Table 1.
qRT-PCR primer sequences and thermocycling conditions.
| Gene locus | Annotation | Primer name | Primer set (5′–3′) | Product size (bp) | Annealing temp. (°C) | Final primer concentration (μM) |
|---|---|---|---|---|---|---|
| SOYBEAN GENES# | ||||||
| GLYMA19G36620 | Phenylalanine ammonia lyase 1 (PAL) | PAL1-F | GTCCAGTACTAAGGGAAGTGATCC | 216 | 54 | 0.15 |
| PAL1-R | ACTCCTTCTCGGGCAGACTC | |||||
| GLYMA03G12240 | Glutamate-5-kinase (G5K) | G5K-F | ACTCTTGCAAAATGGCCACA | 160 | 54 | 0.175 |
| G5K-R | ACGCTTCACTTTGGTGACAA | |||||
| GLYMA10G33650 | Glutathione-S-transferase (GST) | GST-F | GATGACATGTTTTCTGCAGTTATTG | 174 | 54 | 0.2 |
| GST-R | CCCAAAAGCTATGTCCATAATGT | |||||
| GLYMA08G20230 | Lipoxygenase 10 (LOX10) | LOX10-F | ATGCAAAAATGTACAAAAACACTCGTA | 188 | 54 | 0.2 |
| LOX10-R | GGGTGTTCCCAAATCATTGT | |||||
| GLYMA08G45210 | Alpha-glucan phosphorylase (AGP) | AGP-F | TTGAGCTGGAACAAGCTTACTAT | 279 | 51 | 0.2 |
| AGP-R | GCCTACCAAGACCACCATTT | |||||
| GLYMA03G04990 | Alanine-glyoxylate transaminase (AGT) | AGT-F | CTCAAAACTTCCCAGTGATCTC | 156 | 51 | 0.25 |
| AGT-R | GCCATTGTCCCAGTTGCA | |||||
| GLYMA04G01950 | Alpha-amylase (AMY) | AMY-F | GTCAGTGGAATCTGGTGGATAC | 238 | 51 | 0.2 |
| AMY-R | CCAGGTAAGTCACATCCAACTTTA | |||||
| GLYMA02G39320 | Asparagine synthetase (ASN) | ASN-F | GGTACAATCCTCCTTGGTTCTC | 290 | 51 | 0.2 |
| ASN-R | GCCTAGATAGTCAGCAACTTCTT | |||||
| GLYMA15G10480 | Beta-amylase (BAMY) | BAMY-F | AGTTCTTCTTGACCTGGTATTC | 199 | 51 | 0.2 |
| BAMY-R | CGGTATCCGTCTCTATCATTAAG | |||||
| GLYMA05G04290 | Beta-fructofuranosidase or invertase (BFF) | BFF-F | GAACGATCCCAATGGTCCTATG | 248 | 51 | 0.2 |
| BFF-R | CGTTGGTGGAACCTGTGTATAA | |||||
| GLYMA12G05780 | Beta-glucosidase (BGLUC) | BGLUC-F | GACTTCCAGTATGGATGGTTTAT | 247 | 50 | 0.2 |
| BGLUC-R | CATCACGTACAAATGAGGAATTAG | |||||
| GLYMA01G24530 | Delta 1-pyrroline-5-carboxylate synthase 2 (DPSC2) | DPSC2.1-F | AATTTCGTCAGCATCAAACC | 259 | 50 | 0.2 |
| DPSC2.1-R | CCAATATGACTTCATACCCT | |||||
| GLYMA19G01200 | Formate dehydrogenase (FDH) | FDH-F | ATGAACTCCTCAGAATCCTTGT | 223 | 50 | 0.2 |
| FDH-R | GTATTCATCCTAAGTCTATCATAGTAC | |||||
| GLYMA17G13730 | Malate synthase (MLS) | MLS-F | GAAGATCCAGTGGCTAACGAGGTAGC | 204 | 58 | 0.2 |
| MLS-R | TTGCTCGGTGATGTTTGCCCCA | |||||
| GLYMA01G23790 | Phosphenolpyruvate carboxykianse 1 (PEPC) | PEPC-F | GGTGAAAGATGAAGTTACTGAGAATG | 251 | 51 | 0.25 |
| PEPC-R | CTTCGGTAGTTGGTCGAATG | |||||
| GLYMA09G02430 | Non-expresser of PR protein 1 (NPR1) | NPR1-F | TTGAACCTGATTGCGATTATAG | 147 | 54 | 0.2 |
| NPR1-R | ATTTCCCTTCTTTTTCTGATGA | |||||
| GLYMA05G06790 | Pathogenesis-related protein 1 (PR1) | PR1-F | TGTTGCGTATGCTCAAGACT | 195 | 54 | 0.2 |
| PR1-R | CACTTAGGTTACCGGTGCTT | |||||
| GLYMA02G04820 | Pathogenesis-related protein 3 (PR3) | PR3-F | CGAGGACCAATCCAACTTAC | 180 | 54 | 0.2 |
| PR3-R | AGTGATCACAT CATGGCTTG | |||||
| GLYMA18G48730 | Ethylene-responsive element-binding protein 13 (EREBP) | EREBP1-F2 | ATGTCTGAAACCCACCAAGC | 181 | 54 | 0.15 |
| EREBP1-R2 | CAAACTTTCCCCACGGTCTA | |||||
| GLYMA06G04180* | Hypothetical protein unknown 2 (UKN2) | UKN2-F | GCCTCTGGATACCTGCTCAAG | 79 | 58 | 0.2 |
| UKN2-R | ACCTCCTCCTCAAACTCCTCTG | |||||
| R. SOLANI GENES& | ||||||
| ELU42665 | Alpha-amylase (RsAMY) | RS_AMY_F | AAGCGAAGCTGGGAACAA | 268 | 53 | 0.25 |
| RS_AMY_R | TAATATCCGCGAGTTGGTTGAC | |||||
| ELU39168 | Thiamine biosynthesis (RsTHI) | RS_THI_F | TAATATCCGCGAGTTGGTTGA | 136 | 52 | 0.25 |
| RS_THI_R | CCAAGCCTCTTCGAGTAGTTAG | |||||
| ELU42868 | Beta-glucosidase (RsBGLUC) | RS_BGLUC_F | TGGTTCGCAGACCCTATTTA | 201 | 52 | 0.25 |
| RS_BGLUC_R | GGTGTACTGGACGTTTCCTT | |||||
| ELU45264 | Glutathione-S-transferase (RsGST) | RS_GST_F | GGATGCTAAGCTCGATGGATAC | 190 | 52 | 0.2 |
| RS_GST_R | GGATGCTAAGCTCGATGGATAC | |||||
| ELU38450 | Formate dehydrogenase (RsFDH) | RS_FDH_F | CCAAGAAGAACGAGCAGAAAT | 158 | 52 | 0.25 |
| RS_FDH_R | TCCAGCTGCCTTGTACGACCT | |||||
| ELU42795 | Cu/Zn superoxide dismutase (RsSOD) | RS_SOD_F | GCAAGATCACTGGCCTAACA | 195 | 52 | 0.25 |
| RS_SOD_R | CAACTTTGGATTCGCCATTCG | |||||
| ELU41063 | NADH oxidase (RsNOX) | RS_NOX_F | GTGTCGAATTTCAGGCGAAAG | 244 | 52 | 0.25 |
| RS_NOX_R | CGGAATCCACCGGTAACATAA | |||||
| ELU43748 | ABC transporter (RsABC) | RS_ABC_F | AGCATTTGGTGGTGATGTAGAA | 224 | 52 | 0.25 |
| RS_ABC_R | CCAGGCTCTTTGCGATGTAATA | |||||
| ELU38592 | Chitin deacetylase (RsCDC) | RS_CDC_F | GCATGACGTAGTCCTAAGAAGG | 207 | 52 | 0.25 |
| RS_CDC_R | CTCGTTCCCGTCGCTATATTC | |||||
| ELU36963 | Cytochrome P450 monooxygenase pc-12 (RsP450) | RS_P450_F | CAACCTATCGCAGTGGACTTT | 117 | 52 | 0.25 |
| RS_P450_R | GTGAGGATAGGGAAGGGTAGAA | |||||
| ELU37123 | Laccase precursor (RsLAC) | RS_LAC_F2 | CCAAGGGCACGGCTATAAA | 122 | 53 | 0.25 |
| RS_LAC_R | CATCTCGAACGATAGGGACAAG | |||||
| ELU40841 | Pyridoxal-dependent decarboxylase (RsPDX) | RS_PDX_F | GAACAACCAAGCATTACTCGTG | 80 | 53 | 0.25 |
| RS_PDX_R | GACCGGGACGTCAATGATATG | |||||
| ELU41358 | Glycogen synthase (RsGCS) | RS_GCS_F | CTTATCCTGATGCCTTCGGTG | 187 | 52 | 0.25 |
| RS_GCS_R | GGCCATACTTGACCCTTGTAATC | |||||
| ELU43810* | Histone 3 (RsH3) | RS_H3_F | CTTCCAATCATCGGCAGTCCTC | 76 | 52 | 0.2 |
| RS_H3_R | ATTGGTATCTTCGAACAAAGACACGAG | |||||
#
Genes selected for quantification based on Copley et al. (2015a).
*
Housekeeping genes used for normalization.
&
Genes selected for quantification based on unpublished RNAseq analyses (Copley, unpublished data).