Table 3.
A subset of candidate and hub genes adjacent four SNPs associated with soybean seed flooding tolerance at the germination stage
| Candidate Gene ID a | Position (bp)b | Homolog in Arabidopsis | Functional annotationc |
|---|---|---|---|
| Glyma.01G198000 | 53,200,980–53,202,684 | AT4G37850 | Transcription factor bHLH18 |
| Glyma.01G206300 | 53,862,540–53,862,540 | AT5G60900 | G-Type Lectin S-Receptor-Like Serine/Threonine-Protein Kinase |
| Glyma.05G006700 | 608,574–621,690 | AT5G14720 | Protein kinase superfamily protein |
| Glyma.05G008000 | 749,837–753,271 | AT2G02160 | CCCH-type zinc finger family protein |
| Glyma.08G152800 | 11,760,404–11,762,319 | AT3G12610 | Leucine-rich repeat (LRR) family protein |
| Glyma.08G152900 | 11,780,677–11,784,610 | AT5G40410 | Tetratricopeptide repeat (TPR)-like superfamily protein |
| Glyma.08G344500 | 45,957,501–45,962,417 | AT4G17570 | GATA Transcription factor 26 |
| Glyma.08G348500 | 46,292,645–46,301,440 | AT2G15490 | UDP-glycosyltransferase |
| Hub genes | |||
| Glyma.01G207700 | 53,959,688–53,961,931 | AT4G16720 | Ribosomal protein L23/L15e family protein |
| Glyma.05G016800 | 1,491,261–1,493,536 | AT5G08180 | Ribosomal protein L23/L15e family protein |
| Glyma.08G159800 | 12,386,775–12,390,398 | AT3G04770 | 40s ribosomal protein SA B |
aGenes position in Glyma2.0 version obtained from SoyBase while those with bolded font are hub genes (highly connected genes in the network)
bGenes start and end positions in Glyma2.0 version
cPossible functional annotation obtained from SoyBase (https://soybase.org/) and Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html)