BoLA
class II RFLP analysis
RFLP
of the DRB genes
Table 5 shows the 46 DRB RFLP patterns defined
in the fifth BoLA workshop using cDNA
or exon 3 probes. Thirty DRB patterns, including 12 new patterns,
were represented in the workshop panel . DRB patterns are complex,
consisting of 2 to 7 TaqI fragments. The complex patterns indicate
that cattle have multiple DRB genes. DRB patterns can not be grouped
on the basis of the presence of particular fragments. Consequently,
the DRB nomenclature was based on the DQ alleles with which DRB
patterns were first associated (Sigurdardóttir
et al., 1988).
Eleven
DRB2-TM patterns were found in the workshop animals (Table
6). Each pattern consisted of one TaqI and one BglII fragment,
demonstrating the locus-specific nature of the probe. The DRB2-TM
patterns were associated with specific class IIa haplotypes.
RFLP
of DQA genes
The 31 DQA patterns defined thus far using cDNA or exon 2 and
exon 3 probes are shown in Table 7.
This
table indicates the fragments that hybridize selectively with
the W1 exon 2 and exon 3 probes. However, there are two distinct
groups of DQA alleles and exon 2 probes of the DQA5 type have
a different pattern of reactivity than exon 2 probes of the W1
type (Sigurdardóttir
et al., 1991b). Nevertheless, since the majority of fragments
carry exon 3 sequences, the overall patterns defined with probes
of the two types are virtually identical . The sizes of several
high molecular weight fragments were adjusted on the basis of
the BRL 1 kb ladder which includes several high molecular weight
markers. The new size estimates are given in Table
7.
RFLP
of DQB genes
Table 8 gives the 26 DQB RFLP patterns defined
to date using cDNA or exon 2 and exon 3 probes. Table 8 includes
information on the probes that hybridize with each fragment. Although
the DQbeta-1 cDNA probe apparently hybridized with all DQB fragments,
hybridization with fragments only containing exon 2 were sometimes
weak.
Table
9 shows the 12 DQB-TM patterns found in the workshop animals.
With the exception of the DQB-TM*213 pattern which has 2 PvuII
fragments, each pattern is comprised of 1 TaqI and 1 PvuII fragment.
This indicates that the DQB1-TM probe behaves in a locus-specific
manner.
Table
5.
DRB RFLP patterns.
Restriction fragments (kb)a
----------------------------------------------------------
TaqI PvuII
--------------------------------------------------- -----
1 1
7 2 9 8 6 6 6 6 5 5 4 4 4 3 3 2 2 2 2 2 1 1 1 1 1 0 6 1
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
Allele 0 0 0 4 4 3 2 0 4 0 9 4 1 7 3 8 3 2 1 0 9 6 3 2 1 9 1 4
-------------------------------------------------------------------------
1Ab + + + + +
1Bb + + + + +
1C + + + +
1D + + + + +
1Ebc + + + + +
1Fbc + + + + +
1Gbc + + + + +
2Ab + + + + + +
2Bb + + +
2C + + + +
3A + + + +
3B + + + +
3Cbd 5 + + 5 5 5 4 4 4
3Dbc + + + + + + +
3Ebc + + + : + +
3Fbc + + + + + +
3Gbe + + + + +
3Hbc + + + + + + +
3Ibc : + + + + +
4Ab + + + +
4B + +
5Ab + + + +
5Bb + + + + +
5Cbc + + + +
5Dbc + + + + + +
6 + + + +
7Ab + + + + + +
7B + + +
7Db + + + + +
7Eb + + + + +
8Ab + + + + +
8B + + + + +
8Cbc + + + + + +
9A + + + + +
9B + + +
9C + + + + +
10b + + + + +
11Ab + + + +
11C + + + +
11Eb + + + +
12A + + + +
12Bb + + + +
13A + + + +
13B + + + +
13Cb + +
14bc + + + +
---------------------------------------------------------------------------
a
Fragments detected with the DRB2 and A1 exon 3 probes (+); fragments
for which data is equivocal (:).
b Present in workshop animals.
c New patterns.
d DRB*3C was defined in the Fourth BoLA Workshop
and a member of the same Brown Swiss family was included in the
Fifth workshop. However, the fragments assigned to this haplotype
were significantly different: assigned in both workshops (+);
assigned in Fourth Workshop (4); assigned in Fifth Workshop (5).
e This haplotype was called DRB*3C by Joosten et al. (1990). However, two different
DRB*3C patterns have been defined.
Table
6
DRB2-TM RFLP patterns
Fragments (kb)
--------------------
TaqI BglII
----------- -------
1
5 5 4 4 3 1 0 9 7 5
. . . . . . . . . .
Allele 9 4 2 0 7 6 3 0 5 9
---------------------------------------
11 + +
13 + +
21 + +
23 + +
24 + +
25 + +
26 + +
31 + +
32 + +
44 + +
46 + +
---------------------------------------
Table
7
DQA RFLP patterns.
Restriction fragments (kb)a
--------------------------------------------------------------------------
TaqI PvuII
------------------------------------------------- -----------------------
1
8 8 8 8 8 7 7 7 7 7 6 6 6 6 5 5 4 4 4 4 3 2 1 1 0 0 9 9 9 8 7 6 5 4 4 2 2
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Allele 9 7 6 4 2 6 5 4 2 0 9 7 1 0 9 4 7 4 3 1 8 9 7 3 9 5 9 5 0 5 2 3 6 8 6 8 5
--------------------------------------------------------------------------------------
1Ab + +
1Bb 2 + +
1C + +
1Dbc + + +
1Ebc + +
2b + +
3Ab + +
3Bb + +
3Cbc + +
4B + +
5b 3 3 3 3
6A 3 3 3 3
6B 3 3 3 3
7Ab + 3 3 + + 3
7B 3 3 2 + 3 +
7Cb + 3 3 2 3 +
7Db + 3 3 + 3
7Fbc + 3 3 3 3 +
8b + 3 3 2 3 3 +
9Ab 2 3 + + 3
9Bb + 3 + 3
10b + 3 + 3
11Ab + 3 + 3
11Bb + 3 + 3
11Db + 3 + 3
11E + 3 + 3
11Fbc + 3 + 3
12b + 3 3 +
13A 3 3 3 3
13Bb 3 3 3 3
14b + +
a
Fragments
detected with the W1 exon 2, W1 exon 3, DQA5 exon 2+3 and pII-alpha-5
cDNA probes (+); fragments detected with the W1 exon 2 probe (2),
the TaqI 1.7 kb fragment hybridizes with the pII-alpha-5 cDNA
probe and weakly with the DQA5 exon 2+3 probe; fragments detected
with the W1 exon 3, DQA5 exon 2+3 and pII-alpha-5 cDNA probes
(3).
b Present in workshop animals.
c New patterns.
Table
8
DQB RFLP patterns.
Restriction fragments (kb)a
------------------------------------------------------------------------
TaqI PvuII
------------------------------------- ---------------------------------
2 1
0 0 9 8 8 7 7 7 5 5 4 4 3 3 3 3 1 1 1 9 8 8 7 7 6 5 5 4 4 3 2 2 1 1 1 1
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
0 2 3 6 3 5 4 0 8 4 5 2 7 6 2 0 5 4 1 2 3 0 6 2 9 5 3 1 0 4 6 0 8 7 7 3
Allele 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0
------------------------------------------------------------------------------------
1b 3 2 3 3
2b 3 +
3Ab 3 +
3Bb 3 +
3Cbc 3 +
4b 3 +
5b 3 3 c + 3 2 3
6A 3 3 c + + 3
6B 3 3 3 +
7Ab 3 2 3 3 2 3 3
7B 2 3 3 3 3 2
7C 3 2 3 + 3
7Eb 3 2 3 3 3
8b 2 3 3 3 3 2
9Ab 2 3 3 2 + 2 3
9Bb 2 3 3 3 2
10b 2 3 3 2 2 + 3 3
11Ab 2 3 3 + 2 3
11Cb 2 3 3 + 2 3
11D : 3 3 + 2 3
11Eb 3 3 + 2 3
12b 2 3 3 + +
13A 3 +
13Bb 3 +
13C 3 +
14b 3 3 3
a
Fragments
detected with the Y1 exon 2, Y1 exon 3 and DQbeta-1 cDNA probes
(+); fragments detected with the Y1 exon 2 and DQbeta-1 cDNA probes
(2); fragments detected with the Y1 exon 3 and DQbeta-1 cDNA probes
(3); fragments detected with the DQbeta-1 cDNA probe but not with
the genomic probes (c); fragments for which data remains equivocal
(:).
b Present in workshop animals.
c New patterns.
Table
9
DQB-TM RFLP patterns.
Fragments (kb)
----------------------
TaqI PvuII
--------- -----------
9 8 4 4 1 8 7 7 5 3 2
. . . . . . . . . . .
Allele 3 3 5 3 8 0 5 1 6 3 5
-------------------------------------
11 + +
12 + +
13 + +
14 + +
213 + + +
33 + +
42 + +
43 + +
44 + +
45 + +
46 + +
53 + +
