Table 3.
Validation of 27 SSR motifs and polymorphisms for 21 primer pairs in 211 bitter gourd samples.
| Markers | SSR motifs | Markers from published reports | GenBank | Motifs from published reports | Primer sequences (5′–3′) | Allele No | PIC |
|---|---|---|---|---|---|---|---|
| – | – | JY001∗ | JQ358823 | (CT)5(CTT)17 | – | – | – |
| – | – | JY002∗ | JQ358824 | (CTT)9 | – | – | – |
| MC08_106502 | (AAG)26 | JY003 | JQ358825 | (CTT)22 | F:TGCCAAGCAAATACCACAAA R:TGAAGAAGCAACAGCAGCAG | 14 | 0.84 |
| MC04_54893 | (GAA)14 | JY004 | JQ358826 | (CTT)8 | F:GAAAGCGAGAACGAACGAAC R:TGCCATCGGTACTCATCAAA | 9 | 0.74 |
| MC05_69551 | (AG)6 | JY005 | JQ358827 | (AG)6(CTT)7 | F:GGACGATCGACGTACGTTTT R:TAGCAAACGGCTCAAGCTCT | 2 | 0.37 |
| MC10_152791 | (TTC)16 | JY006 | JQ358828 | (CTT)16(CT)6 | F:TTGCAGCTTCCTTTCTGGTT R:AGGAAACACATCTTGGGCTG | 6 | 0.67 |
| – | – | JY007∗ | JQ358829 | (CTT)11 | – | – | – |
| MC10_147313 | (CT)21 | JY008 | JQ358830 | (CT)22 | F:CGGCATGAAGAATGGCTAAT R:GGGGTTTTCCCCTAATTGAA | 5 | 0.62 |
| MC10_143173 | (GA)26 | JY009 | JQ358831 | (CT)23 | F:TGTTGCCTTTGACTGCAAAT R:AGGCAAGAGGAATGGAGGTT | 6 | 0.62 |
| – | – | JY010∗ | JQ358833 | (CTT)13 | – | – | – |
| MC07_95456 | (CT)16 | JY011 | JQ358833 | (CT)15 | F:TTCTTGAGAGACGGTTGGCT R:GATACAAAGAAACGGTGGCG | 7 | 0.64 |
| MC04_46305 | (GA)11(A)10 | N1 | GU166217 | (GA)11(A)9 | F:TCCGAGTTCAAACCAGTTCC R:ATCTGGTTCCTCGGGAGATT | 3 | 0.54 |
| MC03_37553 | (AG)13 | N5 | GU166218 | (CT)13 | F:TCAATAATGCATTCTCCCCC R:AGGGGATTTCCACCAAAAGA | 3 | 0.51 |
| MC09_141866 | (TC)14 | N6 | GQ338437 | (GA)14 | F:TGGCACACTCTGCATGAAAT R:TGTCAGAAGTTGGAACGACG | 4 | 0.51 |
| MC01_5661 | (AG)15 | N9 | GU166219 | (TC)17 | F:GGGGTGGCTGGAATATATGA R:ATCCATCCCCACAAGTTGAA | 5 | 0.57 |
| MC08_111602 | (CT)11tctt(TC)6 | N12 | GU166220 | (AG)9(GA)11 | F:GTGTTTTCGTGAGGGAGGAA R:TGGGTAGTGGAATGATGGGT | 4 | 0.51 |
| MC01_6583 | (GA)13 | N24 | GU166221 | (GA)13 | F:GACGAGTTTAAAAGACTTTCGG R:TGACCAAGCAACCATGTGAT | 3 | 0.49 |
| MC04_42551 | (TC)6ttcctt(TC)11 | S9 | GQ338438 | (TC)6(TC)11 | F:AGAAAGAGGGGGAAAGACCA R:AAGGCATCGTATGGGAAGTG | 3 | 0.42 |
| MC01_4761 | (GA)13 | S12 | GQ338439 | (TC)14 | F:TAACGAAACGGAACGAAACC R:CCTGGCAATTGGAGATCAGT | 5 | 0.51 |
| MC07_92319 | (TC)15 | S13 | GQ338440 | (TC)15 | F:GCAAATCAAAGAAGCCAAGC R:GTAGGGGTTGGGTTGATCCT | 3 | 0.49 |
| MC08_111602 | (CT)11tctt(TC)6 | S15 | GQ338441 | (AG)6(AG)12 | – | – | – |
| MC01_5661 | (AG)15 | S18 | GQ338442 | (AG)15 | – | – | – |
| MC01_3973 | (AG)11 | S20 | GU166222 | (TC)12 | F:GCTCAAACTTTTGGGCTGAG R:AAGCTTGAGCTCCATTTCCA | 2 | 0.20 |
| MC11_158010 | (AG)11 | S24 | GQ338443 | (CT)11 | F:GTCCAAAAATGGAGGCAAAA R:TTGTAGTGGAGGGGATCGAG | 4 | 0.58 |
| MC06_75265 | (GA)13 | S26 | GQ338444 | (GA)13 | F:GCGGTAAATTCAGAATCCCA R:CCTGCTAGTTTGGCTTTTCG | 5 | 0.58 |
| MC06_73242 | (AG)15 | S32 | GQ338447 | (TC)17 | F:AGCGAAGCAGCTTTATCGAG R:CGAAACGCACTATTCCCATT | 16 | 0.70 |
| MC11_160743 | (CT)20 | S33 | GQ338448 | (GA)19 | F:CAGAGCTGGGTCTGTTGTGA R:AAATAATTTAGTGGGGCGGG | 4 | 0.45 |
| Mean | 5.30 | 0.54 | |||||
A total of 27 SSR motifs that were assayed in two previous studies (Wang et al., 2010; Ji et al., 2012) were verified in the ‘Dali-11’ bitter gourd genome. The consistent or complementary motifs between our results and published reports are shown in bold font. ∗Indicates no or multiple blast hints.