Table II.
Sequenced STSs
| STSa | Putative Product | Sizeb | Polymorphismsc
|
|||||
|---|---|---|---|---|---|---|---|---|
| BCIngrid/ Malt. Heda | BCIngrid/ BCPallas | BCIngrid/ Gran. Zweiz. | Malt. Heda/ BCPallas | Malt. Heda/Gran. Zweiz. | Gran. Zweiz./ BCPallas | |||
| ABC152 | Histone H3 | 334 bp | n.p. | n.p. | n.p. | n.p. | n.p. | n.p. |
| ABG53 | None | 292 bp | n.p. | n.p. | n.p. | n.p. | n.p. | n.p. |
| ABG74 | None | 832 bp | 3 subst. | n.p. | 2 subst. | 3 subst. | 5 subst. | 2 subst. |
| ABG373 | S-like RNAse | 449 bp | 1 exchange | n.p. | n.p. | 1 exchange | 1 exchange | n.p. |
| ABG452 | YABBY | 1,671 bp | 1 subst. | n.p. | 1 subst. | 1 subst. | 1 subst. | n.p. |
| ABG494 | Sodium protonexchanger | 1,053 bp | 2 subst.1 indel | n.p. | n.p. | 2 subst.1 indel | 2 subst.1 indel | n.p. |
| ABG500 | None | 499 bp | 10 subst.4 indels | n.p. | n.p. | 10 subst.4 indels | 10 subst.4 indels | n.p. |
| BCD386 | Hypothetical | 1,231 bp | 1 subst.1 indel. | n.p. | 1 subst.2 indels | 1 indel. | n.p. | 2 indels |
| BCD454 | Pyruvate orthophosphatedikinase | 1,215 bp | n.p. | 1 subst. | n.p. | 1 subst. | n.p. | 1 subst. |
| BCD1449 | GTPase activator | 260 bp | n.p. | n.p. | n.p. | n.p. | n.p. | n.p. |
| BPM101 | None | 2,538 bp | n.p. | 1 indel4 subst. | 1 indel5 subst. | 1 indel4 subst. | 1 indel2 subst. | 2 subst. |
| CD098 | mRNA transport regulator | 1,270 bp | 1 subst. | n.p. | 1 subst. | 1 subst. | n.p. | 1 subst. |
| CD01173 | None | 2,156 bp | 1 subst. | n.p. | 1 subst. | 1 subst. | n.p. | 1 subst. |
| CDO1188 | Alanine aminotransferase | 3,294 bp | n.p. | n.p. | 3 subst. | n.p. | 3 subst. | 3 subst. |
| COMT | Caffeic acid O-methyltransferase | 2,137 bp | n.p. | +/− | 7 subst. | +/− | 3 subst. | +/− |
| DGE18 | Hypothetical | 1,117 bp | n.p. | 2 indels | n.p. | 1 indel | n.p. | 1 indel |
| MWG506 | None | 668 bp | n.p. | n.p. | n.p. | n.p. | n.p. | n.p. |
| cMWG758 | Transcription factor | 986 bp | n.p. | 1 subst. | 1 subst. | 1 subst. | 1 subst. | 1 subst. |
| MWG800 | Hypothetical | 1,812 bp | n.p. | n.p. | 3 subst. | n.p. | 3 subst. | 3 subst. |
| MWG896 | Retroviral pol | 698 bp | 2 subst. | n.p. | 4 subst. | 2 subst. | 2 subst. | 4 subst. |
| MWG913 | Lipo amide dehydrogenase | 1,522 bp | n.p. | 4 subst. | n.p. | 4 subst. | n.p. | 4 subst. |
| MWG2056 | None | 2,164 bp | 1 subst. | 1 indel.6 subst. | 1 indel.9 subst. | 1 indel.5 subst. | 1 indel.9 subst. | 8 subst. |
| Total polymorphisms | 29 | 21 | 42 | 46 | 49 | 34 | ||
| Total sequence comparedd | 19,985 bp | 23,702 bp | 21,795 bp | 18,499 bp | 16,578 bp | 18,633 bp | ||
| Sequence polymorphism frequency/basepair | 1.5 × 10−3 | 0.9 × 10−3 | 1.9 × 10−3 | 2.5 × 10−3 | 3.0 × 10−3 | 1.8 × 10−3 | ||
Sequence of 22 STSs were determined from each of six barley parent lines. Most of the STSs were predicted to encode products with similarity to known or hypothetical proteins. The no. and types of polymorphisms observed for each marker/pairwise barley line comparison are shown.
Original RFLP probe type upon which STSs were based: ABC and ABG, barley cDNA and barley genomic DNA, respectively (Kleinhofs et al., 1993); BCD and CDO, barley cDNA and oat cDNA, respectively (Heun et al., 1991); COMT, barley genomic DNA (Lee et al., 1997); DGE18, A. squarrosa genomic DNA (also known as KSUDGE18 and KSUE18; Heun et al., 1991); and MWG and cMWG, barley genomic DNA and barley cDNA, respectively (Graner et al., 1994).
For each barley line pairwise comparison. BCIngrid, BCIngrid mlo-5; BCPallas, BCPallas mlo-5; Gran. Zweiz., Grannenlose Zweizeilige; Malt. Heda, Malteria Heda; indel, insertion/deletions; subst., single or dinucleotide substitutions; exchange, exchange of 5 bp with another 10 bp; +/−, indel polymorphism of several hundred bp; n.p., no polymorphism; indels, single nucleotide substitutions, dinucleotide substitutions, and exchanges were each counted as one polymorphism.
Out of a total of 28,198 bp of STS sequence. Incomplete sequence of some STSs was obtained for some STS/barley line combinations.