全 文 ：Received 24 Sept. 2003 Accepted 6 Feb. 2004
* Contributed equally to this work.
** Author for correspondence. Tel: +86 (0)28 82745350.
http://www.chineseplantscience.com
Acta Botanica Sinica
植 物 学 报 2004, 46 (8): 965-972
Genetic Analysis and Gene Mapping of a Dominant Long-culm Mutant in Rice
DENG Xiao-Jian1, 2*, LI Xiu-Lan1, 3*, WANG Ping-Rong1, WU Cheng2, YANG Zhi-Rong2**
(1. Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
2. College of Life Sciences, Sichuan University, Chengdu 610064, China;
3. College of Life Sciences, Qufu Normal University, Shandong 273165, China)
Abstract: A new long-culm mutant “D111” was discovered in breeding materials of rice (Oryza sativa
L.). Polymorphic analysis of microsatellite markers demonstrated that D111 derived from a gene mutation
in the crossing progenies of two semidwarf varieties 6442S-7 and Shuhui 881. Plant height and culm length
of D111 increased by 63.0% and 87.0%, respectively, compared with those of its parent Shuhui 881.
Genetic analysis suggested that the long-culm trait of D111 was controlled by a pair of dominant genes, and
the long-culm gene of D111 was tightly linked or allelic to that of long-culm control variety Nanjing 6.
Molecular marker analysis showed that the mutant gene of D111 located on the long arm of rice
chromosome 1, 27.7 cM, 25.5 cM and 6.0 cM from microsatellite markers RM212, RM302 and RM472,
respectively. This long-culm mutant gene was designated tentatively as LC (t). It was considered that D111
was the first rice example of dominant long-culm mutant derived from spontaneous mutation of semidwarf
varieties and that LC(t) was the first mapped long-culm mutant gene of rice. In addition, the possible
relationship between LC(t) gene and rice “green revolution gene” sd1 was discussed.
Key words: rice (Oryza sativa); dominant long-culm mutant; long-culm gene; genetic analysis; gene
mapping; microsatellite marker
Plant height is an important agronomic trait in rice. So
far, many studies have been made on the height of rice
plants. This trait has shown genetic models of a major gene
and polygenes in different genetic backgrounds of rice. In
a major gene model, the dwarfism and semidwarfism are
generally inherited with a recessive gene, rarely with a domi-
nant gene (Saeda and Kitano, 1992); the long-culm charac-
ter is generally inherited with a dominant gene, but several
recessive long-culm mutants have been identified (Okuno
and Kawai, 1978a; 1978b；Rutger and Charnahan, 1981；
Liao et al., 1988；Wu and Zhang, 1988； Li et al., 1992；
Sun et al., 1994；Zhu et al., 2000；Yang et al., 2001).
A new long-culm mutant was discovered in the F2 popu-
lation of a cross between two indica semidwarf varieties,
6442S-7 and Shuhui 881. After several generations of self-
fertilization, one homozygous long-culm mutant line was
obtained, designated as “D111”. In present studies, the
mutant was for the first time analyzed genetically, and the
mutant gene was mapped with microsatellite markers.
1 Materials and Methods
1.1 Plant materials and field experiments
D111 is an indica long-culm mutant discovered in the
F2 population of a cross between two semidwarf varieties,
6442S-7 and Shuhui 881, which has been genetically ho-
mozygous after successive self-fertilizations (Fig.1). Shuhui
881, Shuhui 527, Minghui 63, 9311, IR68 and G46B are in-
dica semidwarf varieties. Nanjing 6, an indica long-culm
variety extensively used in rice production in China, was
bred from Nanjing 1 through pedigree method in 1957 (Lin
and Min, 1991).
The long-culm mutant D111, its original semidwarf par-
ent Shuhui 881 and the long-culm control variety Nanjing 6
are basically similar in growth duration, all belonging to
medium or late maturing types. So, the three materials were
planted together in the field at a 17×27 cm spacing. At the
stage of maturity, 20 individual plants from each material
were selected randomly, and their plant height, culm length
and internode length were measured.
The long-culm mutant D111 was crossed to the above-
mentioned semidwarf varieties and the long-culm control
variety Nanjing 6, respectively. Parents, F1 hybrids and F2
populations were planted together in field at a 17×27 cm
spacing, with 20 plants for parents and F1’s, 120-300 plants
for each F2. Plant height was measured individually at
maturity.
6442S-7, another semidwarf parent of D111, is an early
maturing nuclear male-sterile line and has completely
Acta Botanica Sinica 植物学报 Vol.46 No.8 2004966
dominant earliness (Deng et al., 2001; 2002). Therefore,
6442S-7 was not selected as the material for phenotypic
comparison and crossing experiments.
1.2 Extraction of genomic DNA and microsatellite
analysis
Genomic DNA of rice leaf was extracted as described by
McCouch et al. (1988). Microsatellite analysis was per-
formed according to Panaud et al. (1996), Chen et al.
（1997） and Temnykh et al. (2000; 2001), and the amplifi-
cation products were run in 3.0%-3.5% agarose gels.
1.3 Construction of mapping population and molecular
mapping of target gene
The mapping population consisted of 30 dominant long-
culm individual plants and 66 homologous recessive semi-
dwarf individual plants in the F2 population of Shuhui 527/
D111. The leaf of each selected individual was used for
DNA extraction and microsatellite analysis. Then, based
on the segregation data of plant height and microsatellite
markers of the F2 mapping population, the linkage map was
constructed with MAPMARKER/EXP version 3.0b. The
genetic distance (cM) was calculated with Kosambi
function.
2 Results and Analyses
2.1 Phenotypic characteristics of long-culm mutant D111
At maturity, the height of plant and the length of panicle,
culm and internodes of D111, its semidwarf parent Shuhui
881 and long-culm control variety Nanjing 6 were measured
(Table 1). The results showed that D111 had the following
characteristics in plant height and culm length.
2.1.1 Plant height was very significantly increased Un-
der natural condition in Chengdu, Sichuan Province, plant
height of D111, Shuhui 881 and Nanjing 6 were 178.2 cm,
109.3 cm and 151.0 cm, respectively. D111 was 68.9 cm or
63.0% higher than Shuhui 881, and 27.2 cm or 18.0% higher
than Nanjing 6. Therefore, it could be considered that D111
was a highly significant long-culm mutant.
2.1.2 The increase in plant height was completely re-
sulted from the increase in culm length Panicle length of
D111 was 25.6 cm, being slightly shorter than that of Shuhui
881 and Nanjing 6. But culm length of D111 was 152.6 cm,
being 71.0 cm longer or 87.0% higher than that of Shuhui
881, and 31.1 cm longer or 25.6% higher than that of Nanjing
6.
2.1.3 The increase in culm length was primarily re-
sulted from the significant elongation of lower internodes
Firstly, based on the absolute length of internodes, the
first internode (the topmost internode) of D111 was only
4.9 cm longer than that of Shuhui 881; but the second,
Fig.1. Phenotype of the long-culm mutant D111 (middle) and
its two original semidwarf parents, 6442S-7 (left) and Shuhui 881
(right).
Table 1 Comparison of plant height, culm length and internode length between D111 and its original semidwarf parent, Shuhui 881,
and long-culm control variety, Nanjing 6 (Sichuan, 2001)
Trait
D111 Nanjing 6 Shuhui 881
Length (cm) % Length (cm) % Length (cm) %
Plant height 178.2± 5.9 - 151.0± 4.8 - 109.3± 2.3 -
Panicle length 25.6± 1.1 - 29.5± 1.7 - 27.7± 1.4 -
Culm length 152.6± 6.2 100.0 121.5± 4.3 100.0 81.6± 2.2 100.0
First internode length 37.6± 3.2 24.6 45.7± 2.5 37.6 32.7± 1.6 40.0
Second internode length 32.7± 1.9 21.4 33.1± 0.7 27.2 17.8± 0.8 21.8
Third internode length 28.7± 1.0 18.8 21.1± 1.0 17.3 13.6± 0.6 16.7
Fourth internode length 25.2± 1.8 16.5 16.1± 2.6 13.3 10.4± 1.0 12.7
Fifth internode length 19.5± 2.9 12.8 5.6± 1.0 4.6 5.6± 1.0 6.8
Sixh internode length 9.0± 3.8 5.9 0 0 1.6± 0.7 2.0
DENG Xiao-Jian et al.: Genetic Analysis and Gene Mapping of a Dominant Long-culm Mutant in Rice 967
third, fourth and fifth internodes were all about 15 cm longer
and the sixth internode was also 7.4 cm longer than that of
Shuhui 881. Similarly, the first internode of D111 was 8.1 cm
shorter than that of Nanjing 6 and the second internode
corresponded to the latter; but the third, fourth, fifth and
sixth internodes were 7.6 cm, 9.1 cm, 13.9 cm and 9.0 cm
longer than that of Nanjing 6, respectively. Secondly, based
on the relative length of the internodes over the culm length,
i.e. total length of all internodes (being indicated as 100%),
the first internode of D111 was 15.4% shorter than that of
Shuhui 881, and the second internode corresponded to the
latter; but the third, fourth, fifth and sixth internodes were
2.1%, 3.8%, 6.0% and 3.9% longer than that of Shuhui 881,
respectively. Similarly, the first and second internodes of
D111 were 13.0% and 5.8% shorter than that of Nanjing 6,
respectively; but the third, fourth, fifth and sixth intern-
odes were 1.5%, 3.2%, 8.2% and 5.9% longer than that of
Nanjing 6, respectively. Therefore, D111 belonged to “lower
internodes elongation” type of long-culm mutant.
2.2 Polymorphism of microsatellite markers between
D111 and its two original semidwarf parents
D111 was a long-culm mutant discovered in the F2 popu-
lation of a cross between two semidwarf varieties, 6442S-7
and Shuhui 881. So, polymorphism of genomic DNA be-
tween D111 and its two original parents, 6442S-7 and Shuhui
881, were analyzed with the microsatellite markers well-dis-
tributed on the 12 pairs chromosomes of rice (Temnykh
et al., 2000), the results of which are shown in Table 2. It
can be seen in Table 2 that D111 had no new SSR bands
compared with its original parents based on the 205 de-
tected microsatellite loci. This demonstrated that D111 did
derive from the gene mutation in the crossing progenies of
6442S-7 and Shuhui 881 and did not from crossing fertiliza-
tion of a unknown long-culm variety in the field.
2.3 Inheritance of the long-culm trait of D111
D111 was crossed with six semidwarf varieties, i.e. Shuhui
881, Shuhui 527, Minghui 63, 9311, IR68 and G46B. Plant
height of all the F1 progenies exceeded obviously mid-par-
ent value, and closed to or exceeded that of long-culm par-
ent D111. Meanwhile, there was no obvious difference be-
tween reciprocal crossing F1 progenies in plant height (Table
3). In another section, plant height of the individual plants
distributed bimodally in the F2 population of each cross
(Fig.2). Therefore, individual plants in each F2 population
could be classified into two groups, long-culm and
semidwarf, according to the plant height distribution profile.
The segregation ratio of long-culm plants to semidwarf
plants fitted the ratio of 3:1 in each F2 population (Table 4).
These results suggested that the long-culm trait of D111
was controlled by a pair of dominant nuclear genes.
2.4 Allelic test of long-culm genes harbored in D111 and
Nanjing 6
D111 was crossed with long-culm control variety Nanjing
6. Under the natural long-day condition in Chengdu,
Sichuan Province in 2002, the parents and their F1 were
planted. As a result, plant height of D111, Nanjing 6 and the
F1 were 168.6 ± 5.4 cm, 143.4 ± 2.8 cm and 179.5 ± 4.5 cm，
Table 3 Plant height (cm) of F1 progenies from D111 crossed with semidwarf varieties
F1 combinations D111 Semidwarf parent F1
Sichuan, 2001
Shuhui 881/D111 176.9± 5.1 103.0± 4.8 164.4± 3.8
D111/Shuhui 881 103.0± 4.8 165.4± 3.9
G46B/D111 93.0± 4.8 174.7± 5.5
D111/G46B 93.0± 4.8 177.5± 3.2
Sichuan, 2002
Shuhui 881/D111 168.6± 5.4 99.1± 4.5 145.9± 6.5
Shuhui 527/D111 108.8± 2.7 154.1± 4.7
Minghui 63/D111 103.0± 3.1 157.4± 5.6
9311/D111 111.0± 3.7 177.1± 4.1
IR68/D111 108.4± 4.1 171.5± 5.4
Table 2 Polymorphism of microsatellite markers between D111
and its two semidwarf original parents, i.e. 6442S-7 and Shuhui
881
Chromosome Total markers No.
No. of markers with
new SSR bands
1 29 0
2 20 0
3 21 0
4 13 0
5 14 0
6 19 0
7 14 0
8 23 0
9 15 0
10 12 0
11 13 0
12 12 0
Total 205 0
Acta Botanica Sinica 植物学报 Vol.46 No.8 2004968
respectively. Under the natural short-day condition in
Lingshui, Hainan Province from Winter 2002 to Spring 2003,
the parents and their F2 population were planted. As a result,
plant height of D111 and Nanjing 6 were 136.5 ± 6.2 cm and
123.3 ± 4.6 cm, respectively. In the F2 population, except for
four semidwarf plants, plant heights of which were 70 cm,
81 cm, 92 cm and 95 cm, respectively, plant heights of the
other 350 plants varied from 103 cm to 157 cm, averaged
132.1 ± 10.6 cm, and displayed nearly normal distribution
with the mid-parent value basically at the center (Fig.3).
These results suggested that the long-culm gene of D111
was tightly linked or allelic to that of Nanjing 6.
2.5 Molecular mapping of the long-culm mutant gene of
D111
At present, semidwarfism of most indica semidwarf va-
rieties was all controlled by sd1 gene located on the long
arm of rice chromosome 1. Long-culm variety Nanjing 6
had a dominant long-culm gene allelic to sd1 gene. The
Fig.2. Distribution of plant height in the F2 populations of the crosses between D111 and semidwarf varieties (Sichuan, 2001-2002).
Table 4 Segregation of plant height in the F2 populations of the crosses between D111 and semidwarf varieties
F2 combinations
Total No. of No. of long-culm No. of semidwarf
Expect ratio X2 P
plants plants plants
Shuhui 881/D111 588 443 145 3:1 0.020 0.75-0.90
Shuhui 527/D111 294 227 67 3:1 0.65 0.25-0.50
9311/D111 221 160 61 3:1 0.67 0.25-0.50
Minghui 63/D111 121 93 28 3:1 0.13 0.50-0.75
IR68/D111 120 94 26 3:1 0.54 0.25-0.50
G46B/D111 119 93 26 3:1 0.47 0.25-0.50
DENG Xiao-Jian et al.: Genetic Analysis and Gene Mapping of a Dominant Long-culm Mutant in Rice 969
above-mentioned allelic test suggested that the long-culm
gene of D111 was tightly linked or allelic to that of Nanjing
6. So, as the first step of gene mapping, it should be ana-
lyzed whether the long-culm mutant gene of D111 located
on the long arm of rice chromosome 1.
Genomic DNAs from the two parents, D111 and Shuhui
527, of the F2 mapping population were amplified with prim-
ers of microsatellite markers on rice chromosome 1. As a
result, parental polymorphism of microsatellite markers,
RM212, RM302 and RM472 were observed. Then, genomic
DNA of the F2 individuals amplified with RM212, RM302
and RM472, the results of which suggested that the three
microsatellite markers were all linked to the long-culm mu-
tant gene of D111 (Fig.4).
The linkage map of the long-culm mutant gene was con-
structed with the segregation data of the plant height and
microsatellite markers of the F2 mapping population of
Shuhui 527/D111 (Fig.5). The results showed that the long-
culm gene located on one side of the microsatellite markers,
RM212, RM302 and RM472, on the long arm of rice chro-
mosome 1, and the genetic distances from the target gene
to the markers were 27.7 cM, 25.5 cM and 6.0 cM,
respectively. This long-culm mutant gene was designated
tentatively as LC(t).
3 Discussion
Early rice varieties were long-culm types, however, over
higher plant often resulted in plant lodging and output
reducing. Since the end of the 1950s, owing to identifica-
tion and utilization of rice semidwarf gene sd1, many elite
semidwarf varieties that had higher lodging resistance and
responded to heavy applications of nitrogen had been suc-
cessfully developed and very extensively used in rice
production, which remarkably improved the yield potential
of rice and so was praised as “green revolution” in the
world.
Fig.3. Distribution of plant height in the F2 population from
D111 crossed with long-culm control variety, Nanjing 6.
Fig.5. Linkage map of D111 long-culm mutant gene LC(t) on the
long arm of rice chromosome 1.
Fig.4. Segregation of microsatellite marker RM212 in the F2 population of Shuhui 527/D111. L, long-culm plant in F2; M, DL2000
marker; P1, D111; P2, Shuhui 527; S, semidwarf plant in F2.
So far, some long-culm mutants derived from semidwarf
rice have been reported. However, among these mutants,
only one viz LM-3 was a dominant long-culm mutant (Okuno
and Kawai, 1978a; 1978b), and the others belonged to re-
cessive long-culm mutants (Okuno and Kawai，1978a;
1978b；Rutger and Charnahan，1981；Liao et al.,
1988；Wu and Zhang, 1988； Li et al., 1992；Sun et al.,
1994；Zhu et al., 2000；Yang et al., 2001). LM-3 was a
Acta Botanica Sinica 植物学报 Vol.46 No.8 2004970
japonica dominant long-culm mutant induced by chemical
mutagen. Plant height and culm length of LM-3 were about
143 cm and 113 cm, 18%-21% and 15%-19% higher than
that of its original parent Norin 8, respectively. The culm
type of LM-3 belonged to “upper internodes elongation”
type, and the long-culm trait was mainly controlled by a
pair of dominant genes (Okuno and Kawai, 1978a;1978b).
Compared with LM-1, dominant long-culm mutant D111
identified in the present studies had the following
characteristics: (1) effect of its long-culm mutant gene was
greater. Although the long-culm trait was also controlled
by a pair of dominant genes, the plant height and culm
length of D111 amounted to 178.2 cm and 152.6 cm,
respectively, and increased by 63.0% and 87.0% over that
of its semidwarf original parent Shuhui 881, respectively,
and 18.0% and 25.6% over that of long-culm control variety
Nanjing 6, respectively; (2) its culm type belonged to “lower
internodes elongation” type; (3) it was the first indica ex-
ample of dominant long-culm mutant derived from the mu-
tation of semidwarf varieties; (4) it was the first rice example
of dominant long-culm mutant derived from spontaneous
mutation.
For molecular mapping of long-culm mutant genes, the
recessive long-culm gene eui was mapped on rice chromo-
some 5 with RFLP markers, 33.6 cM from RG435 (Wu et al.,
1998), and the recessive long-culm gene eui2 was mapped
on rice chromosome 10 with microsatellite markers, 1.4 cM
from RM304 (Yang et al., 2001). In present studies, the domi-
nant long-culm mutant gene of D111 was mapped on the
long arm of rice chromosome 1, 27.7 cM, 25.5 cM and 6.0
cM from microsatellite markers RM212, RM302 and RM472,
respectively. This gene, being the first mapped dominant
long-culm mutant gene of rice, was designated tentatively
as LC(t).
Up to now, although many new genes for semidwarfism
of rice have been identified (Kinoshita, 1995；Li et al.,
2003), most of indica varieties extensively used in the cur-
rent rice production are still the semidwarf varieties con-
trolled by sd1 gene. sd1 gene was praised as rice “green
revolution gene” (Monna et al., 2002), which located be-
tween RFLP markers RG220 and RG109 on the long arm of
rice chromosome 1, 0.3 cM and 0.9 cM from RG220 and
RG109, respectively (Spielmeyer et al., 2002). This gene
encoded a defective GA20-oxidase, which resulted in the
semidwarf phenotype because of decrease of gibberellin
biosynthesis in rice plant (Monna et al., 2002; Sasaki et al.,
2002; Spielmeyer et al., 2002). In present studies, dominant
long-culm mutant D111 derived from a gene mutation in the
crossing progenies of two indica semidwarf varieties, 6442S-
7 and Shuhui 881. Furthermore, when the linkage map of
dominant long-culm mutant gene LC(t) of D111 (Fig.5) was
compared with the rice molecular linkage maps published
by Causse et al. (1994) and Temnykh et al. (2000;2001), it
was found that LC(t) gene located just on the chromosome
region close to sd1 gene. Therefore, it was inferred that
three kinds of possible relationship between LC(t) gene
and rice “green revolution gene” sd1 might exist as follows:
(1) LC(t) and sd1 located on the same locus. LC(t) resulted
from reverse mutation of sd1 and could encode normal GA20-
oxidase; (2) LC(t) and sd1 belonged to the same gene family.
LC(t) resulted from a dominant mutation of one of the mem-
bers in sd1 gene family and could encode a kind of enzyme
that could remedy action of the defective GA20-oxidase
encoded by sd1 gene; (3) LC(t) located on the chromo-
some region that was not too far from sd1 gene. LC(t) pro-
moted gibberellin biosynthesis in the rice plants carrying
homozygous sd1 gene to a normal level through an un-
known pathway, which resulted in remarkable increase in
plant height. However, it is necessary to carry out further
study to make sure what kind of relationship between LC(t)
and sd1 truly exists.
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