Nuclear DNA sequences homologous to organellar DNAs have been reported
in plant species including rice, as well as animal and microbial species
(Blanchard and Lynch, 2000). However little is known about the distribution
of sequences homologous to the organellar DNAs on the rice nuclear genome.
Here we report the rice loci for some of the organellar DNA homologues
determined by RFLP mapping and the aggregated distribution of the loci
on a rice linkage map.
First we obtained 11 organellar DNA clones from the DNA libraries which
were made of rice total DNA (c.v. 'Nipponbare') to construct an RFLP map
of rice (Saito et al., 1991), based on DNA sequence analysis of
ca.300-400bp of each insert in these DNA clones. Next we found that some
of the hybridizing faint bands produced by these DNA clones showed RFLPs
between an indica rice 'Kasalath' and a japonica line 'FL134' and segregated
in the F2 population derived from the crossing of these two
lines. The F2 population is the same population used to construct
an RFLP map of rice (Saito et al., 1991). In scoring for segregating
genotype in the autoradiograms from probed F2 blotting filters,
we have given the definition of a single locus as described below; when
all the F2 individuals have either one of two bands (A or B)
or both (A and B), these two bands indicate a pair of alleles on a single
locus; when at least one individual has neither of these two bands, the
bands (A and B) indicate two different loci. RFLP segregation data of
these faint bands were analyzed using MAPL (Ukai et al., 1991)
to determine the loci of these bands on the rice RFLP map (Saito et
Table 1 shows the segregation ratios of 19 loci identified with the 11
organellar clones. Five
of the 11 clones (XNpb060, XNpb478, XNpb483, XNpb538 and XNpb543) detected
multiple loci. Two of the 19 loci exhibited significant deviation from
Mendelian inheritance (Table 1). The 19 loci were mapped on 9 chromosomes.
The multiple loci detected with a single clone did not cluster each other,
and scattered either on separate chromosomes or on the same chromosome
without significant linkage (Figure 1). The 19 loci showed random distribution
on the 12 chromosomes and aggregated distribution at 20-cM intervals ('Goodness
of fit test' of observed frequency distribution of the 19 loci at the
12 chromosomes to binomial distribution: chi2 = 0.790, p >
0.5, the number of the loci = 19, df = 2; 'Goodness of fit test' of observed
frequency distribution of the 19 loci at 20-cM intervals to Poisson distribution:
chi2 = 5.120, p < 0.025, the number of the intervals = 100,
df = 1). Ten of the 19 loci formed four clusters on three chromosomes
(chr. 1, 10 and 12). A cluster on chr. 1 consisted of 2 loci, XNpb460
and XNpb466, which were linked with a distance of 3.4 cM. Another
cluster, located on chr. 10, consisted of 3 loci, XNpb483-4, XNpb467
and XNpb060-1, which were linked with distances of 3.6 cM and 2.2
cM in this linear order, respectively. The third and fourth clusters were
located on chr. 12. The third one consisted of 2 loci, XNpb543-2
and XNpb060-2, which were tightly linked with 0 cM distance.
The fourth one consisted of 3 loci, XNpb538-2 - XNpb478-1
- XNpb457, which were linked with distances of 2.8 cM and 0 cM
in this linear order, respectively. Also other two loci, XNpb538-1
and XNpb537, showed close linkage to the loci
of sequences homologous to mitochondrial plasmid-like DNAs (B1 to B4;
Kanazawa et al., 1993), XNpbB1-1 and XNpbB4 on chr.
1 and XNpbB2 and XNpbB3 on chr. 8, respectively.
We have performed preliminary blast search using rice genome databases
of a japonica line 'Nipponbare' made by RGP and TIGR to see if there are
nuclear DNA regions similar to the whole mitochondrial DNA (Accession:
AB076665 and AB076666 by Notsu et al., 2002) at the two pairs of
linked loci with 0 cM distance on chr. 12 which detected with mitochondrial
DNA clones in this study. So far we have found no BAC/PAC clones containing
long sequences similar to the whole mitochondrial DNA from chr. 12 though
there are BAC clones carrying sequences similar to many mitochondrial
DNA fragments some of which are more than 10 kpb (Kishimoto et al.,
Getting together, clustering of the loci for sequences homologous to organellar
DNAs suggests that there may be chromosome regions tending to be inserted
by organellar-originated DNAs. In addition, The 19 loci identified in
this study had a tendency to be located near deduced centromere regions
(Figure 1), suggesting organellar-originated DNAs might be liable to be
transferred to heterochromatic regions, especially those near centromeres.
Blanchard, J. L and M. Lynch, 2000. Organellar genes: why do they end
up in the nucleus? Trends Genet. 16: 315-320.
Kanazawa, A., N. Kishimoto, W. Sakamoto, R. Ohsawa, Y. Ukai, N. Tsutsumi,
A. Hirai and A. Saito, 1993. Restriction fragments homologous to mitochondrial
plasmid-like DNAs are located within limited chromosomal regions on the
rice nuclear genome. Theor. Appl. Genet. 87: 577-586.
Notsu, Y., S. Masood, T. Nishikawa, N. Kubo, G. Akiduki, M. Nakazono,
A. Hirai and K. Kadowaki, 2002. The complete sequence of the rice (Oryza
sativa L.) mitochondrial genome: frequent DNA sequence acquisistion
and loss during the evolution of lowering plants. Mol. Genet. Genomics
Saito, A., M. Yano, N. Kishimoto, M. Nakagahra, A. Yoshimura, A. Saito,
S. Kuhara, Y. Ukai, M. Kawase, T. Nagamine, S. Yoshimura, O. Ideta, R.
Ohsawa, Y. Hayano, N. Iwata and M. Sugiura, 1991. Linkage map of restriction
fragment length polymorphism loci in rice. Jpn. J. Breed. 41: 655-670.
Singh, K., T. Ishii, A. Parco, N. Huang, D.S. Brar, G.S. Khush, 1996.
Centromere mapping and orientation of the molecular linkage map of rice
(Oryza sativa L.). Proc. Natl. Acad. Sci. USA. 93: 6163-6168.
Ukai, Y., R. Ohsawa and A. Saito, 1991. MAPL: A package of microcomputer
programs for RFLP linkage mapping. RGN 8: 155-158.
Xiao, J., T. Fulton, S. McCouch, S. Tanksley, N. Kishimoto, R. Ohsawa,
Y. Ukai and A. Saito, 1992. Progress in integration of the molecular maps
of rice. RGN 9: 124-128.