Table 1.
Summary of 37 candidate genes associated with main flavor-related traits in tomato fruita
| Trait | Chr | BP | Ref | Alt | P | I 2 | Locus name | Candidate gene |
|---|---|---|---|---|---|---|---|---|
| Citrate | 1 | 1749084 | c | g | 3.62 × 10−13 | 0 | Solyc01g007090 | Aluminum-activated malate transporter |
| Citrate | 2 | 47904426 | a | g | 4.30 × 10−13 | 97.9 | Solyc02g084820 | Glycosyl transferase group 1 |
| Citrate | 3 | 52998165 | a | c | 1.84 × 10−15 | 0 | Solyc03g083090 | Glycogen synthase |
| Citrate | 6 | 44955568 | a | c | 7.46 × 10−27 | 98.4 | Solyc06g072920 | Aluminum-activated malate transporter |
| Citrate | 7 | 63601724 | t | g | 4.70 × 10−12 | 0 | Solyc07g055840 | Citrate synthase |
| Fructose | 1 | 3327330 | a | g | 6.37 × 10−11 | 0 | Solyc01g009150 | Glycosyl hydrolase |
| Fructose | 5 | 63485334 | c | g | 4.68 × 10−10 | 0 | Solyc05g053400a | Glucosyltransferase |
| Fructose | 7 | 63757414 | a | c | 4.28 × 10−09 | 0 | Solyc07g055840 | Citrate synthase |
| Fructose | 8 | 64470216 | a | g | 2.33 × 10−10 | 96.2 | Solyc08g081420 | Glycosyltransferase-like protein |
| Fructose | 10 | 422707 | a | t | 6.27 × 10−10 | 0 | Solyc10g005510a | Glyceraldehyde-3-phosphate dehydrogenase |
| Fructose | 10 | 65465775 | t | c | 6.84 × 10−09 | 0 | Solyc10g086720 | Fructose-1 6-bisphosphatase class 1 |
| Glucose | 1 | 1998383 | a | g | 2.36 × 10−10 | 0 | Solyc01g007910 | Succinyl-CoA ligase |
| Glucose | 2 | 43844073 | t | c | 2.87 × 10−09 | 96.7 | Solyc02g079220 | Solute carrier family facilitated glucose transporter member 8 |
| Glucose | 4 | 911809 | a | g | 6.62 × 10−09 | 0 | Solyc04g007160 | Alpha-glucosidase |
| Glucose | 8 | 58158082 | a | g | 4.99 × 10−08 | 0 | Solyc08g069060 | Beta-1 3-galactosyltransferase 6 |
| Glucose | 10 | 332069 | t | g | 1.20 × 10−09 | 0 | Solyc10g005510a | Glyceraldehyde-3-phosphate dehydrogenase |
| Malate | 1 | 2650772 | t | c | 2.08 × 10−15 | 0 | Solyc01g008550 | Cinnamoyl CoA reductase-like protein |
| Malate | 9 | 72364359 | a | t | 1.34 × 10−15 | 0 | Solyc09g098590 | Sucrose synthase |
| Malate | 11 | 55879120 | a | c | 7.14 × 10−16 | 0 | Solyc11g072700 | Glycosyltransferase-like protein |
| Malate | 12 | 1824226 | t | g | 1.75 × 10−19 | 0 | Solyc12g008430 | Malic enzyme |
| Asparagine | 2 | 54365596 | a | g | 3.72 × 10−10 | 94 | Solyc02g093550a | Methyltransferase type 11 |
| Asparagine | 5 | 62468569 | a | g | 8.92 × 10−09 | 0 | Solyc05g052170 | Acetyltransferase GNAT family protein |
| Asparagine | 12 | 64463407 | t | c | 1.13 × 10−09 | 0 | Solyc12g089350 | GDSL esterase/lipase |
| Aspartate | 8 | 60307917 | t | c | 6.35 × 10−09 | 0 | Solyc08g076350 | Abhydrolase domain-containing protein |
| Aspartate | 11 | 4008385 | t | g | 7.24 × 10−11 | 0 | Solyc11g010960 | Alcohol dehydrogenase |
| Aspartate | 12 | 37536492 | a | t | 9.16 × 10−08 | 0 | Solyc12g044940a | Short-chain dehydrogenase/reductase |
| Phenylalanine | 11 | 4002767 | t | c | 9.57 × 10−09 | 0 | Solyc11g010960 | Alcohol dehydrogenase |
| Proline | 3 | 66798980 | t | g | 2.39 × 10−09 | 0 | Solyc03g117770a | Serine incorporator 1 |
| Serine | 3 | 69913055 | a | g | 3.06 × 10−14 | 0 | Solyc03g121910 | Threonine synthase |
| Geranyl acetone | 2 | 40883244 | a | g | 6.00 × 10−15 | 0 | Solyc02g081330 | Phytoene synthase 2 |
| Hexenal | 1 | 1083181 | c | g | 1.45 × 10−10 | 0 | Solyc01g006540 | Lipoxygenase |
| Methyl salicylate | 9 | 69293875 | a | g | 2.34 × 10−19 | 0 | Solyc09g089580 | 1-aminocyclopropane-1-carboxylate oxidase-like protein |
| 1-penten-3-one | 5 | 3036212 | a | g | 7.07 × 10−09 | 0 | Solyc05g008800b | Lipid phosphate phosphatase 3 |
| 2-methyl-1-butanol | 6 | 37782796 | a | g | 5.50 × 10−09 | 0 | Solyc06g059850 | 3-methyl-2-oxobutanoate dehydrogenase |
| 6-methyl-5-hepten-2-one | 3 | 3212583 | t | c | 6.76 × 10−26 | 0 | Solyc03g025720 | Long-chain-fatty-acid--CoA ligase |
| 6-methyl-5-hepten-2-one | 4 | 60345897 | a | t | 3.00 × 10−11 | 0 | Solyc04g074360 | UDP-glucuronosyltransferase |
| 6-methyl-5-hepten-2-one | 10 | 61007386 | a | g | 9.28 × 10−09 | 0 | Solyc10g079470 | L-galactono--lactone dehydrogenase |
aA total of 305 loci for main tomato flavor-related quality traits were identified by meta-analysis of 775 tomato accessions and 2,316,117 SNPs. For each association, associated traits, chromosome (Chr), reference allele (Ref), alternative allele (Alt), the marker-trait association P value (P), heterogeneity I square (I2), locus name (International Tomato Annotation Group 2.4) and candidate genes are shown. All SNP positions were aligned on the tomato reference genome version 2.50. The P-value is reported from the random-effect model performed using the inverse variance-weighted fixed-effect model in METAL25. For those SNPs where heterogeneity occurs (I2 > 25, indicating moderate heterogeneity), we used the Han and Eskin random-effects model (RE2) implemented in METASOFT26. We also treated those candidate genes as new if previous GWAS did not report them though the association might be significant
bSignificant cis expression quantitative trait loci (cis-eQTLs) from a previous transcriptome-wide association study (TWAS)12 mainly based on panel T