Table 3 Polymorphic sites observed and the markers developed for the PA-related candidate genes
Gene | Locus ID | Marker locus | Polymorphic site | Primer sequence (5’-3’) | Annealing Temp (0C) | Expected amplicon (bp) |
|---|---|---|---|---|---|---|
OsLpa1 | LOC_Os02g57400 | M1 | (AG)8 and (AGA)7 in 5' UTR | F: GGACACACACACAACTCCAC R: CTCTCGGCGTCCTCTTCTAC | 58.99 59.34 | 213 |
OsLpa1 | LOC_Os02g57400 | M2 | (T)12 and (G)10 in 5' UTR | F: GCTTCTCGTATCCAGCGTTG R: CCCGTCACCTTTCTTTGTCA | 59.08 58.04 | 191 |
OsLpa1 | LOC_Os02g57400 | M3 | (CTC)6 and (CGC)7 in 5' UTR | F: CAATGCGCCTCCTCAAAACC R: ACGGCAATGTAGAGGAGCTT | 60.11 59.09 | 209 |
OsLpa1 | LOC_Os02g57400 | M4 | (CT)10 in 5' UTR | F: CAACTCATGGGATGCAAGGC R: CGAAGCGGAAGAATCACGAG | 59.54 59.08 | 203 |
OsMIK | LOC_Os03g52760 | M5 | (CTC)9 in 5' UTR | F: TCAACCGCCGCTTTTATTCC R: CATGGATGGAGGAGAAGGGG | 59.19 59.23 | 157 |
OsMIK | LOC_Os03g52760 | M6 | (GGA)5 in CDS | F: CCCCACGCCTACTACTTCTT R: CTCGACCTCATCAAGCCCC | 58.81 59.86 | 172 |
OsMIK | LOC_Os03g52760 | M7 | 4Â bp indel (AGGA) at 3' UTR | F: AATGAACTGACTTCGCTGCC R: GCACTCAGCGATTCCCATG | 58.84 58.98 | 173 |
LPA | LOC_Os04g55800 | M8 | (ATCC)5 in intron | F: GATCGCGTCGCTGATAATGG R: GCCTGCATCCATCCATCAAG | 59.29 59.04 | 244 |
LPA | LOC_Os04g55800 | M9 | (CAA)6 in 5' UTR | F: ATACACACCCCAAACCCTCC R: GCCGTTGTCATTGTAGCCAT | 59.3 58.91 | 152 |
LPA | LOC_Os04g55800 | M10 | (CGC)6 in Intron | F: GCAATTGCGCATCCATAACG R: AGGAGTAGACGCGTGTGTAG | 58.88 58.91 | 211 |
OsIPK1 | LOC_Os04g56580 | - | No SSR or InDel in promoter and gene sequence | - | - | - |
OsMRP5/ OsABCC13 | LOC_Os03g04920 | M11 | (GAT)5 in CDS | F: TCTCCTTCGTGCTCTGTGTT R: CCATGACACCAACCAAGCAG | 58.96 59.4 | 150 |
OsMRP5/ OsABCC13 | LOC_Os03g04920 | M12 | 5Â bp InDel in Promoter | F: ATAATATTCCGGCGCCTCGT R: GACCGATCCACAAGTCCACT | 59.39 59.39 | 232 |
SPDT/ OsSultr3;4 | LOC_Os06g05160 | M13 | (AAG)18 in 3' UTR | F: AGAACAAGGTGCTTCTCGGA R: GAGATCAGCACCCGGAGTTA | 58.95 58.89 | 222 |
OsPT8 | LOC_Os10g30790 | M14 | (GAC)4 and a 3Â bp InDel in CDS | F: GGGATCGGGGTGAGGAAC R: GTCATACACTACGCCGTCTG | 59.09 58.18 | 194 |