Rice Science, 2013, 20(6):

Copyright 2013, China National Rice Research Institute Published by Elsevier BV. All rights reserved DOI: 10.1016/S1672-6308(13)60150-X

Mapping of QTLs of Germination Characteristics under Non-stress and Drought Stress in Rice
Zahra MARDANI1, Babak RABIEI1, Hossein SABOURI2, Atefeh SABOURI1
(1Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht 41635-1314, Iran; 2 Department of Plant Production, Faculty of Agriculture and Natural Resources, Gonbad University, Gonbad 4971799151, Iran)

Abstract: Identification of genetic factors controlling traits associated with seed germination under drought stress conditions, leads to identification and production of drought tolerance cultivars. Present study by using a population of F2:4 derived from a cross between a drought tolerant variety, Gharib (indica) and a drought sensitive variety, Sepidroud (indica), is to identify and compare QTLs associated with traits germination under drought stress and non-stress. Through QTL analysis, using composite interval mapping, regarding traits such as germination rate, germination percentage, radicle length, plumule length, coleorhiza length and coleoptile length, totally 13 QTLs was detected under pole drought stress (-8 MPa poly ethylene glycol 6000) and 9 QTLs under non-stress conditions. Of the QTLs identified in non-stress conditions, QTLs associated with the coleorhiza length (qCOL-5) and germination rate (qGR) explained 21.82% and 19.73% of the total phenotypic variation, respectively. Under drought stress conditions, QTLs associated with coleorhiza length (qCOL-3) and plumule length (qPL-5) explained 18.34% and 18.22% of the total phenotypic variation, respectively. A few droughttolerance-related QTLs identified in previous studies were found to be near the QTLs detected here, and several QTLs are novel alleles. The results showed that the major QTLs like qGR-1, qGP-4, qRL-12 and qCL-4 that were identified in both conditions of stress for traits such as germination rate, germination percentage, radicle length and coleoptile length respectively, should be considered by breeders as the important and stable trait-controlling QTLs in rice seed germination. Those major or minor QTLs could be used to significantly improve drought tolerance by marker-assisted selection in rice. Key words: rice; drought stress; seed germination; quantitative trait locus

Drought stress is a serious limiting factor to rice production and yield stability in worldwide (Dey and Upadhyaya, 1996). As a result, understanding the mechanisms of drought tolerance and breeding for drought-resistant crop plants has been the major goal of plant biologists and crop breeders (Xiong et al, 2006). Furthermore, standard assays used to measure drought tolerance must be enhanced since they are important to success in genetic improvement (Lanceras et al, 2004). Moreover, genotype environment (GE) interaction is a challenge to plant breeders and has been shown to reduce the progress of the quantitative traits from selection. Because of the GE interaction, quantitative trait loci (QTLs) that are important in one environment may not be as important as in another environment in determining the phenotype (Tanksley, 1993). For this reason, QTLs with little GE interaction across a set of environments would be desirable in
Received: 24 March 2013; Accepted: 10 June 2013 Corresponding author: Zahra MARDANI (zahra.mardani64@gmail.com)

marker-assisted breeding programs (Zhang et al, 2005). QTL analysis of seed germination has been reported in Arabidopsis, rice, beans, lettuce and soybean (Mano and Takeda, 1997; Teng et al, 2001; Price et al, 2002; Fujino et al, 2004; Miura et al, 2004; Cheng et al, 2008; Hayashi et al, 2008; Ikeda et al, 2009; Ji et al, 2009; Oh et al, 2009; Park et al, 2009; Yano et al, 2009; Wang et al, 2011; Sasaki et al, 2013). Moreover, QTLs conferring stress tolerance in rice were identified mainly at the seedling stage, but few reports on rice seed germination stage (Wang et al, 2011). Cheng et al (2008) found two main-effect QTLs associated with tolerance to alkali damage on chromosomes 3 and 7, using by 120 double haploid (DH) lines derived from the cross between TN1 (Oryza sativa L. subsp. indica) and Chunjiang 06 (O. sativa L. subsp. japonica). Also, a few efforts have been made on comparative studies of QTLs for germination traits in rice under salt stress and non-stress conditions. For example, Foolad et al (1996) detected several QTLs for seed

Zahra MARDANI, et al. Mapping of QTLs of Germination Characteristics in Rice

germination under cold stress, salt stress and nonstress conditions, using BC1S1 lines. Gong et al (2001) reported two QTLs on chromosome 4 for HD (heading date) and the other on chromosome 6 for GPP (grains number per panicle) under salt stress and non-stress conditions. Kamoshita et al (2002) could find only two stable QTLs among 31 detected for seven traits associated with root morphology in two experiments with different sowing dates under anaerobic conditions. Han et al (2006) mapped several QTLs associated with agronomic traits in rice under different growing environments. Also, MacMillan et al (2006) mapped six QTLs for root traits in four different environments in rice and most QTLs for an identical trait in the four environments were different. Wang et al (2011) detected one QTL qIR-4 for seed imbibition under salt stress and non-stress conditions on chromosome 4 with the recombinant inbred line (RIL) population derived from IR26/Jiucaiqing. Further, Srividhya et al (2011) find five stable QTLs among 24 detected for drought related traits at the seedling stage under the poly ethylene glycol (PEG) induced stress and control conditions in rice. This study focused on comparative investigation of QTLs for drought tolerance trait in a F2:4 population grown under drought stress and non-stress conditions, to disclose the relationship of QTLs detected in both conditions. Moreover, to further identify specific QTLs associated with drought tolerance in Iranian rice at the germination stage, which will be useful in marker-assisted breeding for drought resistance in rice.

used to evaluate drought tolerance, with two replications (Each petri dish contained 40 seeds for each replication). All seeds were surface-sterilized with 0.1% hydrargyrum chloratum solution for 15 min, and then rinsed three times with sterile distilled water. The 40 seeds were then placed in Petri dishes (diameter is 9 cm) with two sheets of filter paper to which 10 mL of solution was added. To determine the suitable PEG 6000 concentration of treatment, the different PEG concentrations were applied among two parents, and the results showed that the -8 Mpa was suitable for drought treatment in this study. Then, the evaluation of seed germination among 148 families and parents were conducted under -8 Mpa and control (distilled water) conditions, respectively. The seeds were incubated in a growth chamber at (30 1) C for 10 d, and the seeds germinability was observed each day to estimate the total germination percentage (GP). In total, 25 randomly selected seedlings were used to measure the length radicle, length plumule, length coleoptile and length coleorhizae. In addition, final count, germination rate (GR) and germination percentage (GP) were calculated by the following formulae (Maguire, 1962): GP = Number of germinated seeds / Total number of seeds planted 100%; GR = X1 / Y1 + (X2 X1) / Y2 ++ (Xn Xn-1) / Yn; Where Xn is the number of germinated seeds on the nth days and Yn is the number of days from the first day experiment. Two replications were conducted and the mean value was used for data analysis. Genotyping DNA was extracted from fresh leaves of each F2 plant and the parental lines. DNA extraction was performed by using the CTAB as described by Saghai Maroof et al (1994). Simple sequence repeat (SSR) markers on 12 rice chromosomes were selected from the Gramene database (http://www.gramene.org) and the linkage map was constructed following McCouch et al (2002) based on their map location. A total of 575 SSR markers of known chromosomal position were used to survey the parents for polymorphism. Polymorphic markers were used to detect the genotype of 148 F2 plants. Polymerase chain reaction (PCR) was carried out in a total volume of 10 L per reaction containing 2 L of template DNA, 0.4 L of forward and reverse primers each of 10 pmol concentration, 0.6 L of dNTPs (2 mmol/L), 0.12 L of Taq polymerase (5 U/L), 0.48 L of MgCl2 (50 mmol/L), 1 L of 10

MATERIALS AND METHODS

Rice materials The rice material was F2:4 population consisting of 148 families each derived from a cross between two Iranian rice varieties Gharib and Sepidroud. Gharib is a drought tolerant variety and other parental line, Sepidroud is a drought susceptible variety. An F2 population derived from a cross of these parents was used in order to construct a genetic linkage map. The genetic material used in phenotype evaluations involved 148 F4 families, each derived from bagged seeds of a single F2 plant. The experiments were conducted in the Faculty of Agricultural Sciences Laboratory, University of Guilan, Iran from 2009 to 2011. Phenotypic evaluation The 148 F4 families and their parental varieties were

Rice Science, Vol. 20, No. 6, 2013

PCR buffer and 5 L of sterile nanopure H2O. PCR amplification was performed in a thermal cycler (Applied Biosystems, Germany). The thermal cycle protocol includes 94 C for 5 min (initial denaturation), followed by 35 cycles of 94 C for 30 s (denaturation), 55 C for 30 s (primer annealing with most of the primers while some were adjusted), 72 C for 2 min (extension) and at least 72 C for 5 min (final extension). PCR products were separated on 6% polyacrylamide gels (19 acrylamide : 1 bisacrylamide). and then stored at 4 C. Parental surveys were conducted to identify polymorphism between the parents using amplified fragment length polymorphism (AFLP) markers. Nine AFLP primer combinations (EcoRI primer and MseI primer) showing polymorphisms between Gharib and Sepidroud were used for genotype analysis of the F2 population. The AFLP protocol developed by Vos et al (1995) was followed, with minor modifications. PCR products were separated on 6% denaturing poly acrylamide gels and visualized by the silver staining method. Genetic linkage map construction and QTL analysis A genetic map was constructed with AFLP and SSR markers. The linkage map was established using the program QTXB17 Map Manager (Wang et al, 2007).

From 575 SSR markers, 131 markers displayed polymorphism, also of 9 primer pair combination AFLP, 105 produced polymorphic bands between two parents and 131 polymorphic markers. All the 131 polymorphic marker loci involved in construction of the genetic map tested for segregation distortion, distortion was detected using the 2 test for goodness of fit to expected allelic frequency for SSR of 1:2:1 and for AFLP of 1:3. The QTLs were mapped using the composite interval mapping (CIM) function of the WinQTL Cartographer v2.5 (Basten et al, 1997). An automatic cofactor selection using a forward/backward regression. The LOD values above 3.3, 3.1, 3.8, 3.0, 3.2 and 3.4 were considered to indicate the presence of QTLs for germination rate, germination percentage, coleoptile length, coleorhizae length, radicle length and plumule length, respectively.

RESULTS
Phenotypic variation Fig. 1 shows the frequency distribution for drought tolerance at germination of the F4 families of Gharib/ Sepidrud. The distributions of the six germination traits among the F4 population showed continuous and

Fig. 1. Phenotypic distribution of six traits related to drought tolerance in 148 F4 families under drought stress.

Zahra MARDANI, et al. Mapping of QTLs of Germination Characteristics in Rice

Fig. 2. Phenotypic distribution of six traits related to drought tolerance in 148 F4 families under non-stress.

significant transgressive segregation with values either larger or smaller than those of the parents. In the nonstress environment, the population showed typical normal distribution for all the six traits investigated (Fig. 2). The mean values and standard deviation (SD) of each trait in the parents and F4 lines together with ttest for evaluating the significant differences between parents are shown in Table 1. The F4 families showed significant variability for the six drought tolerance parameters examined in the present study. All the parameters showed transgressive segregation, suggesting involvement of multiple genes with quantitative inheritance. The female parent, Gharib, was phenotypically more tolerant than the male parent, Sepidroud, for all evaluated traits. Also, differences between parents for all the studied traits were significant (Table 1). For the

six traits, Gharib had greater values than Sepidrud, therefore all traits evaluated in both environments could be analyzed for QTL mapping. Linkage map There are 12 linkage groups. The markers were distributed on each chromosome based on the MacCouchs map ( McCouch et al, 2002 ). A linkage map of 12 rice chromosomes was constructed from genotypic data of 148 F2 plants with 131 SSR and 105 AFLP polymorphic markers. The linkage map covered 12 chromosomes and spanned 2475.7 cM of the rice genome with an average interval of 10.48 cM between marker loci (Fig. 3). QTLs mapping under non-stress and drought stress

Table 1. Phenotypic analysis of physiological traits related to drought tolerance in parents and F4 families. Parent Sepidroud (Mean SD) Gharib (Mean SD) Germination rate (3.52 0.12) 10-3 7.61 0.14 Germination percentage 86.03 0.20 98.75 0.41 Radicle length (cm) (0.48 0.35) 10-3 4.67 0.06 Plumule length (cm) 1.29 0.01 4.00 0.04 Coleoptile length (cm) 0.81 0.01 1.58 0.02 Coleorhiza length (cm) 0.011 0.001 (0.041 0.14) 10-3 **, Indicate significant differences between the two parental lines at P < 0.01. Trait F4 (Mean SD) 5.46 0.13 (94.16 0.83) 10-3 3.55 0.94 2.62 0.08 1.10 0.01 (0.031 0.600) 10-3 T-value (P1 P2) 27.20** 29.31** 72.76** 39.03** 26.92** -75.43**

Rice Science, Vol. 20, No. 6, 2013

Fig 3. Linkage map and QTLs related to drought tolerance in the F2:4 population from the cross Gharib Sepidroud. The numbers of chromosomes (Chr.) are shown at the top and the Kosambi values (cM) and markers are indicated at the right and left sides of the chromosomes, respectively. The QTLs for six studied traits are signed on the chromosomes under drought and non stress.

The results of QTL mapping under drought stress and non-stress are shown in (Table 2). Germination rate (GR) Two QTLs were detected for GR on chromosomes 1 and 4 under drought stress condition. Two QTLs qGR-1 and qGR-4, showed large effects on GR and explained 15.40% and 17.80% of the total phenotypic variation, respectively. The alleles from Gharib at two QTLs had positive effects. In non-stress, one QTL were identified for GR, the QTL on chromosome 1 was located between the two markers RM237RM246 and determined 19.73% of the total variation. Major QTL (qGR-1) mapped to the same region of chromosome 1

in both conditions. Moreover, the QTL detected by the same marker interval across environments indicates that QTL for this trait is stable and not essentially affected by environmental factors. Germination percentage (GP) Three QTLs for GP were identified on three chromosomes under drought condition. Of these, two QTLs (qGP-4 and qGP-7) mapped on chromosomes 4 and 7 with LOD values of 4.19 and 3.74 and phenotypic variation explaining 17.64% and 18.03%, respectively. The increased allele effect of these QTLs was contributed by Gharib. Three QTLs for germination percentage were identified on chromosomes 4, 5 and 7 under non-

Zahra MARDANI, et al. Mapping of QTLs of Germination Characteristics in Rice

Table 2. Putative QTLs for germination traits in F2:4 population under drought stress and non-stress condition. Trait QTL Markers interval a Chr. Position (cM) b LOD Additive effect (A) Dominance effect (D) D/|A| (R2) c DPE d

Drought stress GR qGR-1 RM237RM246 1 0.6 3.86 0.32 0.78 2.43 15.40 GHB qGR-4 RM252E37-M61-6 4 1.3 4.07 0.19 0.22 1.15 17.80 GHB GP qGP-4 E37-M60-3RM8213 4 4.3 4.19 0.81 1.14 1.40 17.64 GHB qGP-7 RM70RM3608 7 5.7 3.74 0.45 1.03 2.28 18.03 GHB qGP-9-b RM3903RM160 9 4.9 3.08 0.76 1.12 1.47 13.75 GHB RL qRL-5 RM421E37-M61-5 5 5.7 3.13 0.11 0.23 2.09 9.80 GHB qRL-12 E36-M61-9RM101 12 11.9 4.12 0.23 1.10 4.78 17.98 GHB PL qPL-1 RM212RM1268 1 1.1 3.56 0.05 0.01 0.20 15.48 GHB qPL-5 E36-M59-10RM440 5 3.5 3.49 0.12 -1.13 -9.41 18.22 GHB COL qCOL-3 RM7RM282 3 3.7 4.04 0.27 0.10 0.37 18.34 GHB qCOL-9 RM434E36-M59-11 9 3.1 3.47 0.10 -0.01 -0.10 10.11 GHB CL qCL-1 RM1287RM237 1 0.3 4.04 0.86 -0.63 -0.73 16.76 GHB qCL-4 RM8213E37-M60-3 4 1.1 4.12 -0.45 -1.03 -2.28 16.24 SPD Non-stress GR qGR-1 RM237RM246 1 0.6 3.67 0.17 0.98 5.66 19.73 GHB GP qGP-4 E37-M60-3RM8213 4 4.3 3.84 0.23 0.91 3.91 16.12 GHB qGP-5 RM480E36-M59-9 5 1.2 3.45 0.25 0.38 1.49 11.98 GHB qGP-7 RM70RM3608 7 5.7 3.39 0.18 0.37 1.97 9.20 GHB RL qRL-12 E36-M61-9RM101 12 11.9 3.01 0.19 0.20 1.05 15.65 GHB PL qPL-8 E36-M59-7E38-M61-1 8 3.6 4.11 0.10 0.58 5.51 15.93 GHB COL qCOL-3 RM7RM282 3 3.7 3.24 -0.33 0.19 0.59 10.44 SPD qCOL-5 RM6320E38-M61-11 5 5.2 4.17 0.02 0.24 0.18 21.28 GHB CL qCL-4 RM8213E37-M60-3 4 1.1 4.87 -1.04 -2.28 -2.19 15.33 SPD GR, Germination rate; GP, Germination percentage; RL, Radicle length; PL, Plumule length; COL, Coleorhiza length; CL, Coleoptile length; Chr., Chromosome. a Underlined markers are more closer to QTL; b QTL position from the nearest flanking marker (cM); c Phenotypic variance explained by each QTL. d DPE, Direction of phenotypic effect, GHB and SPD indicate Gharib and Sepidroud, respectively.

stress. The QTL qGP-4 showed the largest effect on germination percentage and explained 16.12% of the total phenotypic variance. In all the three QTLs, the alleles from Gharib increased germination percentage by 0.66 on average. Further, two QTLs qGP-4 and qGP-7 were also identified under both conditions. Besides, under drought conditions, the QTL qGP-7 was as well detected under non-stress with main effect. Radicle length (RL) Under drought conditions, two QTLs were identified for RL on chromosomes 5 and 12. Furthermore, under non-stress, one QTL associated with radicle length was found on chromosome 12. QTL qRL-12 was detected in vicinity of E36-M61-9RM101 on chromosome 12 and explaining 15.65 % of total variance, putative QTL showed over dominance effects. Plumule length (PL) Two QTLs, one each on chromosome 1 (RM212 RM1268) and chromosome 5 (E36M59-10RM440) were detected for PL under drought stress conditions and explained 15.48% and 18.22% of the total phenotypic variation, respectively. The Gharib alleles of QTL on chromosomes 1 increased PL, while the Sepidrud alleles of QTL on chromosome 5 decreased

PL under severe drought stress. Under non-stress, one QTL was mapped for length plumule on chromosome 8. This QTL showed positive effects on the PL and explained 15.93% of the total phenotypic variance, putative QTL showed over dominance effects. Coleorhiza length (COL) Two QTLs were identified for COL on chromosomes 3 and 9 under stress conditions. One of the QTLs, which identified on chromosome 3 located at the interval RM7RM282 and comprised 18.34% of phenotypic variation also allele inherited from Gharib parent increased COL. Two QTLs were identified for coleorhiza length on chromosomes 3 and 5 under nonstress. QTL qCOL-3 was commonly detected in both conditions. Moreover, The QTL detected by the same marker interval across environments indicates that QTL for this trait is stable and not essentially affected by environmental factors. The major QTL (qCOL-5) was detected only under non-stress and explained 21.28% of the total phenotypic variance, the alleles from Gharib increased coleorhiza length and qCOL-5 exhibited partial dominance for increase this trait. Coleoptile length (CL) Under drought conditions, two QTLs were identified

Rice Science, Vol. 20, No. 6, 2013

for CL on chromosomes 1 and 4. qCL-4 was in a similar position to that found under non-stress and showed greater effect. Similar QTL was found in interval RM1287RM237 and 16.24 and 15.33% of the phenotypic variation was determined by this QTL under drought stress and non-stress, respectively. In addition, putative QTL showed over dominance effects.

DISCUSSION
This study compares the QTLs identified and discusses the genetic relationships between drought tolerance traits at the germination stage under two conditions. Totally of 22 QTLs were detected under both conditions, of which 13 QTLs were detected in drought stress environment and 9 QTLs under nonstress conditions. Under the drought stress, 10 main effect QTLs (qGR-1, qGR-4, qGP-4, qGP-7, qRL-12, qPL-1, qPL-5, qCOL-3, qCL-1 and qCL-4) were located on chromosomes 1, 3, 4, 5, 7 and 12. While under non-stress conditions, six major QTLs (qGR-1, qGP-4, qRL-12, qPL-8, qCOL-5 and qCL-4) were detected on chromosomes 1, 4, 5, 8 and 12. Comparing two treatments, only six QTLs (qGR-1, qCOL-3, qGP-4, qCL-4, qGP-7 and qRL-12) were detected in stress and non-stress environments and they were located on chromosomes 1, 3, 4, 7 and 12 associated with respectively. Putative QTLs for this trait are stable and not essentially affected by environmental factors. One major QTL for GR was found on chromosome 1 under both conditions. Wen et al (2008) detected one QTL for seed dormancy on chromosome 1, which were very close to the QTL (qGR- 1) for GR detected in this study. The QTLs detected for this trait during our study is similar to the results reported by Angaji et al (2008) and Zahng et al (2005), but different to the findings of Liang et al (2006). In this study, QTL qGP-4 for GP was found under both conditions, which might play essential roles in germination percentage. They were placed close to the marker RM8213 on chromosome 4 on both conditions. Wang et al (2011) detected seven QTLs for this trait by using RIL (F2:9) population. They were on chromosomes 4, 7 and 10, qGP-4 with LOD = 2.6 that explained 9% of the total phenotypic variance, this QTL was similar to QTL in this study. The region and variance phenotypic QTL (qGP-4) was also similar to QTL detected by Teng et al (2001). In the present

study, four QTLs related to RL were detected on chromosomes 3, 5, 9 and 12 under non-stress conditions. This result differed for the locations of the QTLs detected for radicle length by other researchers (Redona and Mackill, 1996, Zhang et al, 2005). It is obvious because they studied different trait as well as the ways of phenotyping were different. One QTL for plumule length on chromosome 8 under non-stress conditions was found in similar region reported by Zhang et al (2005). In addition, Sabouri and Sabouri (2008) detected two QTLs for shoot length on chromosomes 3 and 10. Also, the region RM212 on chromosome 1 found in the present study to harbor one QTL for PL trait, which has been reported by many earlier workers. For instance, Price et al (2002), Lafitte et al (2002) and Wang et al (2005) have reported QTLs for drought tolerant in the same region. Thus, this region appears to be a good candidate for breeding for drought tolerance through markerassisted selection as well as for fine mapping and positional cloning of the underlying genes. Coleoptile growth, other factors affect seedling establishment. In this study, we found two QTLs for CL on chromosomes 1 and 4 under both conditions against the chromosomes reported by Redona and Mackill (1996), but putative QTLs were found in agreement with chromosomes reported by Hu et al (2007). Nine QTLs associated with coleoptile length were detected on chromosomes 1 (two QTLs), 2 (two QTLs), 3, 5 (two QTLs), 6 and 7. Furthermore, the locus (qCL-1) mapped on chromosome 1 in this study could be approximately the same locus reported by Hu et al (2007). It is hard to precisely compare the chromosomal location of these QTLs because of different genetic materials and lack of common markers used for mapping, and additional studies are needed to clarify the allelic relationship of these QTLs. In this research, three QTLs were detected associated with COL. In fact, this study reports for the first time the detection of QTL for this trait on chromosomes 3, 5 and 9. The QTLs did not have the same map location and there was no similarity with results of previous researchers. As many as 22 QTLs were detected to be associated with drought tolerant, and some of them are being reported for the first time. Most of the QTLs identified in the current study, showed a range of partial to over dominance effects, indicating complexity of the traits under consideration (Table 2). In most of the cases, degree of dominance (D/|A|) was high, suggesting the

Zahra MARDANI, et al. Mapping of QTLs of Germination Characteristics in Rice

importance of dominance or over dominance effects for the respective QTLs. These high levels of dominance can be related to heterosis. However, these results will provide important information for further functional analysis of drought tolerance genes in rice. In this study, F2:4 population derived from the cross between Gharib Sepidroud, a new source of breeding material and to analysis new QTLs for drought tolerance. These results indicate that QTLs pyramiding by using marker-assisted selection are very useful breeding methods for developing high drought tolerance rice variety.

REFERENCES
Angaji S A. 2008. Mapping QTLs for submergence tolerance during germination in rice. Afr J Biotechn, 7: 25512558. Basten C J, Weir B S, Zeng Z B. 1997. QTL cartographer: A reference Manual and Tutorial for QTL Mapping. Raleigh N C, USA: North Carolina State University. Cheng H T, Hua J, Xue D W, Guo L B, Zeng D L, Zang G H, Qian Q. 2008. Mapping of QTL underlying tolerance to alkali at germination and early seedling stages in rice. Acta Agron Sin, 34: 17191727. Dey M M, Upadhyaya H K. 1996. Yield loss due to drought, cold and submergence in Asia. In: Evenson R E, Herdt R W, Hossain M. Rice Research in Asia: Progress and Priorities. Wallingford, UK: CAB International: 291303. Foolad M R, Lin G Y, Chen F Q. 1996. Comparison of QTLs for seed germination under non-stress, cold stress and salt stress in tomato. Plant Breeding, 118: 167173. Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin S Y, Yano M. 2004. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet, 108: 794799. Gong J M, Zheng X W, Du B X, Qian Q, Chen S Y, Zhu L H, He P. 2001. Comparative study of QTLs for agronomic traits of rice (Oriza sativa L.) between salt stress and nonstress. Sci China: Life Sci, 44: 7382. Han L Z, Zhang Y Y, Qiao Y L, Cao G L, Zhang S Y, Kim J H, Koh H J. 2006. Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genet Sin, 33: 9981006. Hayashi E, Aoyama N, Still D W. 2008. Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome, 51: 928947. Hu S P, Yang H, Zou G H, Liu H Y, Liu G L, Mei H W, Run C, Li M S, LUO L J. 2007. Relationship between coleoptile length and drought resistance and their qtl mapping in rice. Rice Sci, 14(1): 1320. Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H. 2009. A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor Appl Genet, 118: 14771488.

Ji S L, Jiang L, Wang Y H, Zhang W W, Liu X L, Liu S J, Liu S J, Chen L M, Zhai H Q, Wan J M. 2009. Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breeding, 128: 387392. Kamoshita A, Zhang J X, Siopongco J, Sakarung S, Nguyen H T, Wade L J. 2002. Effects of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Sci, 42(1): 255265. Lafitte H R, Courtois B, Arraudeau M. 2002. Genetic improvement of rice in aerobic systems: Progress from yield to genes. Field Crops Res, 75: 171190. Lanceras J C, Pantuwan G, Jongdee B, Toojinda T. 2004. Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol, 135: 384399. Liang C, Lou Q J, Sun Z X, Xing Y Z, Yu X Q, Luo L J. 2006. QTL Mapping of low temperature on germination rate of rice. Rice Sci, 13(2): 9398. MacMillan K, Emrich K, Piepho H P, Mullins C E, Price A H. 2006. Assessing the importance of genotype environment interaction for root traits in rice using a mapping population: II. Conventional QTL analysis. Theor Appl Genet, 113(5): 953964. Maguire J D. 1962. Seed of germination aid in selection and evaluation for seedling emergence and vigour. Crop Sci, 2: 176 177. Mano Y, Takeda K. 1997. Mapping quantitative trait loci for salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L). Euphytica, 94: 263272. McCouch S R, Teytelman L, Xu Y B, Lobos K B, Clare K, Walton M, Fu B, Maghirang R, Li Z K, Xing Y Z, Zhang Q F, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 9: 199207. Miura K, Lin S Y, Araki H, Nagamine T, Kuroki M, Shimizu H, Ando L, Yano M. 2004. Genetical studies on germination of seed and seedling establishment for breeding of improved rice varieties suitable for direct seeding culture. Jpn Agric Res Quart, 38: 15. Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G. 2009. Genome-wide analysis of genes targeted by during seed germination in Arabidopsis. Plant Cell, 21: 403419. Park S J, Kwak K J, Oh T R, Kim Y O, Kang H. 2009. Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol, 50: 869878. Price A H, Townend J, Jones M P, Audebert A, Courtois B. 2002. Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines. Mol Biol, 48: 683695. Redona E D, Mackill D J. 1996. Genetic variation for seedling traits in rice. Crop Sci, 36: 285290. Sabouri H, Sabouri A. 2008. New evidence of QTLs attributed to salinity tolerance in rice. Afr J Biotechn, 7(24): 43764383. Saghai Maroof M A, Biyashev R M, Yang G P, Zhang Q, Allard R W. 1994. Extraordinarily polymorphic microsatillate DNA in barely species diversity, choromosomal location & population dynamics. Proc Natl Acad Sci USA, 91: 54665470.

Rice Science, Vol. 20, No. 6, 2013

Sasaki K, kazama Y, Chae Y, Sato T. 2013. Confirmation of novel quantitative trait loci for seed dormancy at different ripening stages in rice. Rice Sci, 20(3): 207212. Srividhya A, Vemireddy L R, Sridhar S, Jayaprada M, Ramanarao P V, Hariprasad A S, Reddy H K, Anuradha G, Siddiq E. 2011. Molecular mapping of QTLs for yield and its components under two water supply conditions in rice ( Oryza sativa L.). J Crop Sci Biotechn, 14(1): 4556. Tanksley S D. 1993. Mapping polygenes. Ann Rev Genet, 27: 205 233. Teng S h, Zeng D L, Qian Q, Kunihifo Y, Huang D N, Zhu L H. 2001. QTL analysis of rice low temperature germinability. Chin Sci Bull, 46(21): 10811083. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: A new technique for DNA fingerprinting. Nucl Acid Res, 23: 4407 4414. Wang S, Basten C J, Zeng Z B. 2007. Windows QTL Cartographer 25. USA: Department of Statistics, North Carolina University. Wang X S, Zhu J, Mansueto L, Bruskiewich R. 2005. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map. J Zhejiang Univ Sci, 6: 382388. Wang Z F, Wang J F, Bao Y M, Wu Y Y, Zhang H S. 2011. Quantitative trait loci controlling rice seed germination under salt stress. Euphytica, 178(3): 297307. Wen J, Ling J, Zhang W W, Zhai H Q, Wan J M. 2008. Mapping QTL for seed dormancy in weedy rice. Acta Agron Sin, 34(5): 737742. Xiong L M, Wang R G, Mao G H, Koczan J M. 2006. Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic acid. Plant Physiol, 142(3): 10651074. Yano R, Kanno Y, Jikumaru Y, Nakabayashi K, Kamiya Y, Nambara E. 2009. Chottol, a putative double Apetala2 repeat transcription factor, is involved in abscisic acid-mediated repression of gibberellin biosynthesis during seed germination in Arabidopsis. Plant Physiol, 151: 641654. Zhang Z H, Qu X S, Wan S, Chen L H, Zhu Y G. 2005. Comparison of QTL Controlling Seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa). Ann Bot, 95: 423429.