sion is involved. It may be that the inferred homoeology
between pAR219 on Chr. A6 and pAR219b on Chr. 4A is
incorrect. Finally the relative placements of pAR138a on
Chr. 4A and pAR138b on LG D07 requires the assumption
of a post-translocation inversion.
Cytogenetic studies predict that the allotetraploid A
t
ge-
nome will differ from the genomes of
G. herbaceum and
G. arboreum by a second A
t
-specific reciprocal translocation
confounded by a third translocation specific to the A diploid
genome involving the allotetraploid A
t
genome chromosomes
© 1999 NRC Canada
Brubaker et al.
187
Fig. 1. HA1. Probes A1311 and A1437 reveal loci on LG D01 that are inverted relative to their orthologs on D1. The position of
A1311 on D1 is ambiguous and it can be located between A1437 and pAR293 (LOD = –0.38). This would place it beside A1437, as it
is on LG D01 and make D1 and A4 colinear. As a result, however, the position of A1437, A1311, pAR168, and pAR173 on D1 and A4
is altered relative to LG D01. This suggests an inversion centered around pAR173, which is duplicated in LG D01 and D1, and
pAR168, which is duplicated in D1.
1, 2, and 3 (Menzel and Brown 1954; Brown 1980). Thus, it
was not surprising that the compound A genome LG A5 has
homologies to three A
t
LGs, two D genome LGs, and two D
t
LGs (Fig. 8). Reinisch et al. (1994) assigned A
t
LGs Chr.
1A and Chr. 2A to A
t
chromosomes 1 and 2 (Brown 1980),
which is fully consistent with this interpretation (see Menzel
© 1999 NRC Canada
188
Genome Vol. 42, 1999
Fig. 2. HA2. The order of
G1037 and
pAR101 on Chr. 22D is inverted relative to D8.
and Brown’s (1954) Fig. 1). If one accepts this interpretation
of the split affinities of A5, a second A
t
-specific trans-
location becomes apparent, this one involving regions of
chromosomes marked by LGs Chr. 2A and LG A06. As was
the case with Chr. 4A and Chr. 5A in HA7, both of these
LGs show split, non-overlapping homologies to two sets of
otherwise unrelated assemblages of D, D
t
, and A LGs. If
these inferences are correct, A
t
LG A06 corresponds to the
allotetraploid A
t
genome chromosome 3 (Menzel and Brown
1954; Brown 1980).
The only contradictory evidence for the interpretation just
given involves loci revealed by probes pAR250 and A1536.
The former locus maps to LGs in HA8A (A8 and D5) and
HA8B (Chr. 17D), whereas A1536 maps to LGs in HA8B
(Chr. 17D) and HA8C (Chr. 1A). Probe A1536 also reveals
a locus that maps to A5, but that is not by itself contradic-
tory. In light of the unambiguous homology relationships for
a large number of loci, however, this single discrepancy
does not weaken the current interpretation.
Homoeologous associations not accounted by HAs
Of the 659 loci that map to at least one other genome, 235
(36%) were not accounted for by the inferred HAs. In
Figs. 1–11, locus associations with linkage groups outside of
the HA depicted are indicated in brackets next to the
pertinent loci. Many of these inter-HA associations occur in
discrete blocks of loci, providing clues to additional rear-
rangements and past chromosome or chromosome-segment
duplication events. Reinisch et al. (1994) described five ten-
tative “nested” associations between segments of putative
pairs of A
t
and D
t
homoeologues. Two of those are sup-
ported by the present data: A1759 and P6–57 (Chr. 10A/LG
D04 & LG A03/LG D02) and A1751 and P5–61 (Chr.
10A/LG D04 & Chr. 5A). The other three are associated
with the translocations and thus “mimic” nested associa-
tions. Map comparisons among the four genomes studied
here revealed ten “nested” duplications, as follows.
HA1 versus HA2
In HA1, A1826 and A1625 map to the upper end of D1;
A1826 maps to A15, which is associated with the upper end
of A4 to which the other locus, A1625, maps. A1826 and
A1625 also, however, map to the lower end of Chr. 22D in
HA2.
HA1 versus HA5
A number of loci mapped in HA1 have duplicate loci that
map to HA5. Specifically, pAR21 and pAR24 map to D1;
© 1999 NRC Canada
Brubaker et al.
189
HA
Linkage groups involved
Loci
HA1
LG D01
vs.
D1 & A4
A1437
A1311
pAR168
pAR173
HA2
Chr. 22D
vs.
D8
G1037
pAR101
HA3
D6
vs.
A12
pAR288
A1737
A1124
pAR127
Chr. 23D
vs.
D6
A1606
pAR8
HA4
A16
vs.
D4 & LG D03
A1168
pAR309
A1590
pAR118
HA5
D7
vs.
A13
pAR21
pAR319
HA6
D13
vs.
A10
A1591
G1016
G1125
A1720
G1130
G1174
pAR49
pAR8
HA7A
Chr. 20D
vs.
D9
pAR169
pAR65
D9
vs.
A6
A1808
A1650
pAR278
Table 1. Summary of putative rearrangements among the A and
D diploid genomes and the A and D allotetraploid genomes,
organized by homoeologous assemblages (HAs). Loci in boldface
are duplicated in one or more of the LGs.
HA
Linkage groups involved
Loci
HA7B
D12
vs.
A14
G1033
A1172
A1159
pAR206
HA8A
LG A06
vs.
D5
G1164
A1418
PXP2–60
HA8B
LG A06
vs.
D3 & Chr. 17D
pAR185
pAR149
pAR172
HA8C
D2
vs.
Chr. 15D
A1553
A1225
pAR11
P1–3
pAR88
A1720
Chr. 1A
vs.
D2
A1097
A1794
pAR77
HA10
LG D04
vs.
Chr. 10A
pVNC163
A1695
D11
vs.
A9
G1257
A1286
D11
vs.
Chr. 10A
pAR55
A1695
A9
vs.
Chr. 10A
A1183
G1088
D11
vs.
Chr. 10A
A1158
A1751
Table 1 (
concluded).