Table III.
Gene copy number estimated by genomic DNA gel blot for selected candidate genes in A. halleri
Five micrograms of genomic DNA isolated from A. thaliana (Col-0 accession) and from two A. halleri individuals (Lan 3-1 and Lan 5 of the Langelsheim accession) were digested with EcoRI, HindIII, or NcoI, resolved on a 0.9% (w/v) agarose gel, blotted, and hybridized with radiolabelled A. halleri-derived cDNA probes. The size of the detected DNA fragments is given in kilobase pair (detectable fragments were in the range of 0.2 and 14 kb). Note that in A. halleri, there are a maximum of two alleles per gene copy. Blots for the four underlined genes are presented in Figure 5, and other blots are shown in Supplemental Figure 1.
| Gene | Copy No. in A. halleri |
A. halleri Lan 3.1
|
A. halleri Lan 5
|
A. thaliana Col-0
|
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| EcoRI | HindIII | NcoI | EcoRI | HindIII | NcoI | EcoRI | HindIII | NcoI | ||
| ZIP3 | >1 | 3.5 | 6.5 | >10 | 3.5 | 6.5 | >10 | 3.6 | 7.4 | 15.2 |
| 1.2 | 5.8 | 1.2 | 5.8 | (3.8)a | (5.4)a | (7.2)a | ||||
| 1.5 | 1.5 | (1.7)a | ||||||||
| ZIP4 | ∼1 | 4.2 | 2.2 | 0.6 | 4.2 | 2.2 | 0.6 | 0.8 | 7.0 | 2.0 |
| 0.8 | 1.5 | 0.8 | 1.5 | (6.3)b | (5.5)b | (4.5)b | ||||
| (2.0)bc | ||||||||||
| ZIP9 | >1 | 5.5 | 2.5d | 4e | 5.5 | 2.5d | 4e | 4.2d | 4.4 | 4.0e |
| 1.7 | 2 | 3.5 | 1.7 | 2.2 | 0.5 | 0.2 | ||||
| 0.7 | 0.2 | 0.7 | 2 | |||||||
| 0.2 | ||||||||||
| ZIP10 | ∼1 | 3.2 | 2.8 | –c | 3.23 | 3 | 4 | 14.4c | 2.9 | 28.6c |
| 3 | 2.8 | |||||||||
| IRT3 | ∼1 | 1.5 | 2.2e | 9.5 | 1.5 | 2.2e | 9.5 | 6.3 | (7.0)b | 4.5 |
| 0.9 | 2 | 0.8 | 0.9 | 2 | 0.8 | (0.8)b | 5.5f | (2.0)b | ||
| 1.5 | 1.5 | 2.0 | ||||||||
| 1 | 0.06b | |||||||||
| ZIP6 | >1 | 10 | 5.8 | >10 | 5 | 6 | >10 | 2.7c | 8.4 | 11.7 |
| 5 | 4 | 9 | 2.5 | 3.8 | 9 | |||||
| 2.5 | 2.2 | |||||||||
| 2 | ||||||||||
| HMA4 | >1 | 10 | 6d | 9 | 10 | 6d | 9 | 15.7 | 2.8d | 7.3 |
| 8 | 4.5 | 7.5 | 8 | 4.5 | 7.5 | 0.6 | (4.1)g | |||
| 1.7 | 3.8 | 4 | ||||||||
| 1.2 | 1.2 | |||||||||
| 0.6 | 0.6 | |||||||||
| FRD3 | ∼1 | >10 | 3.5ce | 10 | >10 | 3.5ce | 10 | 1.5 | 3.5e | 14.9 |
| 8 | 1.0 | |||||||||
| MTP8 | ∼1 | 5 | 1.1 | –c | 5 | 1.1 | –c | 5.7 | 1.1 | 20.9c |
| PHT1;4 | ∼1 | 1 | –c | 4 | 1 | –c | 4 | 10.0 | 6.0 | 4.1 |
| (2.0)h | (2.5)h | (5.9)h | ||||||||
| PDI1 | ∼1 | 1.5 | 3.3 | 2.2 | 2.4 | 3.3 | 2.2 | (3.4)i | 3.0d,e | 2.2 |
| 1 | 1 | 2.4 | (2.4)i | (2.0)i | ||||||
| 0.7 | 0.7 | (1.5)j | (1.0)i | |||||||
| 0.6 | 0.6 | 0.65 | ||||||||
| 0.56 | ||||||||||
| PDI2 | ∼1 | 1.5 | 3.3 | 2.2 | 2.4 | 3.3 | 2.2 | 3.4 | (3.0)i | 2.8e |
| 1 | 1 | (2.4)i | 2.4d | 2.0 | ||||||
| 0.7 | 0.7 | (1.5)j | 1.0 | (2.2)i | ||||||
| 0.6 | 0.6 | (0.65)i | ||||||||
| (0.56)i | ||||||||||
Cross hybridization of AhZIP3 probe with AtZIP5 genomic sequence.
Cross hybridization of AhIRT3 and AhZIP4 probes with AtZIP4 and AtIRT3 genomic sequences, respectively.
Not detected, predicted fragment given for A. thaliana.
Enzyme cuts once in one of the introns spanned by the cDNA probe.
Enzyme cuts once in the probe.
Enzyme cuts twice in the probe.
Cross hybridization of AhHMA4 probe with AtHMA2 genomic sequence.
Cross hybridization of AhPht1;4 probe with At3g54700 genomic sequence.
Cross hybridization of AhPDI1 and AhPDI2 probes with AtPDI2 and AtPDI1 genomic sequences, respectively. Note that it is likely that cross hybridization also occurs of AhPDI1 and AhPDI2 probes with AhPDI2 and AhPDI1 genomic sequences.
Additional band, identity not known.