Table 2.
Significant SNPs associated with amylose content and texture-related traits identified using several multi-locus GWAS method.
| SNP_ID | Chr | Method(s) used | LOD | r2 (%) | Trait | Gene | Nucleotide change | SNP location/Amino acid change | SWISSPROT |
|---|---|---|---|---|---|---|---|---|---|
| snp_01_3464018 | 1 | pLARmEB; FASTmrEMMA | 3.38; 4.63 | 0.76; 4.04 | SPR | LOC_Os01g07330 | c.-187A>G | Promoter region | No hits |
| snp_01_10014553 | 1 | pLARmEB; ISIS_EM-BLASSO; FASTmrEMMA; mrMLM | 4.50; 5.36; 7.97; 13.09 | 0.33; 3.96; 5.55; 6.54 | ADH | LOC_Os01g17402 | c.-3673C>A | p.Val140Ile | No hits |
| snp_01_31665007 | 1 | FASTmrEMMA; mrMLM; pLARmEB | 3.76; 8.18; 17.48 | 1.65; 3.04; 0.74 | ADH | LOC_Os01g55070 | c.-3673C>A | Downstream gene | No hits |
| snp_01_4991874 | 1 | ISIS_EM-BLASSO; FASTmrEMMA | 3.51; 10.29 | 0.76; 2.43 | AC | LOC_Os01g09680 | c.212-4G>A | Promoter region | Cyclin-B1-3 |
| snp_01_4991874 | 1 | FASTmrEMMA | 5.98 | 2.53 | ADH | LOC_Os01g09680 | c.-926C>T | Promoter region | Pentatricopeptide repeat containing protein |
| snp_02_23917456 | 2 | pLARmEB | 10.44 | 3.08 | HRD | LOC_Os02g39630 | c.*4252G>A | Intergenic region | No hits |
| snp_02_29507254 | 2 | pLARmEB; mrMLM | 3.82; 6.21 | 0.08; 2.26 | AC | LOC_Os02g48184 | c.-5090C>T | Promoter region | No hits |
| snp_02_30672463 | 2 | mrMLM; pLARmEB | 6.89; 6.90 | 7.41; 2.15 | HRD | LOC_Os02g50230 | c.1227C>T | p.Ala399Val | No hits |
| snp_03_30485102 | 3 | pLARmEB; FASTmrEMMA | 3.60; 4.42 | 0.08; 1.36 | AC | LOC_Os03g53150 | c.-1973G>A | Auxin-responsive protein_IAA13 | |
| snp_04_33203256 | 4 | pLARmEB; ISIS_EM-BLASSO | 5.82; 8.86 | 0.13; 2.15 | AC | LOC_Os04g55780 | c.-2831T>C | Intergenic region | No hits |
| snp_04_8836677 | 4 | mrMLM; pLARmEB | 4.57; 13.14 | 1.38; 0.48 | ADH | LOC_Os04g16260 | c.-3159G>A | Promoter region | Arogenate dehydratase/prephenate dehydratase |
| snp_05_12361761 | 5 | pLARmEB; ISIS_EM-BLASSO | 4.36; 5.47 | 3.07; 10.70 | HRD | LOC_Os05g21010 | c.418G>A | p.Val140Ile | No hits |
| snp_05_13977160 | 5 | ISIS_EM-BLASSO; pLARmEB | 3.42; 6.05 | 1.26; 0.27 | AC | LOC_Os05g24190 | c.*3646T>C | Downstream gene | polyprotein |
| snp_05_15589585 | 5 | ISIS_EM-BLASSO; FASTmrEMMA; mrMLM; pLARmEB | 6.11; 11.45; 13.72; 26.36 | 3.05; 5.03; 4.72; 1.22 | ADH | LOC_Os05g26850 | c.-2404T>A | Promoter region | No hits |
| snp_05_21765243 | 5 | pLARmEB; FASTmrEMMA | 4.66; 13.75 | 0.11; 4.42 | AC | LOC_Os05g37225 | c.-2713C>T | Promoter region | No hits |
| snp_05_27396039 | 5 | mrMLM; ISIS_EM-BLASSO | 3.82; 6.36 | 2.29; 3.77 | HRD | LOC_Os05g47790-LOC_Os05g47810 | n.27396039A>G | Intergenic region | No hits |
| snp_06_19437296 | 6 | mrMLM; ISIS_EM-BLASSO; pLARmEB | 3.92; 4.15; 6.69 | 1.47; 1.15; 0.17 | AC | LOC_Os06g33360 | c.-1942C>T | Promoter region | No hits |
| snp_06_27648676 | 6 | pLARmEB; mrMLM | 6.72; 7.82 | 0.32; 3.00 | ADH | LOC_Os06g45650-LOC_Os06g45660 | c.1196C>T | p.Ala399Val | NB-ARC_domain-containing protein |
| snp_06_6710536 | 6 | pLARmEB; mrMLM | 4.56; 7.11 | 0.12; 2.00 | AC | LOC_Os06g12380 | n.27648676A>G | Intergenic region | No hits |
| snp_07_15625737 | 7 | mrMLM; pLARmEB | 3.38; 6.96 | 1.29; 0.21 | ADH | LOC_Os07g26990 | c.52G>A | p.Thr18Thr | No hits |
| snp_07_15950275 | 7 | pLARmEB | 4.01 | 0.7 | SPR | LOC_Os07g27390-LOC_Os07g27400 | n.15950275C>T | Intergenic region | No hits |
| snp_07_15950275 | 7 | ISIS_EM-BLASSO; pLARmEB | 4.61; 7.83 | 3.56; 2.23 | HRD | LOC_Os07g27390-LOC_Os07g27400 | n.15950275C>T | Intergenic region | No hits |
| snp_07_23649340 | 7 | ISIS_EM-BLASSO | 3.06 | 1.5 | SPR | LOC_Os07g39470 | c.-2786T>G | Promoter region | Chitin-inducible gibberellin responsive gene |
| snp_07_26549549 | 7 | pLARmEB | 5.59 | 0.06 | AC | LOC_Os07g44430 | c.513C>T | p.Asp171Asp | phospholipase |
| snp_08_20145633 | 8 | FASTmrEMMA; pLARmEB | 5.90; 6.40 | 1.03; 0.09 | AC | LOC_Os08g32520 | c.*441G>A | Downstream gene | No hits |
| snp_09_14649274 | 9 | pLARmEB; ISIS_EM-BLASSO; mrMLM | 3.72; 3.80; 4.7 | 0.15; 1.82; 2.42 | ADH | LOC_Os09g24590 | c.-3712C>T | Promoter region | polyprotein |
| snp_09_4018179 | 9 | ISIS_EM-BLASSO; pLARmEB; mrMLM | 3.60; 4.18; 6.67 | 1.32; 0.11; 1.91 | ADH | LOC_Os09g07890 | c.*523A>T | 3 prime UTR | No hits |
| snp_10_11723831 | 10 | FASTmrEMMA; mrMLM | 4.07; 6.25 | 1.27; 1.43 | ADH | LOC_Os10g22590 | c.-2300C>T | Promoter region | No hits |
| snp_10_13693521 | 10 | ISIS_EM-BLASSO; FASTmrEMMA | 3.69; 5.76 | 10.69; 0.00 | COH | LOC_Os10g26370 | c.187+112C>A | Intron | allergen and extensin family protein |
| snp_10_5839378 | 10 | mrMLM; pLARmEB | 4.12; 7.89 | 8.67; 5.85 | HRD | LOC_Os10g10580 | c.*4639A>T | Downstream gene | No hits |
| snp_11_10872055 | 11 | pLARmEB; ISIS_EM-BLASSO | 4.29; 5.27 | 0.16; 2.56 | AC | LOC_Os11g19060 | c.*3782C>T | Downstream gene | AP2-like ethylene-responsive transcription famylose contenttor |
| snp_11_22559123 | 11 | ISIS_EM-BLASSO; pLARmEB | 3.35; 3.93 | 1.74; 0.80 | HRD | LOC_Os11g38020 | c.1110+4C>T | Splice variant | small GTP-binding protein |
| snp_11_23638170 | 11 | ISIS_EM-BLASSO; FASTmrEMMA | 3.71; 4.50 | 1.10; 1.49 | ADH | LOC_Os11g39680 | c.*2157G>A | Downstream gene | No hits |
| snp_12_10170782 | 12 | pLARmEB; ISIS_EM-BLASSO; mrMLM | 6.29; 8.71; 10.25 | 2.26; 7.76; 10.68 | HRD | LOC_Os12g17750 | c.830G>A | p.Gly277Asp | No hits |
| snp_12_1204320 | 12 | FASTmrEMMA; mrMLM | 3.10; 5.90 | 3.24; 5.81 | HRD | LOC_Os12g03160 | c.-4154C>T | Promoter region | No hits |
| snp_12_12232293 | 12 | mrMLM; pLARmEB | 3.62; 6.64 | 11.00; 0.27 | SPR | LOC_Os12g21750 | c.-4282G>C | Promoter region | No hits |
| snp_12_12385384 | 12 | ISIS_EM-BLASSO | 4.96 | 2.89 | SPR | LOC_Os12g22020 | c.175-375G>A | Intron | No hits |
| snp_12_12385384 | 12 | ISIS_EM-BLASSO | 6.35 | 12.05 | COH | LOC_Os12g22020 | c.175-375G>A | Intron | No hits |