Life ScienceS | Agriculture
QTL analysis on rice genotypes adapted
to acid sulfate soils in the Mekong river delta, Vietnam
Chi Buu Bui1*, Thi Lang Nguyen2
1Institute of Agricultural Sciences for Southern Vietnam
2Cuu Long Delta Rice Research Institute
Received 16 November 2016; accepted 25 August 2017
Abstract:
Three target points in acid sulfate soils have been identified as: 1) Aluminum
Introduction
(Al) toxicity; 2) Iron (Fe) toxicity; 3) Phosphorous (P) deficiency; and 4)
Acid sulfate soils (Sulfaquefts and
Droughts at the seedling stage. The exploitation of gene pools from wild rice
Sulfaquents) account for 30.1 and 48.5%
species fruitfully obtained a true introgression of desirable traits into high
in the Mekong River Delta and Red River
yielding varieties (HYVs), such as AS996 (IR64/Oryza rufipogon), which are
Delta, respectively [1]. Thus, acid sulfate
tolerant to Al-toxicity, have short durations, high yields, and adaptability to
soils have become the main constraint
acid sulfate soils. Major QTLs on chromosome 3 were detected to control
for rice production in the Mekong delta.
Al-toxicity as identified through an analysis of the RIL population of IR64/O.
rufipogon on control relative root length (RRL). RM232 was considered
as a good marker linked to the target quantitative trait locus (QTL) on
chromosome 3, then SR28 and OSR29 on chromosome 9 were also used.
Four target points in acid sulfate soils
have been identified as aluminum (Al)
toxicity, iron (Fe) toxicity, phosphorous
(P) deficiency, and drought stress at
QTL mapping by 126 SSRs through 225 individuals of the F6 RILs population
of AS996/OM2395 was carried out to find the P-uptake gene on chromosome
12. The promising genotype of OM4498 from the BC population of IR64/
OMCS2000 was selected through MAS with RM235 and RM247 on
chromosome 12 linked to QTL, which controls the P-deficiency tolerance.
Based on the leaf bronzing index (LBI), SSR markers were used to select
promising genotypes tolerant to iron-toxicity, such as RM315 and RM212
on chromosome 1, and RM252 and RM211 on chromosome 2. The intervals
among
RM315-RM212 on chromosome 1, RM6-RM240 on chromosome 2, and
RM252-RM451 on chromosome 4, were continually studied through further
fine mapping.
the seedling stage. The problems and
constraints vary across ecosystems;
therefore, the solutions to the problems
will vary accordingly. The research
thrushes each ecosystem to address these
particular problems. Currently, water
management and agronomic practices
have been recommended. Rice varietal
improvement is also considered as a key
approach. QTL analysis was performed
using the software package QGEN from
Cornell University and MapLfrom Japan
University. MapMarker/QTL(IRRI) was
A backcrossing mapping population that included 217 individuals of BC2F2,
was set up from OM1490/WAB880-1-38-18-20-P1-HB to detect the QTLs
relating to drought tolerance (DT). The QTL was located in the intervals
between RM201-RM511 on chromosome 9. BAC clones 13A9 and 7O3 were
used as pinpoints on the high solution map for new markers designed from
also used to find the location of major and
minor genes. The threshold for declaring
a QTL for P deficiency tolerance was at
LOD > 3. All markers were tested for the
expected 1:1 ratio.
their sequences. The markers became useful to help rice breeders possibly
select the improved genotypes adapting to drought stress in the seedling stage.
Keywords: aluminum tolerance, drought tolerance, iron-tolerance, P-deficiency
tolerance.
Tolerance to Al-toxicity
Since the aluminum (Al) forms of
soils and their solubility have a high
pH of 5 or less, Al-toxicity is one of the
Classification number: 3.1
major growth limiting factors of acidic
soils [2]. Roots injured by high Al-
concentrations are usually stubby, thick,
dark-colored, brittle, poorly branched,
and have reduced root length and volume.
*Corresponding author: Email: buu.bc@iasvn.org
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Life ScienceS | Agriculture
Al-toxicity may inhibit shoot growth
by limiting the supply of nutrients and
Table 1. QTL mapping by 126 SSRs through 225 individuals of the F RIL
population of AS996/OM2395 [10, 11].
water due to poor subsoil penetration
or
lower
root
hydraulic
conductivity.
Chromosome
cM
Number of SSRs
Mean of genetic distance between two markers
Y. Tang, et al. (2000) [3] mapped a
gene for Al-tolerance on the long arm
1
507.5
18
28.19
of chromosome 4H of barley, 2.1-cM
2
206.7
14
14.76
proximal to the marker Xbcd117, and
2.1-cM distal to the markers Xwg464
and Xcdo1395. P. Wu, et al. (2000) [4]
3
4
795.9
216.7
12
13
66.33
16.70
identified several QTLs conferring Al-
5
196.6
11
17.87
tolerance in a random inbred mapping-
population derived from Azucena and
6
101.4
6
16.90
IR1552. V.T. Nguyen, et al. (2001) [5]
7
319.2
13
24.55
also detected five QTLs for Al-tolerance
scattered across five chromosomes with
a major QTL located on chromosome
8
9
115.7
99.9
7
8
16.52
12.48
1. V. Nguyen, et al. (2002) [6] found
10
79.9
5
15.98
ten QTLs located on nine chromosomes
for Al-tolerance using a doubled-
11
115.9
7
16.55
haploid
population
derived
from
the
12
150.1
12
12.50
cross of CT9993 x IR62266. Mapping
using Indica x japonica populations
Total
126
23.05
identified
QTLs
associated
with
a
transgressive
variation
where
alleles
from a susceptible aus or Indica parent
enhanced
Al-tolerance
in
a
tolerant
Japonica background [7].
Three populations of O. rufipogon
were collected by Duncan Vaughan and
Bui Chi Buu in 1989 at Tram Chim - bird
sanctuary (Dong Thap Muoi), which area
has strong acid sulfate soils, and its pH
varies from 2.8 to 3.2 [8].
A total of 274 RFLPs from Cornell
University
and
RGPs
digested
by
EcoRI,
EcoRV,
DraI,
HindIII,
and
XbaI exhibited 14.0, 12.5, 19.8, 27.7,
and 19.5% degrees of polymorphism,
respectively. A population of 171F
recombinant inbred lines were derived
from the cross of IR64 x O. rufipogon
(acc. 106412). Agenetic map, consisting
of
151
molecular
markers
covering
1,755 cM with an average distance of
11.6 cM between loci, was constructed
(Table 1). The seedling stage, a major
QTL for RRL, explained 24.9% of the
phenotypic variations, and was found on
chromosome 3 of the rice varieties (Fig.
1 and 2). These results indicated the
possibilities to use MAS and pyramiding
QTLs for enhancing Al-tolerance in
Fig. 1. QTLs controlling Al-tolerance
related to RRL on chromosome 3.
Fig. 2. Fine mapping on chromosome
9 from BC F of OM1490/WAB880-
1-38-18-20-P1-HB [12, 13].
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Life ScienceS | Agriculture
Table 2. Putative QTLs detected for RRL by interval mapping analysis [9].
analysis
progenies
were conducted among
of mapping populations of
Interval
RG406-RZ252
CDO1395-RG391
Chromosome
1
3
Length (cM)
6.5
0.6
Additive effect (DPE)
0.100 (O)
0.167 (O)
LOD
2.4
8.3
R2
9.0
24.9
Kasalath 47/OM4495 (BC F ) and
AS996/OM2395 (BC2F3).
The genetic nature of some characters
related to P-deficiency tolerance was
RZ629-RG650
RG28-RM223
7
8
29.8
31.0
0.126 (O)
0.104 (O)
5.4
2.5
22.5
20.8
studied using diallele analysis. Suitable
materials were chosen as OM723-
11, OM850, IR64, IR50404, OM997,
RM201-WALI7 9 10.0 0.109 (O) 2.6 9.9
DPe (direction of phenotypic effect): The allelic genetic effect and the o and
I observed shows that the favorable alleles were derived from O. rufipogon
and Ir64, respectively; loD: The maximum-likelihood of loD score for the
and IR59606. The tillering ability was
considered as a good selection criteria.
Maximum tiller numbers were scored at
45 days after transplanting the hybrids
and their parents, constituting a 6 x 6
individual QTl; r2: Phenotypic variation explained by the individual QTl.
diallel set. However, shoot dry weight
Table 3. Nature of gene variation for important characters under P-stress [20].
is the most sensitive plant parameter
to P-deficiency, followed by root dry
weight and the number of tillers. The
Trait
(H1/D)1/2
2s2gca/(2s2gca + s2sca)
H2 (%) (Narrow sense
heritability)
proportion of dominant and recessive
genes in the parent (K /K = 1.6) was
more than one unit, which means that
Tilling capacity
Growth duration
Filled grains/pan.
1.94
0.98
5.80
0.16
0.56
0.01
19.70
33.90
3.10
the dominant gene actions were more
important under P-stress. The tendency
of + ve alleles was clear (H /4H = 0.37)
showing the higher the root dry weight,
Root dry weight
0.81
0.03
20.90
the better tolerance to P-deficiency.
rice varieties [9]. AS997 was officially
released and has become a leading
variety adapted to acid sulfate soil areas
in the Mekong river delta so far. The
exploitation of the gene pool from wild
rice species fruitfully displayed a true
introgression of desirable traits into
high-yielding varieties (HYVs), such
as AS996 (IR64/O. rufipogon), which
is tolerant to Al-toxicity and has short
duration, high yield, and adaptability to
acid sulfate soils.
P-use efficiency, which included a major
one on chromosome 12, that coincided
with QTLs for P-uptake; however,
whereas Indica alleles increased
P-uptake they reduced P-use efficiency
[14]. Three QTLs that were identified for
dry weight and four QTLs for P-uptake
together explained 45.4 and 54.5% of
the variation for the respective traits.
M. Wissuwa, et al. (2002) [15] finally
identified the gene Pup1, which controls
P-deficiency tolerance on chromosome
The variance ratio 2s2gca/(2s2gca
+ s2sca) was computed from expected
components of the mean square
assuming a fixed model to access the
relative importance of additive and
non-additive gene effects in predicting
progeny performance (Table 3).
The tolerance variety of AS996
to P-deficiency is one derivative of
O. rufipogon, whereas high-yielding
varieties of OM2395 are sensitive.
The SSR linkage map consisted of
116 polymorphic SSR markers which
Major QTLs on chromosome 3 were
detected to control Al-toxicity, and this
was observed through the analysis of the
RIL population of IR64/O. rufipogon on
RRL (Table 2) [9].
Tolerance to P-deficiency
P-deficiency in soils is a major
yield-limiting factor for rice production.
Increasing the P-deficiency tolerance
of rice cultivars may represent a more
cost effective solution than relying on
fertilizer application [14]. The QTL
linked to marker C443 on chromosome
12 displayed a major effect. Two of the
12, in acidic soils. Y.J. Zhang, et al.
(2010) [16] identified the interval
of R3375-R367 on chromosome 12,
which controls P-deficiency tolerance.
Common quantitative trait loci (QTLs)
for P-deficiency tolerance have been
mapped on chromosomes 6 and 12 [14,
15, 17]. P-deficiency has been identified
as the main factor in preventing the
realization of high-yielding potentials
of modern varieties in lowland rice
production as well [18]. This problem is
aggravated by the high P-fixing financial
capacity of many soils commonly found
in rice growing regions [19].
showed the location of QTLs associated
with relative shoot length, RRL,
relative shoot dry weight, relative root
dry weight under the Yoshida solution
treatments of P-deficiency (0.5 mg P/
liter), and P-adequate (10.0 mg P/liter).
The map length was 2,905.5 cM with an
average interval size of 23.05 cM. Based
on the constructed map, a major QTL
for P-deficiency tolerance was located
on chromosome 12. Several minor
QTLs were mapped on chromosomes
1, 2, 5, and 9. The study indicated that
the candidate genes linked to RM235
and RM247 on chromosome 12, had an
interval distance of 0.2 cM (Fig. 3 and
three QTLs were detected for internal
The
allelism
test
and
QTL
map
Table 4) [10, 11].
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