Table 3.
List of 28 known chlorophyll-related genes within a ± 3 MB region of the 43 putative candidate SNPs identified from Soybase (www.soybase.org) for extractable chlorophyll a (eChl_A), chlorophyll b (eChl_B), total chlorophyll (eChl_T) and chlorophyll a/b ratio (eChl_R)
| Loci | Gene a | Chromosome | Start | Stop | Soybase b /Pathway/Reference | Distance to SNP (Mb) | Functional annotation | Trait |
|---|---|---|---|---|---|---|---|---|
| 1 | Glyma01g41320 | Gm01 | 528,55,359 | 528,56,591 | Glyma 1.0 | 0.29 | Chlorophyll A-B binding protein | eChl_R |
| Glyma01g43630 | Gm01 | 545,89,487 | 545,98,903 | Glyma 1.0 | 1.80 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_R | |
| Glyma01g43720 | Gm01 | 546,67,132 | 546,69,898 | Glyma 1.0 | 1.80 | Tetrapyrrole biosynthetic process (Porphobilinogen deaminase) | eChl_R | |
| Glyma01g42390 | Gm01 | 545,54,210 | 545,56,460 | Fang et al 2014 | 1.80 | Stay-Green (SGR) gene D2 (Chlorophyll catabolic process) | eChl_R | |
| 2 | Glyma04g04110 | Gm04 | 30,19,987 | 30,21,151 | Glyma 1.0 | 2.64 | Chlorophyll A-B binding protein | eChl_A |
| 3 | Glyma04g37740 | Gm04 | 441,63,842 | 441,70,887 | Glyma 1.1 | 0.98 | regulation of transcription, DNA-templated | eChl_A and eChl_T |
| 5 | Glyma05g01000 | Gm05 | 6,06,608 | 6,08,812 | Glyma 1.0 | 1.11 | Electron transfer flavoprotein-Ubiquinone oxidoreductase | eChl_B, eChl_R and eChl_T |
| 6 | Glyma05g05450 | Gm05 | 47,64,696 | 47,66,688 | Glyma 1.0 | 2.14 | Chlorophyll A-B binding family protein | eChl_B, eChl_R and eChl_T |
| 7 | Glyma06g17360 | Gm06 | 136,67,004 | 136,74,569 | Glyma 1.0 | 0.13 | Regulation of transcription, DNA-templated (ATP-dependent CLP protease) | eChl_R |
| 8 | Glyma07g18470 | Gm07 | 184,08,168 | 184,13,639 | Glyma 1.0 | 1.05 | Prenyltransferase activity | eChl_A and eChl_T |
| 9 | Glyma07g32550 | Gm07 | 374,27,501 | 374,30,163 | KEGG pathway database | 1.69 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_R |
| Glyma07g33320 | Gm07 | 382,60,227 | 382,61,619 | Glyma 1.0 | 2.52 | UbiA prenyltransferase family (prenyltransferase activity) | eChl_R | |
| 12 | Glyma10g13190 | Gm10 | 148,88,257 | 149,01,045 | Glyma 1.1 | 2.86 | Pyridine nucleotide-disulphide oxidoreductase | eChl_B |
| 13 | Glyma10g32080 | Gm10 | 405,24,508 | 405,27,468 | Glyma 1.0 | 0.27 | Chlorophyll A-B binding protein | eChl_A and eChl_T |
| 15 | Glyma15g05790 | Gm15 | 41,14,634 | 41,16,181 | Glyma 1.0 | 1.09 | Chlorophyll A-B binding protein | eChl_R |
| Glyma15g06050 | Gm15 | 42,95,728 | 43,06,099 | Glyma 1.0 | 1.28 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_R | |
| Glyma15g08680 | Gm15 | 61,55,823 | 61,58,347 | Campbell et al 2015 | 2.93 | Magnesium chelatase activity | eChl_R | |
| 16 | Glyma15g16570 | Gm15 | 128,69,848 | 128,76,153 | Glyma 1.0 | 1.49 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_A, eChl_B and eChl_T |
| 17 | Glyma15g42140 | Gm15 | 495,29,893 | 495,34,600 | Glyma 1.0 | 1.51 | ATP-citrate synthase | eChl_R |
| Glyma15g43150 | Gm15 | 514,86,036 | 514,91,942 | Reed et al 2014 | 2.96 | Biogenesis of Photosystem I and II | eChl_R | |
| 18 | Glyma16g24570 | Gm16 | 285,47,662 | 285,50,487 | Glyma 1.0 | 0.65 | Chlorophyll catabolic process (Chlorophyllase.) | eChl_T |
| Glyma16g26130 | Gm16 | 303,09,204 | 303,11,593 | Glyma 1.0 | 2.41 | Chlorophyll A-B binding protein | eChl_T | |
| 19 | Glyma17g15730 | Gm17 | 124,56,729 | 124,58,671 | Glyma 1.0 | 0.41 | Chlorophyll A-B binding protein | eChl_R |
| 21 | Glyma19g30350 | Gm19 | 379,57,536 | 379,60,664 | Glyma 1.0 | 1.17 | Oxidation-reduction process (Rubrerythrin) | eChl_A, eChl_B and eChl_T |
| 22 | Glyma19g32070 | Gm19 | 398,43,036 | 398,49,603 | Glyma 1.0 | 2.97 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_A, eChl_B and eChl_T |
| 23 | Glyma19g40370 | Gm19 | 467,94,372 | 467,99,578 | Glyma 1.0 | 0.27 | Magnesium chelatase activity (chlorophyll biosynthetic process) | eChl_A and eChl_T |
| 24 | Glyma20g35530 | Gm20 | 438,24,060 | 43826992 | Glyma 1.0 | 1.36 | Chlorophyll A-B binding protein | eChl_A, eChl_B and eChl_T |
| Glyma20g38941 | Gm20 | 464,38,179 | 46439540 | Glyma 1.1 | 0.92 | Homogentisate phytyltransferase 1 | eChl_A, eChl_B and eChl_T |
a As reported in Soybase
b Annotation version information based on Soybase