Table 7.
Putative candidate genes associated with chlorophyll fluorescence phenotypes based on the multi phenotype loci (MPL)
| Gene ID | Chromosome | Start | End | Soybase | Mb to nearest MPL-SNP | Functional annotation | Annotation category |
|---|---|---|---|---|---|---|---|
| Glyma.01G017400 | Gm01 | 1,653,678 | 1,657,140 | Glyma 2.0 | 0.5407 | RNA-binding (RRM/RBD/RNP motifs) family protein | Nucleotide Binding |
| Glyma.01G028900 | Gm01 | 3,060,271 | 3,064,492 | Glyma 2.0 | 0.8659 | ATP-citrate lyase A-1 | Chlorophyll biosynthesis |
| Glyma.02G036300 | Gm02 | 3,341,760 | 3,346,084 | Glyma 2.0 | 0.8471 | ATP-citrate lyase A-1 | Chlorophyll biosynthesis |
| Glyma.02G047600 | Gm02 | 4,376,285 | 4,379,912 | Glyma 2.0 | 0.1874 | Ferredoxin-NADP(+)-oxidoreductase 1 | Biochemical |
| Glyma.07G057200 | Gm07 | 5,078,005 | 5,083,913 | Glyma 2.0 | 0.4456 | THYLAKOID RHODANESE-LIKE, TROLa | Protein stability |
| Glyma.07G059600 | Gm07 | 5,317,552 | 5,319,355 | Glyma 2.0 | 0.2061 | NdhV | Protein stability |
| Glyma.10G153100 | Gm10 | 38,772,208 | 38,774,371 | Glyma 2.0 | 0.9477 | Photosystem II reaction center PsbP family protein | PSII protein |
| Glyma.11G094700 | Gm11 | 7,190,632 | 7,195,838 | Glyma 2.0 | 0.9096 | Hydroxymethylbilane synthase. | Chlorophyll biosynthesis |
| Glyma.11G100800 | Gm11 | 7,629,148 | 7,632,965 | Glyma 2.0 | 0.4711 | Photosystem II stability/assembly factor, chloroplast (HCF136) | PSII stability |
| Glyma.11G108800 | Gm11 | 8,294,535 | 8,297,524 | Glyma 2.0 | 0.1943 | IMPAIRED SUCROSE INDUCTION 1a | Photosynthetic gene regulation |
| Glyma.11G108900 | Gm11 | 8,299,154 | 8,302,660 | Glyma 2.0 | 0.1989 | pfkB-like carbohydrate kinase family protein | Photosynthetic gene regulation |
| Glyma.11G110000 | Gm11 | 8,387,146 | 8,394,939 | Glyma 2.0 | 0.2869 | NAD(P)-binding Rossmann-fold superfamily protein. GIANT CHLOROPLAST 1 | Chloroplast structure |
| Glyma.11G111100 | Gm11 | 8,483,000 | 8,499,771 | Glyma 2.0 | 0.3828 | Fructose-bisphosphate aldolase 2 | Calvin cycle |
| Glyma.11G111400 | Gm11 | 8,496,826 | 8,499,771 | Glyma 2.0 | 0.3966 | Fructose-bisphosphate aldolase 2 | Calvin cycle |
| Glyma.11G112900 | Gm11 | 8,633,078 | 8,637,349 | Glyma 2.0 | 0.5329 | CGLD11, CONSERVED IN THE GREEN LINEAGE AND DIATOMS 11a | ATP synthase |
| Glyma.11G114700 | Gm11 | 8,753,784 | 8,755,152 | Glyma 2.0 | 0.6536 | Photosystem II reaction center protein C | PSII protein |
| Glyma.11G119300 | Gm11 | 9,067,166 | 9,070,714 | Glyma 2.0 | 0.9670 | CLP protease proteolytic subunit 6 | Chloroplast structure |
| Glyma.12G044500 | Gm12 | 3,230,504 | 3,235,246 | Glyma 2.0 | 0.7470 | CLP protease proteolytic subunit 6 | Chloroplast structure |
| Glyma.12G061600 | Gm12 | 4,499,104 | 4,499,532 | Glyma 2.0 | 0.1008 | Ribulose-bisphosphate carboxylases | Rubisco |
| Glyma.13G213500 | Gm13 | 32,711,673 | 32,716,430 | Glyma 2.0 | 0.9357 | Deoxyxylulose-5-phosphate synthase | Chlorophyll biosynthesis |
| Glyma.13G215400 | Gm13 | 32,875,517 | 32,877,386 | Glyma 2.0 | 0.7719 | NAD(P)-binding Rossmann-fold superfamily protein | Chlorophyll biosynthesis |
| Glyma.13G225000 | Gm13 | 33,791,887 | 33,794,220 | Glyma 2.0 | 0.1445 | Aldolase-type TIM barrel family protein | Chlorophyll biosynthesis |
| Glyma.13G232500 | Gm13 | 34,356,666 | 34,359,254 | Glyma 2.0 | 0.7093 | CHLI subunit of magnesium chelatase | Chlorophyll biosynthesis |
| Glyma.13G299200 | Gm13 | 39,750,734 | 39,751,715 | Glyma 2.0 | 0.8473 | Photosystem II Psb27 | PSII protein |
| Glyma.13G302100 | Gm13 | 39,924,081 | 39,927,914 | Glyma 2.0 | 0.6739 | Photosystem II reaction center PSB29 protein | PSII protein |
| Glyma.13G302900 | Gm13 | 39,981,657 | 39,984,723 | Glyma 2.0 | 0.6163 | CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE | Cytochrome B6f |
| Glyma.15G253700 | Gm15 | 48,243,955 | 48,247,144 | Glyma 2.0 | 0.8062 | Photosystem II subunit R | PSII protein |
| Glyma.15G262700 | Gm15 | 49,552,224 | 49,552,328 | Glyma 2.0 | 0.5021 | Photosystem II reaction center protein T | PSII protein |
| Glyma.17G228700 | Gm17 | 38,364,416 | 38,367,780 | Glyma 2.0 | 0.3293 | Cytokinin-responsive gata factor 1 | Chlorophyll biosynthesis |
| Glyma.19G212800 | Gm19 | 46,633,685 | 46,639,818 | Glyma 2.0 | 0.8428 | Sucrose synthase 3 | Starch synthesis |
aIndicate annotations refined with the highest scoring homolog from Arabidopsis on www.arabidopsis.org