Table 4 Gene annotation for the significant SNPs linked to phytate, trypsin inhibitors in the soybean. Candidate genes along with their functions are detailed below.
Trait | Method | SNP ID | Chr | Pos (Mb) | Gene ID | Functional annotation | PFAM | Reference |
|---|---|---|---|---|---|---|---|---|
Genome association and prediction integrated tool (GAPIT) | ||||||||
Phytate | FarmCPU | Soy_3_218818 | Gm03 | 218,818 | Glyma.03G001600 | Acid phosphatases | PF03767 | |
Gm03 | Glyma.03G009000 | Phosphatidylinositol N-Acetylglucosaminyltransferase | PF12552 | |||||
Gm03 | Glyma.03G010200 | Plant phosphoribosyltransferase C-terminal (PRT_C) | PF08372 | |||||
Gm03 | Glyma.03G002200 | Protein kinases | PF00069 | |||||
Gm03 | Glyma.03G002000 | O-Glycosyl hydrolases | PF16499 | |||||
Soy_4_45462019 | Gm04 | 45,462,019 | Glyma.04G194600 | Metallo-beta-lactamase superfamily | PF00753 | |||
Gm04 | Glyma.04G195633 | Lycopene epsilon-cyclase | PF05834 | |||||
Gm04 | Glyma.04G206100 | Phosphatidylinositol 4-phosphate 5-kinase 1-related | PF01504 | |||||
Gm04 | Glyma.04G203600 | Protein Suppressor of Gene Silencing 3 (SGS3) | PF03468 | |||||
Gm4 | Glyma.04G205200 | Defensin-like protein 6 (DEFL6) | PF00304 | |||||
Gm4 | Glyma.04G196900 | F-box domain | PF00646 | |||||
Gm4 | Glyma.04G194600 | Beta-lactamase | PF00753 | |||||
Soy_13_23167455 | Gm13 | 23,167,455 | Glyma.13G128200 | Protein phosphorylation | PF07714 | |||
Gm13 | Glyma.13G127800 | Tetratricopeptide repeat | PF07719 | |||||
Gm13 | Glyma.13G132400 | Inorganic pyrophosphatase | PF00719 | |||||
Gm13 | Glyma.13G132700 | Phosphatidylinositol-bisphosphatase | PF03372 | |||||
Soy_20_35904989 | Gm20 | 35,904,989 | Glyma.20G118700 | Glycerophosphodiester phosphodiesterase | PF00069 | |||
Glyma.20G118000 | Metallo-beta-lactamases | PF00753 | ||||||
Glyma.20G119100 | Protein phosphatase 2C 5-related | PF00481 | ||||||
TTI | CMLM | Soy_6_5695090 | Gm06 | 5,695,090 | Glyma.06G074700 | Serine protease inhibitor domain | PF00067 | |
Glyma.06G074300 | Kunitz/Bovine pancreatic trypsin inhibitor (BPTI) domain | PF13639 | ||||||
Glyma.06G077400 | WRKY transcription factor 11-related | PF10533 | ||||||
Glyma.06G078100 | Thioredoxin isoform B-related | PF07649 | ||||||
Glyma.06G074300 | Ring-Type Zinc finger | PF00010 | ||||||
Soy_12_41339023 | Gm12 | 41,339,023 | Glyma.12G241600 | Translation initiation factor 2D | PF01253 | |||
Glyma.12G241600 | Translation initiation factor SUI1 | PF01253 | ||||||
Glyma.12G240800 | Ring finger domain | PF13920 | ||||||
Soy_14_43649238 | Gm14 | 43,649,238 | Glyma.14G176700 | Protein kinase domain | PF00069 | |||
Glyma.14G178200 | Ring finger domain | PF13639 | ||||||
Glyma.14G185100 | Helix-loop-helix DNA-binding domain | PF00010 | ||||||
Multi-locus random-SNP-effect mixed linear model (mrMLM) | ||||||||
Phytate | mrMLM, FASTmrMLM | Soy_14_48672982 | Gm14 | 48,672,982 | Glyma.14G213400 | Diphosphoinositol Polyphosphate Phosphohydrolase | PF00293 | |
Glyma.14G214700 | Protein kinase domain | PF00069 | ||||||
Glyma.14G224300 | Cyclin, N-terminal domain | PF00134 | ||||||
mrMLM, FASTmrMLM | Soy_16_26978144 | Gm16 | 26,978,144 | Glyma.16G126400 | Glycosyl hydrolases family 38 C-terminal domains | PF07748 | ||
Glyma.16G128300 | TSL-Kinase interacting protein 1 | PF00249 | ||||||
TTI | mrMLM, FASTmrEMMA | Soy_13_14029215 | Gm13 | 14,029,215 | Glyma.13G052700 | K-box region | PF01486 | |
Glyma.13G053600 | Protein tyrosine kinase (Pkinase_Tyr) | PF07714 | ||||||
Glyma.13G053733 | U-Box domain-containing protein 50-related | NA | ||||||
Glyma.13G055200 | Eukaryotic translation initiation factor 3 subunit M | PF01399 | ||||||
Glyma.13G055400 | protein SPIRAL1 and related proteins (SPR1) | NA | ||||||
mrMLM, pLARmEB, ISIS EM-BLASSO | Soy_18_4301721 | Gm18 | 4,301,721 | Glyma.18G050400 | Cation efflux family | PF01545 | ||
Glyma.18G051500 | AP2 domain (transcription factors) | PF00847 | ||||||
Glyma.18G051600 | KIP1-like protein | PF07765 | ||||||
Glyma.18G050300 | Homodimerization region of STAR domain protein | PF16544 | ||||||
Glyma.18G050600 | Ribosomal protein L16p/L10e | PF00252 | ||||||
