-ref 24485380 C A 5.38 7.41 Missense Ra_g7012 Expansin-like A1; At3g45970
1-dom-ref 25139841 T C 5.46 7.47 Missense Ra_g7125 Expansin-A20; At4g38210
1-dom-ref 25140011 G A 5.76 7.97 Nonsense Ra_g7125 Expansin-A20; At4g38210
1-dom-ref 25140131 T A 5.76 7.97 Missense Ra_g7125 Expansin-A20; At4g38210
1-dom-ref 25140272 A C 5.81 7.96 Missense Ra_g7125 Expansin-A20; At4g38210
1-dom-ref 26764458 T C 5.38 7.51 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 26765115 G C 5.76 7.97 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 26765139 A G 5.38 7.51 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 26765333 A G 5.38 7.51 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 26765357 G A 5.76 7.97 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 26765634 T G 5.76 7.97 Missense Ra_g7381 Glucan endo-1,3-beta-glucosidase A6; At3g07320
1-dom-ref 27713275 A G 5.38 7.41 Missense Ra_g7552 Probable pectate lyase 8; At3g07010
1-dom-ref 27715029 C T 5.38 7.51 Missense Ra_g7552 Probable pectate lyase 8; At3g07010
1-dom-ref 27715116 A G 5.76 7.97 Missense Ra_g7552 Probable pectate lyase 8; At3g07010
i

Phenotypic r2 estimates were calculated based on single marker prediction models.

iiThe SwissProt and Araport11 databases were interrogated for descriptions of gene homologs and the Arabidopsis homolog identifier following Brůna et al., 2022.

iiiDownstream from candidate end position.

ivUpstream from candidate start position.

v

Not on or near any annotated gene with known role in cell wall disassembly.

All significant SNPs for fruit firmness are listed, but only 22 of 212 significant RDR SNPs were listed. All but one of these 22 SNPs with significant RDR associations were nonsynonymous mutations on genes with previously documented roles in cell wall modification/degradation. The full list of significant genes associated with RDR is available in Supplementary Table 2 .