Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought ...tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge.
Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the -QTL BILs and IR64, four major-effect QTL--one each on chromosomes 2, 4, 9, and 10--were identified. Meta-analysis of transcriptome data from the +QTL/-QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha⁻¹ over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia.
Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Drought is the most important constraint reducing rice yield in rainfed areas. Earlier efforts to improve rice yield under drought mainly focused on improving secondary traits because the broad-sense ...heritability (H) of grain yield under drought stress was assumed to be low, however gains in yield by selecting for secondary traits have not been clearly demonstrated in rice. In present study, the effectiveness of direct selection for grain yield was assessed under lowland reproductive stage stress at Raipur in eastern India and under upland reproductive stage drought stress at IRRI. The selection under severe stress (in both upland and lowland trials) resulted in greater gains under similar stress levels (yield reduction of 65% or greater under stress) in evaluation experiments than did selection under non-stress conditions, with no yield reduction under non-stress conditions. We observed similar H of grain yield under stress and non-stress conditions, indicating direct selection for yield under drought will be effective under both lowland and upland drought stresses. None of the secondary traits (panicle exsertion, harvest index, leaf rolling, leaf drying) included in our study showed a higher estimate for H than grain yield under stress. Secondary traits as well as indirect selection for grain yield under non-stress situation were predicted to be less effective in improving yield under drought in both lowland and upland ecosystem than direct selection for grain yield under the respective stress situations. The low, but positive values observed for genetic correlation (
r
G) between yield under stress and non-stress indicated that it is possible to combine drought tolerance with high-yield potential but low values also indicated that selection for grain yield needs to be carried under stress environments. The study also indicated that under lowland drought stress, the use of highly drought-tolerant donors, as parents in crosses to high yielding but susceptible varieties resulted in a much higher frequency of genotypes combining high-yield potential with tolerance than did crosses among elite lines with high-yield potential but poor tolerance. Breeding strategies that use drought-tolerant donors and that combine screening for yield under managed drought stress with screening for yield potential are likely to result in the development of improved cultivars for drought-prone rainfed rice producing areas.
Flooding is one of the major constraints for rice production in rainfed lowlands, especially in years and areas of high rainfall. Incorporating the Sub1 (Submergence1) gene into high yielding popular ...varieties has proven to be the most feasible approach to sustain rice production in submergence-prone areas. Introgression of this QTL into popular varieties has resulted in considerable improvement in yield after flooding. However, its impact under non-flooded conditions or years have not been thoroughly evaluated which is important for the farmers to accept and adopt any new version of their popular varieties. The present study was carried out to evaluate the effect of Sub1 on grain yield of rice in different genetic backgrounds, under non-submergence conditions, over years and locations. The study was carried out using head to head trials in farmer's fields, which enable the farmers to more accurately compare the performance of Sub1 varieties with their recurrent parents under own management. The data generated from different head to head trials revealed that the grain yield of Sub1 varieties was either statistically similar or higher than their non-Sub1 counterparts under non-submergence conditions. Thus, Sub1 rice varieties show no instance of yield penalty of the introgressed gene.
Background
Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient ...varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of
qDTY
1.1
,
qDTY
2.1
,
qDTY
3.1
and
Sub1.
Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal.
Results
Grain yield advantage of the NILs with
qDTY
1.1
+ qDTY
2.1
+
qDTY
3.1
+
Sub1
and
qDTY
2.1
+
qDTY
3.1
+
Sub1
ranged from 76 to 2479 kg ha
− 1
and 396 to 2376 kg ha
− 1
under non-stress (NS) respectively and 292 to 1118 kg ha
− 1
and 284 to 2086 kg ha
− 1
under reproductive drought stress (RS), respectively. The NIL, IR96322–34-223-B-1-1-1-1 having
qDTY
1.1
+ qDTY
2.1
+
qDTY
3.1
+
Sub1
has been released as variety CR dhan 801 in India. IR 96321–1447-651-B-1-1-2 having
qDTY
1.1
+
qDTY
3.1
+
Sub 1
and IR 94391–131–358-19-B-1-1-1 having
qDTY
3.1
+
Sub1
have been released as varieties Bahuguni dhan-1′ and ‘Bahuguni dhan-2’ respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322–34-223-B-1-1-1-1, IR 96321–1447-651-B-1-1-2 and IR 94391–131–358-19-B-1-1-1 respectively on 6 K SNP Infinium chip.
Conclusion
The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha
− 1
under reproductive stage drought stress and 0.1 to 1.0 t ha
− 1
under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
Key message
The study provides high-throughput protocol for ploidy determination which may accelerate the production of double haploids in rice.
Advancements in anther-culture technique have ...accelerated the production of completely homozygous breeding lines in a shortened time frame. However, the success is dependent upon several factors including precise and accurate determination of ploidy status at callus stage. In the present study, we describe a protocol for nuclei isolation and performed DNA content based ploidy analysis in anther-derived rice callus. Tris-MgCl
2
buffer (200 mM Tris, 4 mM MgCl
2
·6H
2
O, 0.5% (vol/vol) Triton X-100, adjusted pH to 7.5 with 1 N HCl) was used for isolating high-density nuclei suspension. The nuclei were stained with propidium iodide and fluorescence image was captured using Cellista-Acumen Software in high throughput cell analyser (HTCA). The region of interest was defined on stored image and DNA content was calculated on the basis of fluorescence intensity as well as volume. The protocol was validated using anther callus from different indica rice varieties. Thus, the adoption of high-throughput protocol for ploidy determination will accelerate the development of successful double haploids in rice.
BACKGROUND: Drought is the most severe abiotic stress reducing rice yield in rainfed drought prone ecosystems. Variation in intensity and severity of drought from season to season and place to place ...requires cultivation of rice varieties with different level of drought tolerance in different areas. Multi environment evaluation of breeding lines helps breeder to identify appropriate genotypes for areas prone to similar level of drought stress. From a set of 129 advanced rice (Oryza sativa L.) breeding lines evaluated under rainfed drought-prone situations at three locations in eastern India from 2005 to 2007, a subset of 39 genotypes that were tested for two or more years was selected to develop a drought yield index (DYI) and mean yield index (MYI) based on yield under irrigated, moderate and severe reproductive-stage drought stress to help breeders select appropriate genotypes for different environments. RESULTS: ARB 8 and IR55419-04 recorded the highest drought yield index (DYI) and are identified as the best drought-tolerant lines. The proposed DYI provides a more effective assessment as it is calculated after accounting for a significant genotype x stress-level interaction across environments. For rainfed areas with variable frequency of drought occurrence, Mean yield index (MYI) along with deviation in performance of genotypes from currently cultivated popular varieties in all situations helps to select genotypes with a superior performance across irrigated, moderate and severe reproductive-stage drought situations. IR74371-70-1-1 and DGI 75 are the two genotypes identified to have shown a superior performance over IR64 and MTU1010 under all situations. CONCLUSION: For highly drought-prone areas, a combination of DYI with deviation in performance of genotypes under irrigated situations can enable breeders to select genotypes with no reduction in yield under favorable environments compared with currently cultivated varieties. For rainfed areas with variable frequency of drought stress, use of MYI together with deviation in performance of genotypes under different situations as compared to presently cultivated varieties will help breeders to select genotypes with superior performance under all situations.
A large-effect QTL for grain yield under drought conditions (qtl12.1) was reported in a rice mapping population derived from Vandana and Way Rarem. Here, we measured the effect of qtl12.1 on grain ...yield and associated traits in 21 field trials: ten at IRRI in the Philippines and 11 in the target environment of eastern India. The relative effect of the QTL on grain yield increased with increasing intensity of drought stress, from having no effect under well-watered conditions to having an additive effect of more than 40% of the trial mean in the most severe stress treatments. The QTL improved grain yield in nine out of ten direct-seeded upland trials where drought stress was severe or moderate, but no effect was measured under well-watered aerobic conditions or under transplanted lowland conditions. These trials confirm that qtl12.1 has a large and consistent effect on grain yield under upland drought stress conditions, in a wide range of environments.
The genetic diversity of yield and yield attributing characteristics was explored in this research. In the topical study, fifty-two rice genotypes including four checks were used under three ...environmental conditions i.e. irrigated (IR), rainfed (RF) and terminal stage drought (TSD) conditions. The prevalence of genetic divergence was evaluated using clustering and Principal component analysis (PCA) was used to determine the relative contribution of various traits. To fulfill the aim of the study, fifty-two genotypes were grouped into three distinct and non-overlapping clusters among these 3 clusters, cluster-I was the largest with the highest number of genotypes i.e. 47, 49 and 49 under IR, RF and TSD conditions, respectively. The highest average intra-cluster distance was observed in cluster-I, also the genotypes showed high variability under all three conditions. The highest inter-cluster distance between the cluster-II and cluster-III (IR and TSD) and cluster-I and cluster-II (RF) was observed, indicated that genotypes from the group should be considered for direct use as parents in hybridization programme to produce high yield. Only five of the 13 principal components (PCs) have been considered in the study based on the Eigen values and variability criteria. From the complex matrix it was revealed that the first-PC accounted for the highest variability. Genotypes which fall under a common PC were observed to be the most important factor for grain yield.
With the substantial increase in food grain production, much of the emphasis has been put for enhanced grain quality traits. Most of the grain qualities traits are polygenic in nature. Identification ...of QTLs and markers linked to these QTLs can substantially enhance the selection efficiency. In this study, an effort has been made to identify QTLs for these traits. For this purpose two mapping population, RIL Safri17 x Kranti and DH population CT-993-5-10-1-M and IR 62266-42-6-2 were used and evaluated under field conditions. DNA from 112 lines of RIL was extracted, quantified and diluted to the appropriate concentration for PCR-based amplification. Fifty markers were used for detecting parental polymorphism. Five markers exhibiting polymorphism were further used for developing marker profile on the complete set of RIL. This data along with genotyping data for this population was used for QTLs analysis using single marker ‘t’ test. RM 110, RM 202 and RM 212 were associated with grain length, RM 84 and RM 539 was associated with grain width, and RM 163, RM 202, RM 247 and RM 80 were associated to be L/B ratio. For DH population MAPMAKER/ QTL 1.1 was used for interval mapping and to estimate the percentage of total phenotypic variation. A threshold of LOD> 2.4 was used per test to claim the presence of QTL. A total of 8 QTLs were detected for grain width and grain L/B ratio. For grain width 3 QTLs detected on chromosome number 2, 3, 6 which shows 11 percent phenotyping variation. For L/B ratio 5 QTLs were detected, which were present on chromosome 2 3, 6 having 9 to 12.5 percent phenotypic variation. For grain length no QTLS detected.
Rice is a major cereal crop, negatively impacted by soil-salinity, both in terms of plant growth as well as productivity. Salinity tolerant rice varieties have been developed using conventional ...breeding approaches, however, there has been limited success which is primarily due to the complexity of the trait, low yield, variable salt stress response and availability of genetic resources. Furthermore, the narrow genetic base is a hindrance for further improvement of the rice varieties. Therefore, there is a greater need to screen available donor germplasm in rice for salinity tolerance related genes and traits. In this regard, genomics based techniques are useful for exploring new gene resources and QTLs. In rice, the vast allelic diversity existing in the wild and cultivated germplasm needs to be explored for improving salt tolerance. In the present review, we provide an overview of the allelic diversity in the Quantitative Trait Loci (QTLs) like Saltol, qGR6.2, qSE3 and RNC4 as well as genes like
,
(
) and
(salt tolerance level 1 gene) related to salt tolerance in rice. We have also discussed approaches for developing salt-tolerant cultivars by utilizing the effective QTLs or genes/alleles in rice.
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