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Mol Breeding (2015)35:212

DOI 10.1007/s11032-015-0394-2

Molecular marker-directed development of a novel


cytoplasmic male sterile line in rice
Fengfeng Fan . Nengwu Li . Jie Wang .
Xingdan Liu . Jianfeng Liu . Yingguo Zhu .
Shaoqing Li

Received: 3 March 2015 / Accepted: 7 October 2015


Springer Science+Business Media Dordrecht 2015

Abstract In response to the challenge of food


security in the new century, heterosis exploitation is
being intensified as an effective way to increase grain
yield of rice. Thus, breeding of new cytoplasmic male
sterility (CMS) is necessary so as to prevent homogenization of hybrid rice in commercial breeding
programs. As the rapid development of molecular
biology, molecular marker based selection can not
only increase the efficiency and accuracy for breeding,
but also provide us the possibility to create new CMS
by genotypic identification. In this study, we developed a novel CMS rice by screening rice male sterilityinducing cytoplasm and maintainer candidates using
mitotype-specific and nuclear molecular markers,
respectively. Field trials reveal that the newly bred

Electronic supplementary material The online version of


this article (doi:10.1007/s11032-015-0394-2) contains supplementary material, which is available to authorized users.
F. Fan  N. Li  J. Wang  X. Liu  Y. Zhu  S. Li (&)
State Key Laboratory of Hybrid Rice, Key Laboratory for
Research and Utilization of Heterosis in Indica Rice of
Ministry of Agriculture, Engineering Research Center for
Plant Biotechnology and Germplasm Utilization of
Ministry of Education, College of Life Science, Wuhan
University, Wuhan 430072, China
e-mail: shaoqingli@whu.edu.cn
F. Fan  X. Liu  J. Liu (&)
College of Agronomy, Hunan Agricultural University,
Changsha 410128, China
e-mail: liujf501@aliyun.com

CMS line has good general combining ability and


special combining ability for generation of hybrid rice,
which means that the molecular marker system
provides us an efficient and practicable approach for
development of new CMS in rice breeding programs.
Keywords Cytoplasmic male sterility  Mitotype 
Molecular breeding  Molecular marker assisted
selection  Rice

Introduction
In the twentieth century, food security is still a huge
challenge in the world. As has been proven in
agricultural production, heterosis utilization is one of
the most effective ways for increasing yield of crop
plants (Yuan and Peng 2005). As one of the most
important approaches, cytoplasmic male sterility
(CMS) has been widely used for commercial hybrid
rice breeding programs (Wise and Pring 2002; Tan
et al. 2012). Exploration of novel CMS will greatly
enforce the basis for heterosis utilization (Wang et al.
2013). Since discovery of the first rice CMS line
(Shinjyo 1969), over 60 rice CMS lines had been
developed through widecross within or between
species (Luan et al. 2013). However, only a small
part of which have been used for hybrid rice breeding,
which limits diversity of the CMS mitotypes, and will
hamper to breed of desirable rice varieties with high

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yield (Rao et al. 2014). Thus, development of new


CMS with different cytoplasmic genome is necessary
to support the sustainable development of hybrid rice.
Generally, rice CMS lines can be divided into two
types based on the genetic model for pollen sterility,
i.e. gametophytic type and sporophytic type. Molecular characterization revealed that the gametophytic
CMS lines include Honglian-CMS, Boro II CMS and
CW-CMS etc. carry chimeric gene orf(H)79 (Li et al.
2007; Wang et al. 2013), and the sporophytic CMS
lines are mostly controlled by mitochondrial gene
orf352 (Luo et al. 2013). These genes can be used as
molecular markers to monitor the CMS-inducing
cytoplasm. Recently, there are over five mitochondrial
genomes from different rice varieties being
sequenced, and a great many of DNA sequence
variations being characterized among them (Fujii
et al. 2010; Luan et al. 2013). Which provide us
possibility to develop mitotype-specific molecular
markers from mitotype-specific sequences (MSS) that
can be used for detection of rice cytoplasm (Xie et al.
2014).
Traditional breeding of new CMS by random
crossing is time-consuming and inefficiency because
of the non-target selection. Molecular marker based
screening can not only increase the efficiency and
accuracy for selection, but also provide us the
possibility to create new CMS type in rice breeding
programs by genotype identification (Xu et al. 2012).
In this study, we developed a novel rice CMS by
screening rice male sterility-inducing cytoplasm and
elite maintainer candidates using mitotype-specific
and nuclear molecular markers, respectively. Further
estimation confirmed the newly bred CMS line has
good general combining ability and special combining
ability for generation of hybrid rice, it suggests that
this method is highly efficient for development of
novel CMS in rice breeding programs.

Mol Breeding (2015)35:212

(Supplementary Table S1). Among them, seven commercial sporophytic CMS lines, including Maxie A, II32 A, K17 A, Yue4 A, Xieqingzao A, Gang46 A, and
Zhenshan97 A and their maintainer lines were used as
controls for screening of CMS-inducing cytoplasm,
and elite maintainer lines, respectively. The rice
accessions were kindly provided by IRRI, Hunan
Agricultural University, Jiangxi Academy of Agricultural Sciences, and Hubei Academy of Agricultural
Sciences. All the accessions were planted in the
experimental field within Wuhan University campus
in the summer and Hainan Island in the winter during
20092013. The hybrid rice combinations and their
corresponding parents used for combining ability
analysis were planted in the experimental field within
Hunan Agriculture University campus in the summer
of 2014.
DNA extraction and PCR amplification
Total genomic DNA was extracted from young leaves
using the CTAB method (Murray and Thompson
1980). The mitotyping of O. glaberrima and wild rice,
and nuclear genotyping of O. sativa were referenced to
the methods of Xie et al. (2014), and Li et al. (2012),
respectively. For the analysis of CMS and restorer
related genes, PCR were performed with the primers
listed in Supplementary Table S2.
PCR was carried out in a total volume of 10 ll
containing 50 ng of total genomic DNA, 1 ll
10 9 PCR buffer, 0.25 lM of each primer, 75 lM
of each dNTP and 0.25 units of Taq DNA polymerase
(Fermentas). The PCR procedure was as follows:
denaturation at 94 C for 5 min, followed by 32 cycles
of 94 C for 30 s, 5057 C (dependent on the
primers) for 30 s, 72 C for 1 min, and a final
incubation at 72 C for 5 min. All the PCR products
were analyzed by electrophoresis on agarose gel.

Materials and methods

Phylogenetic analysis

Plant materials and culture

Each band produced by MSS and SCAR primers was


treated as a unit character and scored as a binary code
(1/0). The phylogenetic trees were drawn using
NTSYSpc 2.10 based on the 1/0 matrix (Rohlf
1992), and genetic relation were assayed using
unweighted pair group method with the arithmetic
mean (UPGMA) cluster analysis.

A total of 151 cultivar and wild rice accessions,


including 90 O. sativa, 11 O. glaberrima, 19 O.
rufipogon, 9 O. nivara, 6 O. punctata, 5 O. longistaminata, 4 O. officinalis, 3 O. rhizomatis, 2 O.
latifolia and 2 O. minuta, were used in this research

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Mol Breeding (2015)35:212

Combining ability analysis


In order to evaluate the combing ability of new CMS
line Luofei A, thirty-five F1 hybrids were generated
from Luofei A and other four commercial CMS lines
Rongfeng A, Xie A, Zaofeng A and Wufeng A by
crossing as maternal parents with seven elite restorer
lines (Supplementary Table S1) using a 5 9 7
incomplete diallele cross (NCII) design. Excellent
three-line hybrid rice variety Tianyou-huazhan which
has a similar growth period to the tested hybrids was
used as control to assay the grain yields of each hybrid.
The experiments were carried out in the experimental
field of Hunan Agricultural University using a randomized complete block design with three replications
(plots). Each plot contained five rows, and each row
had ten plants. The general combining ability effects
and special combining ability variance effects of the
parents were estimated with the fixed model described
by Griffing (1956).

Results
Screening of new CMS-inducing cytoplasm
from wild rice and O. glaberrima
Eleven O. glaberrima and 50 wild rice accessions
were screened with orf(H)79, a specific gametophytic
CMS marker, to rule out gametophytic cytoplasm.
Analysis revealed that there are eight wild rice
accessions carrying orf(H)79 alleles (Fig. 1a). The
rest 53 accessions were further screened using orf352
genes, of which, 22 accessions were detected carrying
orf352, and selected for further mitotype analysis
(Fig. 1a).
In order to select differential mitotype of carring
CMS-inducing cytoplasm in the wild rice and O.
glaberrima accessions, the mitochondrial genomes of
the 22 accessions were further investigated using 27
MSS markers which cover the whole mitochondrial
genome (Xie et al. 2014). PCR analysis shows that,
relative to the seven sporophytic CMS control, the
selected 22 CMS lines show clearly polymorphic
profiles (Fig. 1b). Then, a dendrogram was constructed based on the data matrices derived from the
profiling of the 27 MSS markers using the UPGMA
method (Fig. 1c). From the dendrogram, two monophyletic groups are identified at the similarity

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coefficient value of 0.40, and designated as Mt-I and


Mt-II. Group Mt-I consist of four subgroups including
m1, m2, m3, and m4. Subgroup m1 comprise all seven
CMS lines that are currently used in China, which
show less differences among them in the mitochondrial genomes. Subgroup m2 and m3 each contain only
one O. rufipogon accession. Subgroup m4 is comprised by two accessions: an O. nivara and an O.
rufipogon. Group Mt-II is clearly distinct from the
group Mt-I. This group is divided into four subgroups
named m5, m6, m7, and m8. Subgroup m5 consist of
nine accessions which include four O. glaberrima and
five O. longistaminata lines. Analogously, two O.
punctata and four O. glaberrima lines comprise
subgroup m6. Subgroup m7 consist of one O. glaberrima line, and subgroup m8 is comprised by one O.
rufipogon and one O. nivara lines. Relatively, the
mitotype of the three accessions in subgroup m7 and
m8, are prominently distinct from that of the commercial CMS lines and the other rice accessions,
which means that these three accessions can be
potentially used as candidates for creating new CMS
line. Allowing for that the currently used sporophytic
CMS are mainly derived from common wild rice, in
order to enlarge the diversity of CMS, we selected
potential alternative accessions from O. glaberrima
population (Fig. 1b). Of which, the accession 86258
shows different cytoplasmic profile from others in the
O. glaberrima group (Fig. 1c), and was selected as the
female parent for creation of new CMS.
Screening of elite maintainer lines
To select an elite maintainer line for sporophytic CMS,
firstly we have to rule out the potential alternatives
which carry restorer genes Rf3 and Rf4 for sporophytic
CMS, thus, 62 elite early rice varieties or lines (early
rice in the region of Yangtze River are usually
maintainer for sporophytic CMS) were detected using
Rf3 and Rf4 tightly linked markers (Ahmadikhah and
Karlov 2006; Majid et al. 2008; Tang et al. 2014).
Analysis reveal that 39 lines each has one or two bands
that are identical to that of the elite sporophytic CMS
restorer line Minghui 63, it means that only the rest 23
early rice lines that contain neither Rf3 nor Rf4 can be
the potential maintainer candidates (Fig. 2a). In order
to enlarge the diversity of the nuclear genomes
between the maintainer lines, the genomic difference
of the candidate maintainer lines were further detected

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Mol Breeding (2015)35:212

Fig. 1 PCR amplification and phylogenetic tree of screened


CMS-inducing cytoplasm with mitotype-specific molecular
markers. a PCR amplification with orf(H)79 and orf352. M:
DL2000, DNA marker. YTA was used as a control. b PCR
amplification with MSS markers. Mitochondrial gene atp6 was

used as a control. c Phylogenetic tree of seven rice CMS lines


and 22 rice candidate materials by the UPGMA dendrogram
using 27 MSS markers. The Mt-I, Mt-II and m1m8 represent the
names of different groups and subgroups, respectively

using 23 pairs of polymorphic SCAR (sequence


characterized amplified region) markers which cover
the whole 12 rice chromosomes (Li et al. 2012). The 23
early rice lines are perfectly differentiated each other
by the distinctively different genomic profiles
(Fig. 2b). Phylogenetic analysis show that all rice
accessions are clearly classified into three groups,
designated Nu-I, Nu-II and Nu-III (Fig. 2c). Group NuI comprise four subgroups including n1n4, and group
Nu-II comprise four subgroups including n5n8. The
group Nu-III consist of one early rice variety Xiangzaoxian 24, which shows bad flowering character. Thus,
the potential candidate maintainer lines fall in the
group II, which is clearly distinct from the commercial
maintainer lines fallen in Group Nu-I. Of which, the
rice accessions of Ezaoxuan, Xiangzaoxian13 and
Xiangzaoxian31 are apparently different from others in
the same group. In consideration of the integrative
agronomic traits including plant stature, growth period,
flowering, resistance to disease and rice quality,
Ezaoxuan was finally chosen as the male parent for
creating new CMS.

Development of new CMS line through


interspecific hybridization

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After selection both of the candidate rice lines, a cross


was made by crossing the O. glaberrima line 86258 as
maternal parent with Ezaoxuan in the summer of 2009.
The F1 hybrid of 86258/Ezaoxuan were further
backcrossed to the recurrent male parent Ezaoxuan.
In the BC1 population, only the sterile plants were
selected to backcross with Ezaoxuan. After seven
generations of backcross, the sterile plant look like the
same as Ezaoxuan in phenotype, but pollen sterility
stably reaches over 99.99 %, and the bagged spikelet
fertility is zero (Supplementary Fig. 1). I2-KI staining
show that the aborted pollen of the CMS line look like
irregular (Fig. 3c), a typical character of sporophytic
CMS. Thus, a new CMS line was developed, and
named Luofei A; correspondingly, Ezaoxuan was
named Luofei B.
Luofei A plant height is about 60 cm, has a compact
plant stature, large panicle with about 160 grain
number per plant, strong tillering with effective

Mol Breeding (2015)35:212

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Fig. 2 PCR amplification and phylogenetic tree of screened


elite maintainer lines with nucleus molecular markers. a Screening of early rice lines by restorer-linked markers. M: DL2000,
DNA marker. SSR markers RM490 and RM6100 are cosegregated with Rf3 and Rf4, respectively. ZS97A and MH63 were

used as the control. b PCR profiles of SCAR markers. Reference


gene actin was used as a control. c Phylogenetic tree of seven
sporophytic maintainers and 23 early rice lines based on the 23
SCAR markers using the UPGMA dendrogram. Nu-I, Nu-III and
n1n8 present the name of groups and subgroups, respectively

panicle number about 1012/plant, high percentage of


ear bearing tiller, tidy spike-layer and good flowering
habit (Fig. 3a, b). The growth duration from seeding to
heading of Luofei A is about 68 days in the summer of
Wuhan, and the full-bloom stage occurs on the fourth
day after heading. Besides, the new CMS line Luofei
A shows significantly different cytoplasmic profile
from other CMS lines (Supplementary Fig. 2, 3).
These characters show that Loufei A is an excellent
sporophytic CMS line.

combining ability and special combining ability could


be used to evaluate parent performance (Supplementary Table S4).
As has been proven in breeding practice, desirable
special combining ability and general combining
ability are the critical standards to evaluate an elite
parent for hybrid rice, and parent with a high general
combining ability would be conducive to increase the
concentration of beneficial alleles (Marilia et al. 2001;
Qu et al. 2012; Song et al. 2014). That is, an ideal
parent for hybrid rice should have high general
combining ability and special combining ability
variance effects. Compared with the other CMS lines,
Luofei A has the best general combing ability for grain
number and plant height, but its grain yield and
1000-grain weight are inferior to Rongfeng A
(Table 1). Relatively, the general combining ability
of Luofei A and Rongfeng A are better than the other
three CMS lines.
Further investigations on the special combining
ability of the five CMS lines reveal that the grain yield
has higher special combining ability variance among

Analysis of the combining ability of the new CMS


line
When the hybrid plants matured, grain yields and
yield-related agronomic traits were carefully assayed
for combining ability analysis (Supplementary
Table S3). Variance analysis of the combining ability
reveal that effects of the general combining ability (P1
or P2) and special combining ability (P1 9 P2) are
significantly correlated with most of the agronomic
characters. This suggests that the effects of the general

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Mol Breeding (2015)35:212

Fig. 3 Performance of the new CMS line Loufei A. a Gross


morphology of Loufei A (left) and Loufei B (right). Scale bar
0.5 m. b The flowering habit of Loufei A. Scale bar 1 cm. c,

d Pollen fertility of Loufei A (c) and Loufei B (d) assessed by


1 % I2-KI staining. Darkly stained pollen is fertile, and slightly
stained pollen is sterile, Scale bar 50 lm

Table 1 Effects of the general combining ability of the five CMS lines
CMS Lines

Plant height

Rongfeng A

-0.21

3.67

-6.69

3.02

4.00

8.08

-1.97

10.13

-5.64

2.38

3.17

Xie A
Zaofeng A

1.30
-6.18

-2.69
3.73

4.51
-4.91

-0.11
0.99

-2.92
-0.73

-0.58
-1.37

Wufeng A

-2.56

-2.83

-3.14

1.80

-2.93

-6.14

Luofei A

Effective panicle

Grain number/panicle

the six investigated characters (Table 2). In comparison, Luofei A ranks the third for the special combining ability of grain yield, which means that Luofei A

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Seed setting rate

1000-grain weight

Grain yield/plant
5.10

has not only good general combining ability but also


good special combining ability, it is an ideal CMS line
for production of excellent hybrid rice.

Mol Breeding (2015)35:212

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Table 2 Variance of the special combining ability of the five CMS lines
CMS Lines
Rongfeng A

Plant height

Effective panicle

Grain number/panicle

Seed setting rate

1000-grain weight

Grain yield/plant

3.05

103.28

39.52

5.94

6.73

48.42

12.08

6.54

21.84

9.87

8.58

50.66

Xie A
Zaofeng A

4.46
5.52

51.06
91.84

10.52
22.99

48.03
15.13

8.42
14.95

32.48
65.82

Wufeng A

1.52

32.08

30.94

10.65

3.89

63.79

Luofei A

Discussion
Hybrid rice has been made a great progress, and
contributed greatly to the increase of rice production in
China during the last decades (Cheng et al. 2007; Rao
et al. 2014). Exploitation of new CMS resource is one
of the important means to ensure high yield and avoid
the potential threat of genetic vulnerability of the CMS
lines, which will help to enforce the basis for hybrid
rice sustainable development (Fujii and Toriyama
2009). Traditional breeding is difficult to create new
CMS by random outcrossing, because it is hard for us
by naked eyes and experiences to estimate which rice
carries new CMS-inducing mitotype or an expectant
genotype with recessive restorer genes. Thus, it is
eventually impossible to avoid being homogenization
for the commercial CMS lines, just as shown in our
results that the seven commercial CMS lines show
very similar PCR profiles, and are clustered in the
same subgroup (Fig. 1c). However, our results indicate that a great many of mitotypes actually exist in the
wild rice and O. glaberrima accessions (Fig. 1b), and
can be well differentiated by MSS molecular markers
(Xie et al. 2014), Which highlights the dominant and
significant role of MSS-based selection on new CMS
development from rice wild relatives.
Concomitantly, elite maintainer lines which do not
carry any restorers for a certain CMS, and have a
different genotype from the other maintainers can also
be effectively detected based on the SCAR and Rfspecific markers (Fig. 2). Comprehensively use both
of the mitotype- and Rf-specific molecular markers
make MAS-based selection directional and high
efficiency in the development of novel CMS. This is
agreement with the results of combining ability
analysis. It is well known that combining ability for
a new CMS line depends mainly on the nucleus, a
certain level of distance between parents can make
expectant heterosis of a hybrid (Makumbi et al. 2011).

Traditionally, it is difficult to prejudge the genetic


distance of a potential maintainer line to other used
commercial lines only from the plant morphologies. In
our results, the early rice lines from different resources
are distinctively differentiated using 23 SCAR markers, the accessions in each of the subgroups are
basically corresponded to different genetic backgrounds (Fig. 2c). Which imply that these Rf-specific
and SCAR markers combined with the MSS markers
become a powerful approach to direct the development of novel CMS of rice.
Although a lot of CMS-related markers have been
developed in different reports, no systematic molecular breeding methods for new CMS lines have been
proposed (Rajendran et al. 2007; Ngangkham et al.
2010; Luan et al. 2013). Here, for the first time, we
reported a systematic molecular breeding method
which can be employed to develop novel sporophytic
CMS line with expected genetic background, good
general combining ability and special combining
ability. This implies that molecular marker-directed
development of CMS is completely practicable, which
will help to effectively direct the breeding of new
CMS in molecular breeding programs.
Acknowledgments This research was partly supported by the
863 program (2014AA10A604-9) and the National Transgenic
Research and Development Program (2011ZX08001-004) of
China.

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