Table 3 Position of the 36 polymorphisms detected in the 91 accessions sequenced, after eliminating 26 singletons and one SSR, and structure of the 15 haplotypes observed
From: Specific patterns of genetic diversity among aromatic rice varieties in Myanmar
Pos. | Zone | P | Nature | Freq. | Cons | H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 | H9 | H10 | H11 | H12 | H13 | H14 | H15 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
695 | I2 | snp | nc | 2.2 | C | C | C | C | C | C | C | C | C | C | C | C | G | G | C | C |
825 | I2 | snp | nc | 7.7 | C | C | C | C | C | C | T | C | C | C | C | C | C | C | C | C |
829 | I2 | snp | nc | 3.3 | T | T | T | T | T | T | T | T | T | T | T | T | C | C | C | T |
839 | I2 | indel | nc | 29.7 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
876 | I2 | snp | nc | 2.2 | A | A | A | A | A | A | A | A | G | A | A | A | A | A | A | A |
915 | I2 | snp | nc | 25.3 | C | C | C | C | C | C | T | T | T | T | T | T | C | C | C | C |
918 | I2 | snp | nc | 2.2 | T | T | T | T | T | T | T | T | C | T | T | T | T | T | T | T |
1082 | I2 | snp | nc | 21.9 | T | T | T | T | T | T | C | C | C | T | T | T | T | T | T | T |
1112 | I2 | snp | nc | 25.3 | A | A | A | A | A | A | T | T | T | T | T | T | A | A | A | A |
1113 | I2 | indel | nc | 25.3 | 3 | 3 | 3 | 3 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 3 | 3 |
1316 | I2 | snp | nc | 7.7 | G | G | G | G | G | G | A | G | G | G | G | G | G | G | G | G |
1340 | I2 | snp | nc | 23.1 | C | C | C | C | C | C | G | G | G | G | C | C | C | C | C | C |
1819 | I4 | snp | nc | 25.3 | T | T | T | T | T | T | A | A | A | A | A | A | T | T | T | T |
2142 | I4 | snp | nc | 26.4 | T | T | T | T | T | T | A | A | A | A | A | A | T | T | T | A |
2144 | I4 | snp | nc | 8.8 | T | T | T | T | T | T | A | T | T | T | T | A | T | T | T | T |
2205 | I4 | snp | nc | 26.4 | A | A | A | A | A | A | G | G | G | G | G | G | G | A | A | A |
2219 | I4 | snp | nc | 25.3 | G | G | G | G | G | G | A | A | A | A | A | A | G | G | G | G |
2889 | E7 | snp | c | 25.3 | A | T | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
2891 | E7 | snp | c | 25.3 | A | T | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
2893 | E7 | snp | c | 24.2 | A | G | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
2894 | E7 | indel | c | 25.3 | 8 | 0 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 | 8 |
3003 | I7 | indel | nc | 7.7 | T | T | T | T | T | T | 0 | T | T | T | T | T | T | T | T | T |
3031 | I7 | snp | nc | 3.3 | G | G | G | G | G | G | G | G | G | G | G | G | T | T | T | G |
3219 | I8 | snp | nc | 12.1 | C | C | C | C | T | C | C | C | C | C | C | C | T | T | C | C |
3220 | I8 | snp | nc | 25.3 | G | G | G | G | G | G | A | A | A | A | A | A | G | G | G | G |
3372 | I8 | snp | nc | 25.3 | C | C | C | C | C | C | G | G | G | G | G | G | C | C | C | C |
3467 | I8 | snp | nc | 25.3 | T | T | T | T | T | T | C | C | C | C | C | C | T | T | T | T |
3988 | I9 | snp | nc | 2.2 | T | T | T | T | T | T | T | T | T | T | G | G | T | T | T | T |
4423 | I10 | snp | nc | 2.2 | C | C | C | C | C | C | C | C | C | C | G | G | C | C | C | C |
4452 | I10 | snp | nc | 2.2 | A | A | A | A | A | A | A | A | A | A | A | A | G | G | A | A |
5233 | E13 | indel | c | 14.3 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
5491 | I13 | snp | nc | 2.2 | A | A | A | A | A | A | A | A | T | A | A | A | A | A | A | A |
5531 | I13 | snp | nc | 29.7 | G | G | G | G | G | G | A | A | A | A | A | A | A | A | A | A |
5688 | I14 | snp | nc | 4.4 | A | A | A | G | A | A | A | A | A | A | A | A | A | A | A | A |
6049 | 3'UTR | snp | nc | 3.3 | T | T | T | T | T | T | T | T | T | T | A | T | T | A | A | T |
6086 | 3'UTR | indel | nc | 24.2 | 43 | 43 | 43 | 43 | 43 | 43 | 0 | 0 | 0 | 0 | 43 | 43 | 0 | 43 | 43 | 43 |
Aroma | Ar | M | M | M | Ar | M | M | Ar | Ar | Ar | Na | Ar | Ar | Na | Na | |||||
No acc. | 23 | 15 | 4 | 9 | 13 | 7 | 10 | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | |||||
Myanmar | 6 | 13 | 2 | 6 | 13 | 7 | 7 | 0 | 2 | 1 | 0 | 1 | 1 | 1 | 0 |