Ⅲ-4. Radiation Chemistry & Biology

RIKEN Accel. Prog. Rep. 49 (2016)

newphysicalphysical mapping
mapping of the Silene latifolia Y chromosome
AAnewchromosome† †Y. Kazama,*1 K. Ishii,*1 W. Aonuma,*2 T. Ikeda,*1 H. Kawamoto,*2 A. Koizumi,*2 D.A. Filatov,*3 M.V. Chibalina,*3R. Bergero,*4 D. Charlesworth,*4 T. Abe,*1 and S. Kawano*2
The majority of angiosperms are hermaphrodites and only
6% are dioecious (with separate males and females); some ofthese plants have sex chromosomes. Plant sex chromosomes
are excellent for studying the early stages of sex chromosome
evolution because they have evolved independently indifferent species, more recently than in animals.
Dioecious plants have sex-determining systems that arethought to involve two different genes, a stamen promoting
gene and a pistil-suppressing gene. The dioecious plant,
Silene latifolia, has such two sex determining genes on the Y
chromosome (gynoecium-suppressing function; GSF, andstamen-promoting function; SPF). These sex-determining
genes have not yet been identified, and their evolution has
not yet been studied. Maps of the genes on the X and Ychromosomes are needed to identify Y-linked sexdetermining genes, compare gene orders in the X and Y, anddetermine whether the Y has lost regions present on the X
chromosome. However, most of the Y chromosome is nonrecombining, making genetic mapping impossible. Mapping
Y-chromosome deletion mutants is therefore the only way tomap the Y chromosome. Previous Y chromosome maps 1), 2)
used small numbers of markers. We developed a new S.
latifolia Y map with more markers to achieve high reliability
and developed a new deletion mapping software tool,DelMapper.
We collected 41 mutants with Y-chromosome deletions
from progeny plants derived from seeds or pollen irradiatedby carbon-ion beams or γ-rays as described previously.3) The
mutants include 15 hermaphrodites, one female-like mutant,
10 asexuals, 14 mutants with non-maturing anthers, and one
male plant. These mutants were genotyped for thepresence/absence of deletions at 71 Y-linked markers byPCR amplification (STS-markers). Hermaphroditic mutants
must have deletions of the GSF, while asexual mutants havelost the SPF. Our use of numerous genic markers improves
our ability to locate the GSF and SPF regions in comparison
with the use of non-genic markers.
To find the marker order, DelMapper obtains the best fit to
the data by solving a “Travelling Salesman problem”,
minimizing the number of chromosome breaks required.
Minimization of the chromosome breaks is a standard
approach for deletion mapping, and the novelty of ourmethod is that it can deal with many markers. We verified
this approach by testing DelMapper using simulated datasets†Condensed from the article in Scientific Rep. 5, 18917 (2016)
RIKEN Nishina Center*2
Department of Integrated Sciences, Graduate School of Frontier Sciences,
The University of Tokyo*3
Department of Plant Sciences, University of Oxford*4
Institute of Evolutionary Biology, University of Edinburgh*1- 259 -with known gene orders. The
accuracy of DelMapper depends
strongly on the number of individuals
with mutant phenotypes, and on the
total number of deletions in thedataset, but the number of markers
used is less important. Our
simulations allow us to determine theaccuracy of maps made using
DelMapper.
The analyzed data included 442
instances of deleted markers amongthe 41 mutants. Based on oursimulations, the accuracy of a map
based on such a dataset is expected tobe 90%. Our new Y-chromosome
map infers that markers MK17 and
ScQ14 are the closest to the GSF andSPF genes, respectively,1),2) and it
locates both of them on the putative parm (the chromosome arm that does
not include the pseudo autosomal
region (PAR): see Fig. 1). We locate
GSF between MK17 and genic
contig20685Y, in an interior region ofthe p arm. SPF is located between
ScQ14 and the genic contig 03376Y.
This new map with these added genic
markers provides improved ability tolocate the GSF and SPF regions, incomparison with the previous maps.
Our new map will greatly facilitate
the isolation of sex-determining
factors and will be instrumental inother research focusing on sex
chromosomes.
Fig.1 The new S. latifolia Y map.
Markers indicated by bars areclosely linked and their orders were
not determined.

References

1) S. Lebel-Hardenack et al., Genetics 160, 717 (2002).
2) J. Zluvova et al., Genetics 170, 1431 (2005).
3) N. Fujita et al., G3 (Bethesda) 2, 271 (2012).