A large-effect QTL for rice grain yield under upland drought stress on chromosome 1

Drought is a major abiotic stress factor limiting rice production in rainfed areas. In this study we identified a large-effect quantitative trait locus (QTL) associated with grain yield under stress in five different populations on chromosome 1. The effect of this QTL was further confirmed and characterized in five backcross populations in a total of sixteen stress and non-stress trials during 2006 and 2008. In all the stress trials (eight in total) qDTY1.1 showed strong association with grain yield explaining on average 58% of the genetic variation in the trait. Homozygotes for the tolerant parent allele (Apo) yielded on average 27% more than the susceptible parent allele (IR64) homozygotes. Using an Apo/^3*IR64 population, the peak of this QTL (qDTY1.1) was mapped to an interval between RM486 and RM472 at 162.8?cM at a LOD score of 9.26. qDTY1.1 was strongly associated with plant height in all the environments; this was probably due to the presence of the sd1 locus in this genomic region. In a Vandana/^3*IR64 population segregating for sd1, a strong relation between plant height and yield under stress was observed. The observed relation between increased height and drought tolerance is likely due to tight linkage between qDTY1.1 and sd1 and not due to pleiotrophy of sd1. Thus there is a possibility of combining reduced plant height and drought tolerance in rice. The large and consistent effect of qDTY1.1 across several genetic backgrounds and environments makes it a potential strong candidate for use in molecular breeding of rice for drought tolerance.     

Genetics of yield component traits under salt stress at flowering stage and selection of salt tolerant pre-breeding lines for rice improvement

Genetica - Rice is highly vulnerable to salt stress at both seedling and flowering stage. While research efforts largely focused on seedling stage salinity tolerance, flowering stage salt tolerance...     

Defining selection criteria to improve yield under drought

The many selection criteria that have been proposed to increase drought resistance of our crops have had little, if any, impact on improving crop yields in dry environments. There are several likely reasons for this lack of success. Some of these are: (i) criteria proposed have been related more to survival mechanisms under drought than to productivity, (ii) criteria are inappropriate to the target environment, and (iii) criteria are temporal and are therefore likely to have minimal impact on growth and yield over the entire lifecycle. Another important reason is that breeders have not been convinced the proposed criteria will be successful as they are too difficult to measure. On the other hand, empirical breeding programmes to improve yield under drought have been successful. Surprisingly, some of the greatest successes have been achieved by breeding in environments where water is non-limiting. This paper reviews breeding approaches to improve yield under drought. It focuses on critical factors that must be considered to identify likely plant attributes that can be targeted. These factors, their link with yield, the nature of the target environment, the level of organisation where the trait is expressed are discussed. Three quite different examples are given to emphasize the above considerations and which show substantial promise in targeting traits to improve yield under drought. They are drought at flowering, improving transpiration efficiency and improving early leaf area development.     

干旱胁迫条件下冷型小麦灌浆结实期的农田热量平衡

冷型小麦具有代谢功能较好、活力较旺盛、抗早衰能力较强的特征,因而,培育出越来越多的冷型小麦并将其推向生产对于小麦的高产、稳产十分重要。在干旱频繁出现的今天,小麦生产受到了极大的影响,因而研究干旱胁迫下冷型小麦的农田热量平衡,对明了冷型小麦农田小气候的形成机理、改善农田小气候环境具有重要意义。通过对相关气象要素和小麦生态指标的测定,研究了干旱胁迫条件下冷型小麦灌浆结实期的农田热量平衡,揭示了冷型小麦对干旱胁迫的适应机制。结果表明:①冷型小麦农田净辐射较暖型小麦偏低16.35-47.57W/m²,但经统计检验,两者差异未达显著水平。②活动层内0.2m-2/3株高和2/3株高-冠顶冷型小麦的潜热通量较暖型小麦分别偏高29.09-48.61W/m²和47.41-134.89W/m²,湍流热通量分别偏低12.48-62.57W/m²和29.37-85.81W/m²;活动层与大气之间的潜热通量,冷型小麦较暖型小麦偏高50.30-124.20W/m²,湍流热通量偏低30.50-102.40W/m²。③冷型小麦的土壤热通量比暖型小麦偏低24.60-65.19W/m²。④冷型小麦加热植株体的热量Q_A +Q_T较暖型小麦偏低43.70W/m²。在干旱胁迫条件下,冷型小麦田的能量分配创造出了冷湿的小气候环境,有利于小麦的生长发育和产量的提高。     

Challenges in breeding for yield increase for drought

Crop genetic improvement for environmental stress at the molecular and physiological level is very complex and challenging. Unlike the example of the current major commercial transgenic crops for which biotic stress tolerance is based on chemicals alien to plants, the complex, redundant and homeostatic molecular and physiological systems existing in plants must be altered for drought tolerance improvement. Sophisticated tools must be developed to monitor phenotype expression at the crop level to characterize variation among genotypes across a range of environments. Once stress-tolerant cultivars are developed, regional probability distributions describing yield response across years will be necessary. This information can then aid in identifying environmental conditions for positive and negative responses to genetic modification to guide farmer selection of stress-tolerant cultivars.     

Effect of soil mechanical impedance on root growth of two rice varieties under field drought stress

Two upland rice varieties, Azucena and Bala, were screened for root growth under droughted and irrigated treatments in two field sites at the West Africa Rice Development Association (WARDA) experimental farm, Côte d’Ivoire, during the dry season of 1999/2000. The sites were chosen to represent contrasting soil profile penetration resistance (PR) characteristics on upland sites, although both were relatively impeding. The number of nodal root axes per unit area passing through horizontal transects (root density) was counted at 35, 56, 77 and 98 days after sowing (DAS) at 10 cm depth intervals. Azucena consistently maintained a greater root density than Bala and a greater proportion of Azucena roots grew to 30 cm depth (22.7% vs. 8.4% at 77 DAS). There was little detectable effect of water regime on root distribution but evidence of lower root numbers at depths below 20 cm in the higher PR site was revealed. A site by variety by soil depth interaction suggests that Azucena roots are more strongly affected by very high PR than those of Bala. PR between 0–30 cm depth increased greatly with decreasing soil water content during the drought as the soil dried. This increase is likely to have prevented or greatly impaired further nodal root growth within this layer. At 40 cm depth, PR was high (3–4 MPa) but did not increase during the drought. At this depth root growth rate was likely to be greatly reduced despite the availability of water. These results demonstrate that varietal differences in root morphology characterised in the laboratory can be also detected in impeding field soils as differences in the density of roots at depth. Relatively poor root growth in these fields in the absence of drought was probably due to the high mechanical impedance and/or the physiological stress of the plants in the dry season. Our results indicate that high mechanical impedance was a more fundamental constraint on root growth than soil water availability during the drought. Thus, varietal differences in root penetration ability might be very important for drought avoidance in soils of this type.     

Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population

A recombinant inbred population developed from a cross between high-yielding lowland rice (Oryza sativa L.) subspecies indica cv. IR64 and upland tropical rice subspecies japonica cv. Cabacu was used to identify quantitative trait loci (QTLs) for grain yield (GY) and component traits under reproductive-stage drought stress. One hundred fifty-four lines were grown in field trials in Indonesia under aerobic conditions by giving surface irrigation to field capacity every 4 days. Water stress was imposed for a period of 15 days during pre-flowering by withholding irrigation at 65 days after seeding. Leaf rolling was scored at the end of the stress period and eight agronomic traits were evaluated after recovery. The population was also evaluated for root pulling force, and a total of 201 single nucleotide polymorphism markers were used to construct the molecular genetic linkage map and QTL mapping. A QTL for GY under drought stress was identified in a region close to the sd1 locus on chromosome 1. QTL meta-analysis across diverse populations showed that this QTL was conserved across genetic backgrounds and co-localized with QTLs for leaf rolling and osmotic adjustment (OA). A QTL for percent seed set and grains per panicle under drought stress was identified on chromosome 8 in the same region as a QTL for OA previously identified in three different populations.     

Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis

An F_4:5 population of 490 recombinant inbred lines (RILs) from the cross Apo/^2*Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY _3.1 ) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY _2.1 ) had a highly significant effect on grain yield in lowland drought stress (R ² = 13–16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY _3.1 on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.     

Breeding implications of drought stress under future climate for upland rice in Brazil

Rice is the most important food crop in the developing world. For rice production systems to address the challenges of increasing demand and climate change, potential and on‐farm yield increases must be increased. Breeding is one of the main strategies toward such aim. Here, we hypothesize that climatic and atmospheric changes for the upland rice growing period in central Brazil are likely to alter environment groupings and drought stress patterns by 2050, leading to changing breeding targets during the 21st century. As a result of changes in drought stress frequency and intensity, we found reductions in productivity in the range of 200–600 kg/ha (up to 20%) and reductions in yield stability throughout virtually the entire upland rice growing area (except for the southeast). In the face of these changes, our crop simulation analysis suggests that the current strategy of the breeding program, which aims at achieving wide adaptation, should be adjusted. Based on the results for current and future climates, a weighted selection strategy for the three environmental groups that characterize the region is suggested. For the highly favorable environment (HFE, 36%–41% growing area, depending on RCP), selection should be done under both stress‐free and terminal stress conditions; for the favorable environment (FE, 27%–40%), selection should aim at testing under reproductive and terminal stress, and for the least favorable environment (LFE, 23%–27%), selection should be conducted for response to reproductive stress only and for the joint occurrence of reproductive and terminal stress. Even though there are differences in timing, it is noteworthy that stress levels are similar across environments, with 40%–60% of crop water demand unsatisfied. Efficient crop improvement targeted toward adaptive traits for drought tolerance will enhance upland rice crop system resilience under climate change.     

Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities

Fine-mapping studies on four QTLs, qDTY(2.1), qDTY(2.2), qDTY(9.1) and qDTY(12.1), for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and bayesian interval mapping analyses resolved the originally identified qDTY(2.1) region of 42.3 cM into a segment of 1.6 cM, the qDTY(2.2) region of 31.0 cM into a segment of 6.7 cM, the qDTY(9.1) region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY(12.1) region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY(9.1) and qDTY(12.1)) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY(2.1) and RM24334 within qDTY(9.1) showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.     

Morphophysiology, morphoanatomy, and grain yield under field conditions for two maize hybrids with contrasting response to drought stress

In the northern region of the state of Minas Gerais, lack of rainfall limits crop production in the field, which is possible only with irrigation. Agricultural and physiological practices have been intensively searched to overcome drought effects and consequently increase production. In this context, the objective of this study was to characterize morphophysiological and morphoanatomical changes and evaluate the attributes of grain yield under field conditions in two hybrids contrasting for drought tolerance. The experiment was carried out for 2 years (2010 and 2011) and the water deficit was imposed by stopping irrigation for 22 days at the pre-flowering stage. At the end of the stress treatment, leaf and root anatomy and morphophysiological characteristics (leaf water potential, chlorophyll content, percentage of dry leaves, leaf area, stomatal conductance, chlorophyll fluorescence, and anthesis-silking interval) were evaluated. For a better interpretation of tolerance of the hybrids in the evaluated characteristics, an index was used stress index. Hybrid DKB 390 (tolerant) surpassed hybrid BRS 1030 (sensitive) in grain yield. Furthermore, it presented lower percentage of dry leaves, higher flowering synchronization, higher stomatal conductance, and higher Fv/Fm relationship. In the root, DKB 390 showed higher amount of aerenchyma in the cortex, an increase of exodermis width, and numerous metaxylem with smaller diameter. In the leaf, it presented higher number of stomata and smaller distance between the vascular bundles in the leaf blade. The study concluded that significant morphophysiological and morphoanatomical changes, which are related to drought tolerance, occurred in DKB 390, leading to a higher yield in the field.     

Hybrid breeding of rice via genomic selection

Hybrid breeding is the main strategy for improving productivity in many crops, especially in rice and maize. Genomic hybrid breeding is a technology that uses whole‐genome markers to predict future hybrids. Predicted superior hybrids are then field evaluated and released as new hybrid cultivars after their superior performances are confirmed. This will increase the opportunity of selecting true superior hybrids with minimum costs. Here, we used genomic best linear unbiased prediction to perform hybrid performance prediction using an existing rice population of 1495 hybrids. Replicated 10‐fold cross‐validations showed that the prediction abilities on ten agronomic traits ranged from 0.35 to 0.92. Using the 1495 rice hybrids as a training sample, we predicted six agronomic traits of 100 hybrids derived from half diallel crosses involving 21 parents that are different from the parents of the hybrids in the training sample. The prediction abilities were relatively high, varying from 0.54 (yield) to 0.92 (grain length). We concluded that the current population of 1495 hybrids can be used to predict hybrids from seemingly unrelated parents. Eventually, we used this training population to predict all potential hybrids of cytoplasm male sterile lines from 3000 rice varieties from the 3K Rice Genome Project. Using a breeding index combining 10 traits, we identified the top and bottom 200 predicted hybrids. SNP genotypes of the training population and parameters estimated from this training population are available for general uses and further validation in genomic hybrid prediction of all potential hybrids generated from all varieties of rice.     

The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions

Drought conditions limit agricultural production by preventing crops from reaching their genetically predetermined maximum yields. Here, we present the results of field evaluations of rice overexpressing OsNAC9, a member of the rice NAC domain family. Root‐specific (RCc3) and constitutive (GOS2) promoters were used to overexpress OsNAC9 and produced the transgenic RCc3:OsNAC9 and GOS2:OsNAC9 plants. Field evaluations over two cultivating seasons showed that grain yields of the RCc3:OsNAC9 and the GOS2:OsNAC9 plants were increased by 13%–18% and 13%–32% under normal conditions, respectively. Under drought conditions, RCc3:OsNAC9 plants showed an increased grain yield of 28%–72%, whilst the GOS2:OsNAC9 plants remained unchanged. Both transgenic lines exhibited altered root architecture involving an enlarged stele and aerenchyma. The aerenchyma of RCc3:OsNAC9 roots was enlarged to a greater extent than those of GOS2:OsNAC9 and non‐transgenic (NT) roots, suggesting the importance of this phenotype for enhanced drought resistance. Microarray experiments identified 40 up‐regulated genes by more than threefold (P < 0.01) in the roots of both transgenic lines. These included 9‐cis‐epoxycarotenoid dioxygenase, an ABA biosynthesis gene, calcium‐transporting ATPase, a component of the Ca²⁺ signalling pathway involved in cortical cell death and aerenchyma formation, cinnamoyl CoA reductase 1, a gene involved in lignin biosynthesis, and wall‐associated kinases¸ genes involved in cell elongation and morphogenesis. Interestingly, O‐methyltransferase, a gene necessary for barrier formation, was specifically up‐regulated only in the RCc3:OsNAC9 roots. Such up‐regulated genes that are commonly and specifically up‐regulated in OsNAC9 transgenic roots may account for the altered root architecture conferring increased drought resistance phenotype.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

In vitro selection and field responses of somaclonal variant plants of rice cv PR113 for drought tolerance

Drought is the major environmental stress that limits rice productivity worldwide. In vitro somaclonal variation using different selection agents has been used for crop improvement. Here, rice plants of cv PR113 were selected in vitro on 30, 50 and 70 g L^-1 polyethylene glycol 6,000 (PEG). Callus growth, proliferation, calli volume (first and second culture) and plantlet regeneration (third culture) were found to be decreased upto a certain level to acquire tolerance to PEG-induced drought. From the field data, 30 g L^-1 PEG lines showed higher vegetative growth (plant height, tiller number, leaf number, shoot weight and root growth) as compared with 50 g L^-1 PEG selected somaclone lines under limited irrigation. The yield parameters-panicle length, panicle weight, grains per panicle, 1,000-grain weight, grain yield per plant, harvest index and grain straw ratio were also higher in 30 g L^-1 PEG lines as compared with 50 g L^-1 PEG lines. The results, therefore indicate that 30 g L^-1 PEG selected somaclone lines were more suited than 50 g L^-1 PEG selected somaclone lines under stress as compared with WT. The finding suggests that rice cv PR113 somaclones generated on PEG are found to be drought tolerant under field condition with better yield.     

QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress

Cell-membrane stability (CMS) is considered to be one of the major selection indices of drought tolerance in cereals. In order to determine which genomic region is responsible for CMS, 104 rice (Oryza sativa L.) doubled haploid (DH) lines derived from a cross between CT9993–5-10–1-M and IR62266-42–6-2 were studied in the greenhouse in a slowly developed drought stress environment. Drought stress was induced on 50-day-old plants by withholding water. The intensity of stress was assessed daily by visual scoring of leaf wilting and by measuring leaf relative water content (RWC). The leaf samples were collected from both control (well-watered) and stressed plants (at 60–65% of RWC), and the standard test for CMS was carried out in the laboratory. There was no significant difference (P>0.05) in RWC between the two parental lines as well as among the 104 lines, indicating that all the plants were sampled at a uniform stress level. However, a significant difference (P<0.05) in CMS was observed between the two parental lines and among the population. No significant correlation was found between CMS and RWC, indicating that the variation in CMS was genotypic in nature. The continuous distribution of CMS and its broad-sense heritability (34%) indicates that CMS should be polygenic in nature. A linkage map of this population comprising of 145 RFLPs, 153 AFLPs and 17 microsatellite markers was used for QTL analysis. Composite interval mapping identified nine putative QTLs for CMS located on chromosomes 1, 3, 7, 8, 9, 11 and 12. The amount of phenotypic variation that was explained by individual QTLs ranged from 13.4% to 42.1%. Four significant (P<0.05) pairs of digenic interactions between the detected QTLs for CMS were observed. The identification of QTLs for this important trait will be useful in breeding for the improvement of drought tolerance in rice. This is the first report of mapping QTLs associated with CMS under a natural water stress condition in any crop plants. Received: 8 September 1999 / Accepted: 13 October 1999