American Journal of Plant Sciences, 2013, 4, 1949-1953 Published Online October 2013 (
Physicochemical Characteristics and QTL Mapping
Associated with the Lipid Content of High-Lipid Rice
Na-Hye Kim, Jae-Keun Sohn, Kyung-Min Kim*
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, South Korea.
Email:,, *
Received July 17th, 2013; revised August 17th, 2013; accepted September 10th, 2013
Copyright © 2013 Na-Hye Kim et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
This study was conducted to examine the physicochemical characteristics and perform QTL mapping of genetic factors
associated with the lipid content of rice. A rice strain with a high lipid content, “P31-2-2-2-B-B”, was developed from
mutants of “Dongjin” created by T-DNA insertion. The lipid content of “P31-2-2-2-B-B” brown rice was 4.42% where-
as that of the donor cultivar “Dongjin” was 2.56%. The total fatty acid content of the high-lipid mutant brown rice was
7.82% and that of “Dongjin” was 3.43%. The unsaturated fatty acid composition of the mutant brown rice was 2.73%
oleic acid, 2.74% linoleic acid, and 0.34% linolenic acid. In contrast, the fatty acid composition of the donor cultivar
“Dongjin” was 1.30% oleic acid and 0.99% linoleic acid. The percentage of unsaturated fatty acid to total fatty acid in
the high-lipid mutant was higher (74.3%) than that of “Dongjin” (66.8%). Continuous frequency distribution and trans-
gressive segregation of the lipid content were observed in the F3 family (seeds) derived from a cross between the
high-lipid mutant “P31-2-2-2-B-B” and a tongil-type cultivar “Samgang”. This result implied that the lipid content was
a quantitative trait controlled by a polygene. Additionally, the broad sense heritability of lipid content was estimated to
be 89.6% based on analysis of the F3 seeds. A significant QTL, qRLC5, was identified on chromosome 5 with a LOD
score of 2.37, and was flanked by 5007 and 5014. Results of the present study should be useful for improving rice nutri-
tional quality through marker-assisted selection.
Keywords: Lipid Content; Fatty Acid Content; Quantitative Trait Loci (QTLs); Rice (Oriza Sativa L.)
1. Introduction
Rice is a staple cereal crop for more than half the world’s
population. In most Asian countries including South Ko-
rea, 60% - 70% of the daily nutrients are supplied by rice.
However, rice consumption has been declining over the
years in Asia. It is important to improve the chemical
composition and physical properties of rice in order to
encourage rice consumption and diversify the use of this
grain. Milled rice contains 372 Kcal per 100 g, and is
mostly composed of carbohydrates, proteins, and fats [1].
In addition, rice contains nutrients such as numerous
minerals and vitamins. Rice lipid is mainly concentrated
in the embryo, bran, and aleurone layer. Brown rice is
rich in oleic acid, linoleic acid, and various trace com-
ponents such as γ-oryzanol, sterols, tocopherol, and to-
cotorienol [2,3]. In general, lipid content amounts to
1.6% - 3.02% at 14% moisture in brown rice [4-6]. The
lipids found in rice, especially unsaturated fatty acids,
greatly influence grain appearance and quality [3,6-11].
Changes in the crude fat content of rice are associated
with aging and deterioration of rice. Oxidation reduces
both the total lipid and free fatty acid contents, which are
related to the quality of stored rice [6,9,12]. Lipids de-
rived from rice enhance the immune system and help to
overcome fatigue. Additionally, these lipids reduce se-
rum and LDL cholesterol while elevating HDL choleste-
rol levels [13-15]. Thus, lipids from rice have been iden-
tified as food-derived functional compounds. Heritability
of the lipid content in rice is relatively high (60.90% -
68.25%) [7], and has been reported to be a quantitative
trait controlled by a polygene [10,11,16]. Hu et al. [10]
detected three QTLs (Quantitative Trait Loci) on chro-
mosomes 1, 2, and 5 associated with the lipid content of
rice. Cho et al. [17] identified 12 QTLs on chromosomes
1, 3, 4, 5, 7, 8, and 12. Liu et al. [6] found 14 QTLs rela-
ted to lipid content on chromosomes 1, 3, and 5 - 9. Yu et
al. [18] detected four QTLs controlling the lipid content
of brown rice on chromosomes 3, 5, 6, and 8. Further-
*Corresponding author.
Copyright © 2013 SciRes. AJPS
Physicochemical Characteristics and QTL Mapping Associated with the Lipid Content of High-Lipid Rice
more, Qin et al. [3] found QTLs associated with the lipid
content of brown rice on chromosomes 1, 2, 3, and 5 - 9.
In the present study, we analyzed the physicochemical
properties and fatty acid composition of a high-lipid mu-
tant rice strain, “P31-2-2-2-B-B”. In addition, we identi-
fied that QTLs influence lipid content. The results of our
investigation may be used as a basis to further develop
varieties of high-lipid rice.
2. Materials and Methods
2.1. Plant Materials
The selected high-lipid rice strain by the bulk and pedi-
gree breeding method, “P31-2-2-2-B-B”, derived from
“P31” was used for this study. “P31” is a lipid mutant
line derived from “Dongjin” by T-DNA insertion from
POSTECH (located in Pohang of South Korea) in 2005.
Donor cultivar “Dongjin” was also included in our analy-
ses for comparison purposes. Experimental trials were
carried out in the experimental plots of Kyungpook Na-
tional University (KNU) in Gunwi (South Korea) from
2007 to 2010. One plant per hill was transplanted with 30
cm between rows and 15 cm between plots. Field man-
agement was conducted according to the normal cultiva-
tion practices recommended by Rural Development Ad-
ministration (RDA) of South Korea with an application
for fertilizer (N-P2O5-K2O) at the rate of 90, 45, and 57
2.2. Analysis of Rice Chemical Content
Damage, red, green, and broken grains of the brown rice
were removed before the test. The amylose, lipid, protein,
and starch contents of the brown rice for three replication
per each line was determined with near-infrared spec-
troscopy (NIRS) using a spectrophotometer (Foss 6500).
Crude fat and fatty acid contents were analyzed by the
Local Innovation Center of KNU. To extract crude fat
from the rice, the Soxhlet extraction method was used
with ethyl ether as a solvent. To recover fatty acids, a
solution (37:36:20:5:2, v:v:v:v) was added to 300 mg of
each of rice powder sample. After heating to 80˚C, the
single phase was cooled to room temperature. Fatty acid
composition was measured using a previously described
method [19] which involved preparing fatty acid methyl
esters by direct transmethylation and analyzing them
with a gas chromatography instrument (Agilent 6890 N).
Detailed running conditions for the GC were also previ-
ously described [20].
2.3. Analysis of Genetic Factors Associated with
Lipid Content
To evaluate the broad sense heritability of lipid content,
the F3 family, which consisting of 170 plants derived
from a cross between japonica variety “P31-2-2-2-B” and
tongil-type cultivar “Samgang” cultivated in a greenhouse
at KNU during the winter of 2010, was evaluated. Lipid
contents of the rice were evaluated by NIRS using a
spectrophotometer (Foss 6500). T-test of F3 family was
calculated by the program of SAS 9.1.
2.4. QTL Analysis to Identify Factors Associated
with Lipid Content
The mapping population consisted of 90 lines (F2 popu-
lation), derived from a cross between “P31-2-2-2-B” (ja-
ponica) and “Samgang” (Tongil-type). The molecular
marker data were essentially the same as described in
Qin et al. [3], which consisted of 56 simple sequence re-
peats (SSR) and 116 sequence tagged site (STS) markers
covering 12 chromosomes. A genetic linkage map with
one SSR and eight STS markers was created using
MAPMAKER/EXP version 3.0 [21]. WinQTL cart 2.5
[22] and QTLMAPPER version 1.6 [11] were used for
the QTL analysis. Composite interval mapping (CIM) was
operated for the whole genome scanning on QTLs detec-
tion by one thousand permutation test at a 0.05 signifi-
cant level at a threshold of LOD2.0 [22]. QTL nomencla-
ture used in our study was previously described by
McCouch et al. [23].
3. Results
3.1. Analysis of Rice Chemical Content
Chemical content of the high-lipid mutant “P31-2-2-2-
B-B” rice determined by NIRS is shown in Table 1. The
amylose and starch contents of “P31-2-2-2-B-B” brown
rice (22.57% and 73.39%, respectively) were higherthan
those of the donor cultivar “Dongjin” (20.32% and
71.44%, respectively). Lipid level in the high-lipid mu-
tant was about 1.6 times higher (3.00%) than that of
“Dongjin” (1.83%). Crude fat content of the high-lipid
mutant ‘P31-2-2-2-B-B’ rice determined by the Soxhlet
method was about 1.7 times higher (4.42%) than that of
“Dongjin” rice (2.56%). The fatty acid compositions of
“P31-2-2-2-B-B” and “Dongjin” were measurably diffe-
rent (Table 2). The oleic acid and linoleic acid contents
of “P31-2-2-2-B-B” were 2.73% and 2.74% respectively,
which was about 2.1 and 2.8 times higher than the levels
found in “Dongjin” (1.30% and 0.99%, respectively).
The linolenic acid content of “P31-2-2-2-B-B” was
0.34%; this was not measured in the donor cultivar
“Dongjin” The ratio of unsaturated fatty acids to total
fatty acidsin “P31-2-2-2-B-B” was relatively higher
(74.3%) than that of “Dongjin” (66.8%).
3.2. Analysis of Genetic Factors Associated with
Lipid Content
Continuous frequency distribution and transgressive
Copyright © 2013 SciRes. AJPS
Physicochemical Characteristics and QTL Mapping Associated with the Lipid Content of High-Lipid Rice 1951
Table 1. Chemical contents of the high-lipid mutant “P31-2-
2-2-B-B” and “Dongjin” brown rice.
Chemical content (%)a
Amylose Lipid Protein Starch
P31-2-2-2-B-B 22.57 ± 0.75b 3.00 ± 0.16 8.05 ± 0.54 73.39 ± 0.62
Dongjin 20.32 ± 0.44 1.83 ± 0.08 8.25 ± 0.15 71.44 ± 0.73
aMeasured by NIRS. bData are presented as the mean ± SD.
Table 2. Crude fat contents of the high-lipid mutant “P31-2-
2-2-B-B” and “Dongjin” brown rice.
Cultivar Crude fat content (%)a Ratio
P31-2-2-2-B-B 4.42 ± 0.17b 1.73
Dongjin 2.56 ± 0.28 1.00
aMeasured by the Soxhlet method. bData are presented as the mean ± SD.
segregation of lipid content were observed in seeds from
the F3 family derived from a cross between the high-lipid
japonica variety “P31-2-2-2-B-B” strain and tongil-type
cultivar “Samgang” (Figure 1). The approximately nor-
mal distribution was observed, indication quantitative in-
heritance of lipid content. T-test results showed that there
were significant differences in lipid content between the
two parental lines. A lipid content value ranged from
1.72% to 3.29% in the F3 has relatively high broad sense
heritability (89.6%; Table 3).
3.3. QTL Analysis of Factors Affecting Lipid
A QTL specific for lipid content was detected on chro-
mosome 5. QTL a qRLC5 was located on chromosome 5
between markers 5007 and 5014 with an LOD score of
2.37, accounting for 20.0% of the phenotypic variation.
At this locus, alleles from the “P31-2-2-2-B-B” parent
strain increased the lipid content by 0.12% (Figure 2,
Table 4).
4. Discussion
The lipid content of rice is low and most is composed of
unsaturated fatty acids. Additionally, according to the
previous report, the lipid content of rice material in-
creases the immune system and improves HDL level [13-
15]. In the present study, crude fat content of the high-
lipid mutant “P31-2-2-2-B-B” determined by the Soxhlet
method was about 1.7 times higher than that of “Dong-
jin” (Table 5). Differences in composition between the
two rice strains observed this analysis (Table 5) are si-
milar to the ones found with NIRS. The total fatty acid
level in “P31-2-2-2-B-B” was greater (7.82%, about 2.3
times) than that of “Dongjin” (3.43%). Similarly, “P31-
2-2-2-B-B” had a high concentration of total unsaturated
fatty acids (5.81%) which was about 2.5-times higher
Table 3. Fatty acid composition of the high-lipid mutant
“P31-2-2-2-B-B” and “Dongjin” brown rice.
Fatty acid composition
(% total)
(% total)
Saturated fatty acids
Palmitic acid, C16:0 1.55 ± 0.02a (19.8) 0.78 ± 0.04 (22.7)
Stearic acid, C18:0 0.46 ± 0.006 (5.9) 0.36 ± 0.02 (10.5)
Subtotal 2.01 ± 0.03 (25.7) 1.14 ± 0.06 (33.2)
Unsaturated fatty acids
Oleic acid, C18:1 2.73 ± 0.04 (34.9) 1.30 ± 0.06 (37.9)
Linoleic acid, C18:2 2.74 ± 0.04 (35.0) 0.99 ± 0.08 (28.9)
Linolenic acid, C18:3 0.34 ± 0.004 (4.3) -
Subtotal 5.81 ± 0.08 (74.3) 2.29 ± 0.14 (66.8)
Total 7.82 ± 0.11 (100) 3.43 ± 0.20 (100)
aData are presented as the mean ± SD.
Table 4. Lipid content and heritability estimated from the
analysis of F3 seeds produced by a cross between the high-
lipid “P31-2-2-2-B-B” mutant rice and tongil-type cultivar
Cultivar Lipid content (%)
P31-2-2-2-B-B (P1) 3.25 ± 0.05**
Samgang (P2) 2.08 ± 0.01
F3 seeds
Mean ± SD 2.32 ± 0.13
Range 1.72 - 3.29
H 89.6
Data are presented as the mean ± SD. **Indicates significant difference at a
level of 1%.
BF3 P1P2F3
HV1 2VVV100% .
Table 5. QTL locations and biometrical parameters associ-
ated with the lipid content of rice.
QTL Interval
markers LOD R2 (%)a A
b Increasing allele
qRLC55007-50142.37 20.0 0.12 P31-2-2-2-B-B
aR2: Percentage of phenotypic variation explained. bA: a positive value in-
dicates the genotype from the parent “P31-2-2-2-B-B” toward increasing the
trait value.
than that observed in “Dongjin” (Table 2). The percent-
ages of each fatty acid relative to the total fatty acid lev-
els in “P31-2-2-2-B-B” were 19.8% for palmitic acid,
34.9% for oleic acid, and 35.0% for linoleic acid. Similar
results were reported by the USDA [24], Choi et al. [25],
and Koshen [26]. However, the percentage of linolenic
acid in the high-lipid strain observed in the current study
was higher (4.3%) than that previously reported by the
USDA (1.5%; 1998). In this study, lipid content was a
quantitative trait controlled by a polygene as previously
Copyright © 2013 SciRes. AJPS
Physicochemical Characteristics and QTL Mapping Associated with the Lipid Content of High-Lipid Rice
Figure 1. Frequency distribution of lipid contents in F3
seeds from a cross between the high-lipid “P31-2-2-2-B-B”
mutant and tongil-type cultivar “Samgang”.
Figure 2. Chromosomal locations of QTLs associated with
the lipid content of rice.
reported by Kang et al. [16], Chen et al. [9], and Hu et al.
[10]. However, Qi et al. [7] reported that the broad sense
heritability was 60.90% - 68.25%. Compared to this pre-
vious study, the result (89.6%) obtained in our investiga-
tion should be higher due to the different genotype and
smaller number of samples. Thus, more stable heritability
will be estimated from the larger number of samples in a
future study. The interval distance of qRLC5 between
5007 and 5014 observed in the present study was rela-
tively wide (38.3 cM). This was due to a small number of
markers. If we were to perform this analysis using more
polymorphic markers, the distance of between the qRLC5
markers would be narrow. As shown in Figure 2, qRLC5
was detected at a location different from the one reported
by Qin et al. [3]. Additionally, previous studies were de-
tected to analyze QTL of lipid content after marker 5048
loci [6,10,17,18]. Therefore, fine mapping of chromo-
some 5 could enable us to identify QTLs with high aver-
age LOD scores that affect lipid content. In the present
study, we analyzed the physicochemical properties of a
high-lipid mutant strain and identified QTLs that influ-
ence lipid content. This result may be used as a basis to
further develop varieties of high-lipid rice and improve
rice nutritional quality through marker-assisted selection.
5. Acknowledgements
This work was supported by a grant from the Next-Ge-
neration BioGreen 21 Program (No. PJ0080912013), Ru-
ral Development Administration, Republic of Korea.
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