Table 3.
Annotation of significantly associated SNPs for peduncle length in C. baccatum var. pendulum.
| Marker | P-Value | −log10(P-Value) | FDR | Locus ID | Location | Ma → Mi | Sy/NSy | Annotation/Function |
|---|---|---|---|---|---|---|---|---|
| S7_19145046 | 1.13E−06 | 5.947 | 0.015 | CA07g03460/CA07g03470 | Intergenic | G → C | – | Oxidoreductase family protein/Arogenate dehydrogenase |
| S7_19145048 | 1.13E−06 | 5.947 | 0.007 | ” | ” | C → T | ” | Oxidoreductase family protein/Arogenate dehydrogenase |
| S7_19145066 | 1.13E−06 | 5.947 | 0.005 | ” | ” | T → A | ” | Oxidoreductase family protein/Arogenate dehydrogenase |
| S7_19145073 | 1.13E−06 | 5.947 | 0.004 | ” | ” | C → T | ” | Oxidoreductase family protein/Arogenate dehydrogenase |
| S2_134518344 | 3.89E−06 | 5.410 | 0.010 | CA02g11490 | Exon | G → C | R → P* | Phospho-n-acetylmuramoyl-pentapeptide-transferase |
| S11_725918 | 7.48E−06 | 5.126 | 0.016 | CA11g00270/CA11g00280 | Intergenic | C → G | – | GABA-specific permease/Unknown protein |
| S2_121116327 | 2.01E−05 | 4.697 | 0.038 | CA02g09090 | Exon | G → T | T → K* | LON peptidase N-terminal domain and RING finger protein |
| S3_12740983 | 2.22E−05 | 4.653 | 0.036 | CA03g04980 | Intron | C → T | – | Eukaryotic translation initiation factor 2 subunit alpha |
| S11_190326151 | 3.12E−05 | 4.505 | 0.046 | CA11g12020 | Exon | G → A | S → S | Tho2 protein |
| S11_3937182 | 5.13E−05 | 4.289 | 0.061 | CA11g01740 | Exon | T → A | Q → L* | Hydroxyproline-rich glycoprotein |
| S3_200716267 | 6.71E−05 | 4.173 | 0.073 | CA03g17680 | Intron | A → C | – | Pre-mRNA cleavage factor IM |
| S11_246730373 | 0.0001 | 3.916 | 0.122 | CA11g15960 | Intron | G → A | – | ATP-dependent RNA helicase |
| S4_137196865 | 0.0001 | 3.864 | 0.128 | CA04g10860/CA04g10870 | Intergenic | C → T | – | Amino acid transporter/UDP-glucose 6-dehydrogenase |
| S4_137196912 | 0.0001 | 3.864 | 0.120 | ” | ” | C → A | ” | Amino acid transporter/UDP-glucose 6-dehydrogenase |
| S10_223493543 | 0.0002 | 3.807 | 0.128 | CA10g17500/CA10g17510 | Intergenic | C → G | Cytochrome b559 subunit alpha/Aluminum-activated malate transporter | |
| S8_126682716 | 0.0002 | 3.730 | 0.144 | CA08g09170 | Exon | C → T | G → R* | Ribosomal protein S11 |
| S8_126682746 | 0.0002 | 3.730 | 0.136 | ” | ” | C → A | A → S* | Ribosomal protein S11 |
| S9_252073885 | 0.0004 | 3.449 | 0.195 | CA09g18340 | Promoter | G → A | – | Reticulon-like protein B21 |
| S9_252073890 | 0.0004 | 3.449 | 0.187 | ” | ” | G → A | ” | Reticulon-like protein B21 |
| S11_190326131 | 0.0004 | 3.449 | 0.180 | CA11g12020 | Exon | G → A | S → L* | Tho2 protein |
| S10_229515157 | 0.0004 | 3.412 | 0.188 | CA10g19840 | Exon | G → A | S → F* | Uncharacterized protein |
| S6_2635088 | 0.0004 | 3.381 | 0.195 | CA06g01230/CA06g01240 | Intergenic | T → C | – | Late blight resistance protein Rpi-blb2/Detected protein of confused Function |
| S8_142510499 | 0.0005 | 3.315 | 0.219 | CA08g18030 | Exon | A → T | M → L* | Serine/Threonine-protein kinase SMG1 |
| S1_96976222 | 0.0005 | 3.285 | 0.227 | CA01g16010 | Exon | T → C | T → T | Phytochrome |
| S2_139076418 | 0.0005 | 3.263 | 0.231 | CA02g13050 | Intron | T → G | – | Ureidoglycolate hydrolase |
| S3_70295226 | 0.0006 | 3.220 | 0.247 | CA03g11420/CA03g11430 | Intergenic | C → T | – | Detected protein of confused Function/NADH dehydrogenase subunit |
| S3_257225287 | 0.0006 | 3.188 | 0.251 | CA03g36710/CA03g36720 | Intergenic | C → T | – | LRR receptor protein kinase/LRR receptor protein kinase |
| S11_257395608 | 0.0007 | 3.183 | 0.246 | CA11g19730 | Exon | C → T | H → H | ABC transporter |
| S11_257395610 | 0.0007 | 3.183 | 0.239 | ” | ” | C → A | A → D* | ABC transporter |
| S2_130946711 | 0.0007 | 3.180 | 0.234 | CA02g10590/CA02g10600 | Intergenic | C → T | – | Nucleic acid binding protein/cleavage and polyadenylation specificity factor CPSF30 |
| S3_252341359 | 0.0008 | 3.078 | 0.289 | CA03g33810 | Intron | T → G | – | DNase I-like superfamily protein |
| S1_131644198 | 0.0009 | 3.046 | 0.303 | CA01g17480 | Promoter | A → G | – | Diacylglycerol kinase variant B |
*
Nonsynonymous mutation on amino acid due to minor/major allele SNP variation.