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Dissecting QTLs for Reproductive Stage Salinity Tolerance in Rice from BRRI dhan 47
Plant Breed. Biotech. 2019;7:302-312
Published online December 1, 2019
© 2019 Korean Society of Breeding Science.

Sejuti Mondal1,2,3, Teresita H. Borromeo4, M. Genaleen Q. Diaz5, Junrey Amas6, M. Akhlasur Rahman7, Michael J. Thomson2*, Glenn B. Gregorio1,4*

1International Rice Research Institute, Los Baños, Laguna 4031, Philippines
2Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
3Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
4Institute of Crop Science, College of Agriculture and Food Science, Univerity of the Philippines Los Baños, Laguna 4030, Philippines
5Institute of Biological Sciences, University of the Philippines Los Baños, Laguna 4031, Philippines
6Department of Agriculture-Caraga Region, Butuan City 8600, Philippines
7Bangladesh Rice Research Institute, Gazipur 1701, Bangladesh
Corresponding author: *Michael J. Thomson,, Tel: +19798457526, Fax: +19798450456
*Glenn B. Gregorio,, Tel: +63-286571300 Ext. 1000, Fax: +63-495367097
Received September 18, 2019; Revised October 30, 2019; Accepted October 31, 2019.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Salinity is a common and increasing problem in many coastal rice producing areas around the world. Salinity tolerance at the reproductive stage in rice is crucial as it determines grain yield. An F2 mapping population was developed from two modern rice cultivars contrasting in tolerance: NSIC Rc222 (a high-yielding salt-sensitive variety released in the Philippines) and BRRI dhan 47 (a salt-tolerant variety released in Bangaldesh). The performance of the F2 population showed transgressive segregation in the yield components under salinity stress of EC 10 dS/m under salinized field conditions. Ninety-six single nucleotide polymorphism (SNP) markers using 96-plex FluidigmTM genotyping were used to construct a linkage map of 1306.2 cM (Kosambi), with an average interval size of 13.6 cM. Seven putative quantitative trait loci (QTLs) for reproductive stage salinity tolerance traits having LOD values ranging from 2.9 to 4.1 were identified on chromosomes 1, 2, 5 and 11, explaining 13.4 to 18.4% of the phenotypic variation. Results of this mapping study identified a genomic region on chromosome 2 that confers salinity tolerance at the reproductive stage as measured by the number of filled spikelets, percent filled spikelets and yield. This study reports the molecular mapping of QTLs controlling reproductive-stage salinity tolerance-related traits, which will be useful in marker-assisted selection and breeding population development in rice.
Keywords : Rice, Oryza sativa, Salinity tolerance, Reproductive stage, SNP marker, Quantitative trait locus (QTL)

Rice is a diploid (2n = 2x = 24) glycophyte, of tropical origin, and is considered a model crop species for genetic studies. About 90% of the rice in the world is grown in Asia and 85% is devoted for human consumption. To meet the projected demand for rice, it has been estimated that global annual rice production needs to double by 2050; however, current rates of annual yield increase in rice are insufficient to meet this demand (Ray et al. 2013). Various abiotic stresses greatly affect rice yield, and among the abiotic stresses, salinity is the second most prevalent soil problem in rice growing countries of the world and is a serious threat to increasing rice production worldwide (Gregorio 1997).

Salinity tolerance in rice is a quantitative trait that is polygenic in nature. Rice is very sensitive at the seedling and reproductive stages; but the reproductive stage is crucial as it ultimately determines grain yield. However, the importance of the seedling stage cannot be ignored as it affects crop establishment. Hence, pyramiding of contributing traits at both stages is needed to develop resilient salt-tolerant cultivars for stress-prone environments (Moradi et al. 2003). Salinity at the reproductive stage depresses grain yield much more than the vegetative stage. Conventional breeding has been used to develop stress-tolerant high-yielding varieties of rice, but plant selection for salt tolerance using conventional methods is not easy due to the large environmental effects and low heritability of salt tolerance (Gregorio and Senadhira 1993; Gregorio et al. 2002).

DNA-based molecular markers have been extensively used to assess the genetic diversity across most crop species and to map quantitative trait loci (QTLs) across a large number of traits. Molecular markers can measure the contribution to phenotype for a set of QTLs, as well as enabling the selection of favorable alleles at these loci in a marker-assisted selection (MAS) scheme that aims to accelerate genetic advancement in rice. Thus, identifying molecular markers that are linked to genes controlling salinity tolerance can assist selection for salinity tolerance having low heritability and expressivity (Singh et al. 2007). Moreover, single nucleotide polymorphism (SNP) markers have great potential to further increase the efficiency and number of available markers for high-throughput genotyping techniques and whole genome marker scans; consequently, molecular breeding is becoming more efficient (Thomson 2014). High-throughput SNP techniques have been applied to investigate QTLs in this study.

Rice is a transplanted crop and it is sometimes possible to use early maturing genotypes to avoid terminal salinity that occurs under coastal saline conditions (Singh and Flowers 2010); however, in most salt-prone areas, it is generally not possible to avoid salinity stress at the reproductive stage. Therefore, studies investigating the genetic components of salinity tolerance at the reproductive stage will be essential in developing high yielding rice varieties with salt tolerance. Mapping of QTLs for salinity tolerance at seedling and reproductive stages of rice can aid in the identification of the genetic control of salinity tolerance leading to development of varieties with improved tolerance by precisely transferring QTLs into adapted varieties (Thomson et al. 2010a). Considerable efforts have been diverted towards the development of salinity tolerance at the seedling stage of rice, such as with the characterization of the Saltol QTL (Thomson et al. 2010b); however relatively few attempts have been made to identify QTLs associated with the reproductive stage salinity tolerance in rice (Zeng et al. 2002; Mohammadi et al. 2013; Bimpong et al. 2014; Hossain et al. 2015). Therefore, the main objective of this study was to identify QTLs for reproductive-stage salinity tolerance from the cross between modern salt-tolerant (BRRI dhan 47) and salt-sensitive (NSIC Rc222) varieties using a F2 mapping population and genotyping with SNP markers.


Reproductive stage salinity tolerance phenotyping

The salinity tolerance phenotyping was conducted in an artificially salinized field of the International Rice Research Institute (IRRI) experimental station in Los Baños, Laguna, Philippines, which was similar to naturally saline field conditions (minus the soil heterogeneity). A modern salt-tolerant IRRI-bred variety released in Bangladesh and Philippines, BRRI dhan 47 (IRRI line IR63307-4B-4-3), and a modern high yielding salt-sensitive IRRI-bred variety released in the Philippines, NSIC Rc222 (IRRI line IR78581-12-3-2-2), were used in the experiment as parents to develop the mapping population. The tolerant donor parent (IR63307-4B-4-3) is a medium-maturing, advanced breeding line in an indica background that was bred for salt tolerance at IRRI, and is a cross between a somaclonal variant of Pokkali (TCCP 266-2-49-B-B-3) and the breeding line IR51511-B-B-34-B, which itself was derived from a cross between the breeding line IR8909 and the cultivar IR34 (Gregorio et al. 2002; Reddy et al. 2014; Angeles-Shim et al. 2019). The cross was conducted by the Plant Breeding Division crossing program and F1 seeds were generated and selfed to produce the F2 population. The 92 F2 progenies were chosen randomly and used for the mapping population. The initial salinity level of EC 6 to 8 dS/m was imposed beginning in the early vegetative stage, i.e. two weeks after transplanting, and it was increased to EC 10 dS/m at the panicle initiation stage. A few days before harvesting, salinity scoring was performed to identify the tolerant and sensitive plants based on visual symptoms by using the Modified Standard Evaluation System (SES) of IRRI (Table 1). Data on yield, yield components and important agronomic parameters such as plant height, number of productive, unproductive and total tillers, percentage of productive and unproductive tillers, fresh weight, number of filled, unfilled and total spikelets, percentage of filled and unfilled spikelets and grain yield were collected from the population.

SNP genotyping

The ninty-two F2 individuals were genotyped with SNP markers at the Genotyping Services Laboratory (GSL) of IRRI. Leaf samples were collected from the ninety-two F2 plants and their parents for DNA extraction using a modified CTAB protocol. After extracting DNA, samples were run in agarose for DNA quantification and quality control. Then a 96-plex FluidigmTM high-throughput SNP genotyping protocol was used for SNP analysis with 96 SNP markers, with allele calling performed by the GSL using the clusters from the Fluidigm SNP genotyping software.

QTL mapping analysis

QTL analysis using the yield components and other agronomic traits was performed by composite interval mapping (CIM) with the Java-based QGENE software version 4.0 (Joehanes and Nelson 2008). CIM analysis was performed to precisely identify the location of the identified QTLs for salt tolerance. A default LOD threshold score of 2.9 was used and interval map distances based on the result of linkage map analysis were used to determine the association between markers and QTL.


Physio-morphological variation of F2 progenies at the reproductive stage

The phenotypes of the NSIC Rc222 (sensitive parent) and BRRI dhan 47 (tolerant parent) and their F2 progenies salinized at EC 10 dS/m showed significantly different responses at the reproductive stage. Most of the traits, including plant height, number of productive and unproductive tillers, and total tillers, exhibited mean values of their progenies which were similar to the mid parental value, suggesting that alleles from the two parents contributed equally to the expression of those traits (Table 2). Although the mean values of the F2 progenies were higher than the mid parental values for fresh weight and percent unfilled spikelet, the F2 progenies mean values were lower than the mid parental values for percent filled spikelet and grain yield (Table 2).

Correlation analysis of yield and yield components

Correlation analysis was performed in order to determine the relationship between grain yield and other yield components under salt stress conditions. Positive and significant correlations were observed with grain yield to number of filled spikelets (0.979), percent filled spikelet (0.731), number of unfilled spikelets (0.697), total spikelets (0.846), number of productive tillers (0.669), percent productive tiller (0.589), and total tillers (0.336) (Table 3). On the other hand, and as expected, percent unproductive filled spikelet, percent unproductive tiller, and the number of unproductive tillers showed a negative and significant correlation with grain yield under salinity stress (Table 3).

Salinity tolerance QTL mapping at reproductive stage

QTLs related with yield and yield components and several important agronomic components under salinity stress were identified through CIM using QGENE software. The total length of the distribution of the 96 SNP markers was 1306.2 cM, with an average interval size of 13.6 cM. The proportion of the total phenotypic variation explained by each QTL was calculated as R2 value (R2 = PVE, phenotypic variation explained by the QTL). A total of seven QTLs identified in six traits: plant height (PLH), number of total tillers (TT), number of filled spikelets (FS), total spikelets (TS), percent filled spikelet (PFS) and yield, were detected on chromosomes 1, 2, 5 and 11, as described below (Table 4, Fig. 1). The phenotypic variation of the identified QTLs individually accounted for 13.4 to 18.4% phenotypic variation. The chromosomal location, nearest marker, peak LOD, phenotypic variation explained by QTL (R2) and direction of the phenotypic effect (additive effect) for each QTL are presented in Table 4.

Plant height

One QTL (qPLH1.1) was identified for plant height on chromosome 1 (Table 4). The QTL was mapped at 98.1 cM near the marker id1013920 on the long arm of chromosome 1, and phenotypic variation was 14.9% with a 3.2 LOD value. BRRI dhan 47 (tolerant parent) was responsible for contributing towards taller plant height.

Total tillers

Two QTLs for total tillers were detected, one on chromosome 5 (qTT5.1) and another on chromosome 11 (qTT11.1), both of which had a 2.9 LOD value (Table 4). The positions of these QTLs were 53.8 cM and 10.9 cM on the genetic map of chromosomes 5 and 11, respectively; with 13.4% phenotypic variation explained for both QTLs. BRRI dhan 47 was responsible for contributing towards a higher number of total tillers. The QTL qTT5.1 was mapped near the marker id5005551 on the long arm of chromosome 5, and qTT11.1 was mapped near the marker id11000858 on the short arm of chromosome 11.

Number of filled spikelets

The number of filled spikelets is an important yield component of the salinity tolerance at the reproductive stage. In the present study, one QTL was identified for this trait on the short arm of chromosome 2. The LOD value of this QTL was 3.4 and phenotypic variation was 15.3% (Table 4, Fig. 2). BRRI dhan 47 (tolerant parent) was responsible for contributing towards a larger number of filled spikelets.

Total spikelets

The total spikelets is also a main component of the grain yield. At panicle initiation, salinity stress reduced the total spikelets of the plant, especially the more sensitive plants. One QTL on chromosome 11 (qTS11.1) near SNP marker id11000858 was detected for total spikelets with a 3.5 LOD value. This QTL qTS11.1 explained 15.8% of the phenotypic variation (Table 4, Fig. 3).

Percent filled spikelet

Percent filled spikelet is one of the most important yield components. Generally, due to salinity stress, the percentage of filled spikelets will be reduced. But if the percentage is moderate to high, the population is considered as tolerant to moderately tolerant. For that reason it is a good indicator for determining salinity tolerance of the population. Re sults showed that one QTL (qPFS2.1) was identified on the long arm of chromosome 2 with LOD value of 4.1 and showed the highest phenotypic variation (18.4%) explained (Table 4, Fig. 2). The alleles of this QTL came from the tolerant parent, BRRI dhan 47, and the position of the QTL was 122.1 cM.


Yield is the most important and ultimate factor for determining salinity tolerance at reproductive stage. The findings of the current study detected one QTL (qYLD2.1) on chromosome 2 with LOD value of 3.1 and accounting for 14.6% of the phenotypic variation. The position of this QTL was 40.1 cM and near id2004774 SNP marker (Table 4, Fig. 2). BRRI dhan 47 was the source of the increased grain yield at this QTL.


The study was carried out to identify the QTLs that are associated with salinity tolerance at the reproductive stage of rice using F2 individuals of a NSIC Rc222 and BRRI dhan 47 cross. Both are modern rice varieties released and commercially produced; however, NSIC Rc222 is sensitive to salinity stress, while BRRI dhan 47 (IRRI line IR63307-4B-4-3) is a salt-tolerant variety derived from a cross between a somaclonal variant of Pokkali (TCCP 266-2-49-B-B-3) and the breeding line IR51511-B-B-34-B. Somaclonal variation is variation that occurs in plants that have been produced by plant tissue culture, which leads to the creation of additional genetic variability in the plant (Larkin and Scowcroft 1981). As a result of novel mutations during in vitro culture, a number of trait characteristics can be selected, including tolerance to high salt concentration, mineral toxicity and tolerance to environmental or chemical stress (Krisna et al. 2016). The highly salt-tolerant variety Pokkali underwent cell culture to produce somaclonal variation with improved agronomic traits, resulting in a variant, TCCP 266-2-49-B-B-3, with desirable agronomic characteristics and retained salinity tolerance similar to Pokkali (Gregorio et al. 2002). It is vigorous in growth, semi-dwarf and lodging resistant, with white pericarp and improved cooking quality compared to Pokkali. Although these characteristics make the somaclonal variant superior to Pokkali as an improved genetic donor for crop improvement programs, it should have retained the natural genetic variation for salt tolerance from the original Pokkali parent.

Salinity stress injury scoring (rated as a SES score) was performed to evaluate the performance of each F2 individual in the population, but was not considered as a reliable parameter to represent the tolerance level of the population, since the correlation between grain yield and SES score was positive but not significant. This suggests that using the SES score alone may not always be a reliable parameter to measure salinity tolerance at the reproductive stage because the amount of visual salinity stress damage (represented by the SES score) cannot consider the overall effect of salinity at reproductive stage, unlike at seedling stage. Yield is the ultimate stress indicator, as well as several important yield components such as the percent filled spikelets, number of filled spikelets, total spikelets, number and percentage of productive tillers and total tillers, all of which were significantly correlated with yield under stress. Moreover, the percent unfilled spikelet was highly correlated with grain yield under salinity stress as well. This was unexpected, but a possible reason behind this may be the ability of the tolerant genotype BRRI dhan 47 to produce enough spikelets at panicle initation stage since its not affected by saline stress but at the later reproductive stage it produced a higher percent of unfilled spikelets, but still had more filled spikelets overall than the sensitive genotypes.

No QTLs were identified for the number of productive and unproductive tillers per plant, percent of productive and unproductive tillers, fresh weight and percent unfilled spikelet, possibly due to similar underlying genetic control of these traits between the two parents and fact that the salinity stress was introduced at the vegetative stage where the plants are almost at their maximum tillering stage. There is also the possibility that constraints in the study design (92 individuals × 96 SNPs markers) could have limited the number of detected QTLs, especially on chromosomes 7, 9 and 12 which had several gaps in the chromosome coverage. However, a total of seven QTLs were successfully detected in this study across multiple traits, several of which were located in regions previously identified as having QTLs under salinity stress. For example, one QTL was identified for plant height (qPLH1.1) on chromosome 1. Several plant height QTLs under stress had been previously observed on chromosome 1: Hossain et al. (2015) identifed QTLs on chromosome 1, 4 and 7 for plant height and Mohammadi et al. (2013) identified QTLs on chromosomes 1, 3, 4 and 7. Two QTLs were identified for total tiller number (qTT5.1 and qTT11.1). QTLs for total tillers were identified by Hossain et al. (2015) on chromosomes 7 and 8, but in this experiment, the QTLs were identified on chromosome 5 and 11, indicating that these may be novel QTLs.

One QTL for number of filled spikelets per plant (qNFS2.1) was identified on chromosome 2. QTLs were also detected for number of filled grains by previous studies on several chromosomes, including chromosome 2 (Jubay 2012; Mohammadi et al. 2013). The LOD value of the QTL qFRSP2.1s was 3.3 with 6.3% phenotypic variation and the position of this QTL was around 16.8 cM to 39.4 cM. The current study was similar to the findings of Mohammadi et al. (2013) as the QTL was also detected in a similar region on the short arm of chromosome 2 with a 3.4 LOD value. Likewise, the QTL identified for total spikelets per plant (qTS11.1) was on a different chromosome than the ones detected by Mohammadi et al. (2013) on chromosomes 4, 7 and 9. This indicates that the QTL for total spikelets per plant is potentially novel. However, the QTL identified in this study for percent filled spikelet (qPFS2.1) is similar to the one found by Mohammadi et al. (2013) on chromosome 2. In case of both studies, the QTL came from the salt tolerant variety.

Moreover, a single QTL was detected for yield per plant (qYLD2.1), which was in a similar region on chromosome 2 as a previously published QTL with 6.9% phenotypic variation and 3.6 LOD value from the Sadri/FL478 population (Mohammadi et al. 2013). Likewise, Hossain et al. (2015) also identified a QTL for yield under stress on chromosome 2 explaining 12.2% of the phenotypic variation with 7.9 LOD value. These results suggest that the QTL on chromosome 2 for grain yield under salinity stress may be conserved across several salt-tolerant genetic donors and is being passed to the modern salt tolerant varieties.

Among the seven QTLs observed in this experiment, the QTL qPFS2.1 on chromosome 2 near SNP id2013434 showed the largest effect with 4.1 LOD value and 18.4% of the phenotypic variation explained. A separate region on the other end of chromosome 2 affects salinity tolerance at reproductive stage through alterations in the number of filled spikelets and grain yield, at the SNP marker id2004774. These loci present promising targets for marker-assisted selection activities aimed at improving reproductive-stage salininty tolerance. Another interesting region is on chromosome 11, where QTLs were identified for total tillers and total spikelets.

Although beneficial QTLs have been identified, more work is needed to make use of them in a molecular breeding program to improve reproductive-stage salinity tolerance in rice. Many studies using unimproved genetic donors (i.e. landraces such as Pokkali and Nona Bokra) require specialized genetic populations (such as Advanced Backcross or Backcross-Inbred Lines) or extensive backcrossing to transfer novel QTLs into elite genetic backgrounds. The current study employed a F2 population structure; however, one advantage of using two elite varieties as parents is that the F2 individuals can be directly used in a variety development program without negative linkage drag. The beneficial QTLs can then be transferred using marker-assisted selection with flanking SNP markers to select for the tolerant allele. The QTLs identified in this study for reproductive-stage salt tolerance can also be further confirmed in near-isogenic lines (NILs) and fine-mapped to demonstrate their usefulness for future studies and identify candidate genes underlying the QTLs. The identification of the genes constituting these major QTLs would help in dissecting the molecular mechanisms of salinity tolerance at the reproductive stage of rice and provide valuable tools for breeding salinity tolerant lines with high yield under stress.


The assistance of the Genotyping Services Lab, led by Maria Ymber Reveche, for running the SNP genotyping is greatly appreciated. Also the assistance of the Salinity Tolerance breeding team of IRRI in the field preparation and salinity stress maintenance as well as data collection is greatly appreciated as well.


Modified Standard Evaluation System (SES) for scoring of visual salt injury at seedling and reproductive stages in rice.

Score Observation Rating
1 Normal growth, no leaf symptoms Highly tolerant
3 Nearly normal growth, but leaf tips or few leaves whitish and rolled Tolerant
5 Growth severely retarded, most leaves are rolled; few elongating Moderately tolerant
7 Complete cessation of growth; most leaves dry; some plants dying Sensitive
9 Almost all plants dead or dying Highly sensitive

Mean values of yield and agronomic characters of NSIC Rc222/BRRI dhan47 F2 progenies and their parents grown under salt stress of EC 10 dS/m at reproductive stage in the artificially salinized field condition.

Traits NSIC Rc222 BRRI dhan47 Mid parent F2 progenies

Range Mean Skewness
Plant height (cm) 74.00 98.00 86.00 66-106 92.00 ‒0.71
No of productive tillers 10.00 14.00 12.00 0-24 11.00 0.00
No of unproductive tillers 9.00 7.00 8.00 0-19 6.39 0.84
Total tillers 19.00 21.00 20.00 7-34 17.00 0.90
Percent productive tillers 52.63 66.67 59.65 0-100 62.74 ‒0.92
Percent unproductive tillers 47.47 33.33 40.40 0-100 37.26 0.92
Fresh weight (g) 42.55 71.71 57.13 5.2-178.3 64.83 0.98
Percent filled spikelets 8.24 88.03 48.13 0-88.03 20.07 0.30
Percent unfilled spikelets 91.76 11.97 51.87 0-100 75.59 ‒2.05
Yield (g/plant) 6.20 14.50 10.35 0-14.4 4.00 0.83

Correlation coefficients for grain yield under stress and yield components using the 92 individuals (F2) of NSIC Rc222 × BRRI dhan47 under salt stress of 10 dS/m.

Salscr 0.123 ‒0.386** ‒0.16 ‒0.193 ‒0.318** 0.048 ‒0.048 ‒0.638** 0.132 0.136 0.145 ‒0.016 0.157 0.109
DAM ‒0.004 ‒0.216* 0.196 ‒0.041 ‒0.232* 0.232* 0.083 ‒0.121 ‒0.166 ‒0.164 ‒0.155 0.13 ‒0.126
PLH 0.460** ‒0.123 0.388** 0.325** ‒0.325** 0.584** 0.396** 0.434** 0.455** 0.288** ‒0.066 0.420**
PT ‒0.517** 0.611** 0.809** ‒0.809** 0.380** 0.662** 0.751** 0.782** 0.519** 0.015 0.669**
UPT 0.357** ‒0.895** 0.895** 0.221* ‒0.445** ‒0.457** ‒0.489** ‒0.445** ‒0.188 ‒0.425**
TT 0.048 ‒0.048 0.650** 0.316** 0.406** 0.408** 0.166 ‒0.072 0.336**
PPT ‒1 0.026 0.600** 0.672** 0.701** 0.557** 0.155 0.589**
PUPT ‒0.026 ‒0.600** ‒0.672** ‒0.701** ‒0.557** ‒0.155 ‒0.589**
FW 0.146 0.197 0.196 0.053 ‒0.026 0.197
FS 0.670** 0.832** 0.779** ‒0.252* 0.979**
UFS 0.969** 0.298** 0.173 0.697**
TS 0.481** 0.045 0.846**
PFS ‒0.342** 0.731**
PUFS ‒0.285**

*Significant at P < 0.05.

**Significant at P < 0.01. Salscr: Salinity Score, TT: Total tiller (no), UFS: Unfilled spikelet (no), DAM: Damage (%), PPT: Percent productive tiller, TS: Total spikelets, PLH: Plant height, PUPT: Percent unproductive tiller, PFS: Percent filled spikelet, PT: Productive tillers (no), FW: Fresh weight, PUFS: Percent unfilled spikelet, UPT: Unproductive tillers (no), FS: Filled spikelet (no), YLD: Yield.

QTLs identified with composite interval mapping using QGENE for yield and agronomic components in rice F2 population of NSIC Rc222/BRRI dhan47 under salt stress of 10 dS/m.

Traits Chromosome QTL Nearest marker Position LOD R2 (%) Additive effect Allelic effect
Plant height 1 qPLH1.1 id1013920 98.1 3.2 14.9 ‒12.51 BRRI dhan47
Total tillers 5 qTT5.1 id5005551 53.8 2.9 13.4 ‒0.56 BRRI dhan47
11 qTT11.1 id11000858 10.9 2.9 13.4 ‒0.76 BRRI dhan47
Filled spikelet (no) 2 qNFS2.1 id2004774 40.1 3.4 15.3 ‒75.00 BRRI dhan47
Total spikelet (no) 11 qTS11.1 id11000858 14.0 3.5 15.8 ‒19.9 BRRI dhan47
Filled spikelet (%) 2 qPFS2.1 id2013434 122.1 4.1 18.4 ‒5.4 BRRI dhan47
Yield 2 qYLD2.1 id2004774 40.1 3.1 14.6 ‒1.17 BRRI dhan47

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