Ⅲ-4. Radiation Chemistry & Biology

RIKEN Accel. Prog. Rep. 49 (2016)

Improvement ofof DelMapper:
DelMapper: software
software for
Improvementfor deletiondeletion mapping
mapping ofof
non-recombining
regionnon-recombining region
K. Ishii,＊1 Y. Kazama,＊1 T. Ikeda,＊1 and T. Abe＊1
Genetic mapping is usually constructed by calculating
recombination rate as a measure of distance between
genetic markers. However, this method cannot be applied to
the non-recombining region such as sex chromosomes. To
map the DNA markers or genes on the Y chromosome inSilene latifolia, we have developed new deletion mappingsoftware, Del Mapper.1) Deletion mapping is an approachfor mapping DNA markers or genes in the non-recombining
region by collecting mutants having deletion on themapping region and ordering the markers to have the least
total number of chromosomal breakpoints in all mutants.
DelMapper conducts deletion mapping with a new approachthat boils down seeking the best marker order to solving
traveling salesman problem.
DelMapper calculates the numbers of breakpoints in all
possible permutations of the markers by applying thebranch and bound algorithm. To promote greater efficiency
of calculation, markers are clustered and each cluster istreated as a single virtual marker. When calculating thenumbers of breakpoints in each permutation, DelMapper
adds two virtual markers to the both ends of the mappingregion. One virtual marker represents the essential
chromosomal region that cannot be deleted and is presumed
to be present in all mutants. There are two alternatives forthe other virtual marker. Under the “Del” option, themapping region is assumed to be located on the terminal ofthe chromosome and the virtual marker is regarded to bedeleted. Under the “Any” option, the region is assumed tobe located on the intermediate of the chromosome and thepresence/absence of the marker is dependent on that of theneighboring marker. When run with the “Del” option, aprevious version of DelMapper tends to output an increased
number of marker orders with the least number ofbreakpoints. This problem is potentially caused byA

ClusterMarkerMutant1
Mutant2
Mutant3
Mutant4
Mutant5
Mutant6
TotalL1
1111
1

A
BC
A1 A2 A3 B1 B2 B3 C1 C2 C3
1 0 0 0 0 0 1 1 10 0 0 0 0 0 0 1 1
1 1 1 1 0 0 0 0 0
1 1 0 0 0 0 1 1 1
1 1 1 1 1 0 0 0 0
1 1 1 0 0 0 0 0 0

concentrated deletions on the specific marker (e.g., marker
B3 in Fig. 1). Such situation can be produced by thecollection of mutants showing the same phenotype. In suchcases, the concentrated deletions are located next to theterminal virtual marker. At the same time, “solitarydeletions” that do not extend beyond the border of clusters
appears due to disjunction of deletions that are to becontinuous (Fig. 1; deletions in clusters B and C in Mutants
3, 5, and 6).
To cope with this problem, we added a routine tocalculate the number of “solitary deletions.” In addition to
the number of breakpoints, DelMapper counts the numberof “solitary deletions” in all given permutations of markers.
Users can adopt the permutation(s) of the markers with theleast number of “solitary deletions” in those with the least
number of breakpoints as the mapping result. As averification of the effects of the routine, we made 30 virtual
maps that consisted of 71 markers, 41 mutants, and 500
instances of deleted markers and had a tendency of biased
deletion on the specific markers by a Perl script
DelMapMaker.1) We tested DelMapper whether it could
reconstruct these maps. DelMapper run with the “Any”
option output an average of 1.3 marker orders with the least
number of “solitary deletions” in those with the least
number of breakpoints regardless of the implementation of
the routine. On the other hand, DelMapper run with the“Del” option output an average of 2.5 marker orders before
the implementation, while after the implementation, it did
an average of 1.3 marker orders, which was the same value
as that with the “Any” option.
In this study, we successfully decreased the number ofthe false-positive best marker orders from the output of
DelMapper with the “Del” option, which enables users toconduct more clear deletion mapping.

B

R
000000P
3
313
1
1
12

S
0000000

ClusterMarkerMutant1
Mutant2
Mutant3
Mutant4
Mutant5
Mutant6
Total

L111
111

C
C2 C3 C1
1 1 1
1 1 00 0 0
1 1 10 0 00 0 0AB
A1 A2 A3 B1 B2 B3 R
1 0 0 0 0 0 0
0 0 0 0 0 0 0
1 1 1 1 0 0 0
1 1 0 0 0 0 0
1 1 1 1 1 0 0
1 1 1 0 0 0 0

P
1
13133
12

S
0
0
202
2
6Fig.1 Two examples of the result of DelMapper with the “Del” option. L and R indicate virtual markers representing the endsof the mapping region. “0” and “1” indicate that the markers are absent and present in the corresponding mutant,respectively. P and S indicate the numbers of breakpoints and “solitary deletion,” respectively. The routine calculating“solitary deletions” helps users to determine that the marker order of (A) is more plausible than (B) because of the smaller
number of “solitary deletions” although the numbers of breakpoints are same.
Reference＊11) Y. Kazama and K. Ishii et al.: Sci. Rep. 6, 18917 (2016).

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