Development of drought-resistant cultivars using physiomorphological traits in rice

Drought is a major problem for rice grown under rainfed lowland and upland conditions, but progress in breeding to improve drought resistance has been slow. This paper describes patterns of water-stress development in rice fields, reviews genetic variation in physio-morphological traits for drought resistance in rice, and suggests how knowledge of stress physiology can contribute to plant breeding programmes that aim to increase yield in water-limiting environments. To provide a basis for integrating physiological research with plant-breeding objectives we define drought resistance in terms of relative yield of genotypes. Therefore, a drought-resistant genotype will be one which has a higher grain yield than others when all genotypes are exposed to the same level of water stress.A major reason for the slow progress in breeding for drought resistance in rice is the complexity of the drought environment, which often results in the lack of clear identification of the target environment(s). There is a need to identify the relative importance of the three common drought types; early-season drought which often causes delay in transplanting, mild intermittent stress which can have a severe cumulative effect, and late stress which affects particularly late-maturing genotypes. In addition, in rainfed lowland rice, flooded and non-flooded soil conditions may alternate during the growing season, and affect nutrient availability or cause toxicity.Several drought-resistance mechanisms, and putative traits which contribute to them, have been identified for rice; important among these being drought escape via appropriate phenology, root characteristics, specific dehydration avoidance and tolerance mechanisms, and drought recovery. Some of these mechanisms/traits have been shown to confer drought resistance and others show potential to do so in rice. The most important is the appropriate phenology which matches crop growth and development with the water environment. A deep root system, with high root length density at depth is useful in extracting water thoroughly in upland conditions, but does not appear to offer much scope for improving drought resistance in rainfed lowland rice where the development of a hard pan may prevent deep root penetration. Under water-limiting environments, genotypes which maintain the highest leaf water potential generally grow best, but it is not known if genotypic variation in leaf water potential is solely caused by root factors. Osmotic adjustment is promising, because it can potentially counteract the effects of a rapid decline in leaf water potential and there is large genetic variation for this trait. There is genotypic variation in expression of green leaf retention which appears to be a useful character for prolonged droughts, but it is affected by plant size which complicates its use as a selection criterion for drought resistance.There is a general lack of drought related research for rice in rainfed lowland conditions. This needs to be rectified, particularly considering their importance relative to upland conditions in Asian countries. We suggest that focussing physiological-genetic research efforts onto clearly defined, major target environments should provide a basis for increasing the relevance of stress physiology and the efficiency of breeding programmes for development of drought-resistant genotypes.     

Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking quality. However, the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast disease. The genetic improvement of Varalu was done by introgressing a major yield QTL, qDTY_12.1, along with two major blast resistance genes i.e. Pi54 and Pi1 through marker-assisted backcross breeding. Both traits were transferred till BC₂ generation and intercrossing was followed to pyramid the two traits. Stringent foreground selection was carried out using linked markers as well as peak markers (RM28099, RM28130, RM511 and RM28163) for the targeted QTL (qDTY_12.1), RM206 for Pi54 and RM224 for Pi1. Extensive background selection was done using genome-wide SSR markers. Six best lines (MSM-36, MSM-49, MSM-53, MSM-57, MSM-60 and MSM-63) having qDTY_12.1 and two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%-96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were identified. These lines showed yield advantage under drought stress as well as irrigated conditions. MSM-36 showed better performance in the national coordinated trials conducted across India, which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice production. The present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.     

栽培稻抗旱性研究的现状与策略

 水资源短缺正成为制约我国农业发展的重要因素。培育抗旱的栽培稻品种并实现水稻旱作，不但可在很大程度上节约水资源，而且有利于增产稳产，节约能源和减少环境污染。抗旱性包括逃旱性、避旱性、耐旱性和复原抗旱性。形态生理学的研究揭示出大量的与栽培稻抗旱性有关的形态特征和生理特性，如根系和叶片性状、生育期、渗透调节、脱落酸含量与栽培稻抗旱性密切相关，且已利用分子标记对上述性状进行了基因定位（QTL）研究。旱稻品种改良也已取得重大进展。在进行抗旱品种改良的基础上，通过引进相应的栽培技术，节水种植，实现水稻旱作，并达到稳产与增产的目的，是抗旱性研究的战略目标。在增产、稳产和优质的前提下，以培育耐旱性极强的水稻（或旱稻）为中心，建立有代表性的抗旱性研究基地, 进一步加强稻属抗旱基因资源的发掘和创新、抗旱生理学和遗传学的研究、利用现代生物技术实现不同物种间抗旱基因的转移、建立节水种植栽培技术新体系是目前抗旱性研究的主要内容。     

Genetic analysis of rainfed lowland rice drought tolerance under naturally-occurring stress in eastern India: Heritability and QTL effects

Drought tolerance is an important rainfed rice breeding objective, but because the heritability (H) of yield under drought stress is thought to be low, secondary physiological traits are considered better targets for selection than yield under stress per se. This assumption has rarely been tested, and there are no reports on H for yield under drought stress from experiments repeated over seasons in rainfed lowland rice. To assess the potential for improving yield under drought stress via direct selection, and to identify associated quantitative trait loci (QTL), doubled haploid lines with a narrow range of flowering dates, derived from the population CT9993-5-10-1-M/IR62266-42-6-2, were screened under full irrigation and severe drought stress induced by draining the paddy before flowering in 2000–2002 at Raipur, India. Drought stress reduced mean yield by 80%. H was similar in stress and non-stress trials, as was the relative magnitude of the genotype and genotype × year variances. The genetic correlation between yield in stress and non-stress conditions was 0.8, indicating that about 64% of the genetic variation for yield under stress was accounted for by differences in yield potential also expressed in irrigated environments. These results indicate that direct selection for yield under drought stress can produce yield gains under stress without reducing yield potential. There was no secondary trait for which selection resulted in greater predicted response in yield under stress than direct selection for stress yield per se. A QTL was detected on chromosome 1 near sd1 that explained 32% of the genetic variation for yield under stress, but only 4% under non-stress. Its effect was consistent across years. This QTL accounted for much of the variation in drought yield not accounted for by variation in yield potential.     

Genetic Diversity Analysis of Rice Germplasm in Tripura State of Northeast India Using Drought and Blast Linked Markers

We genotyped 74 rice germplasms including Tripura's local landraces, improved varieties, cultivars and breeding lines and other rice varieties using molecular markers for genetic diversity, drought QTLs, and blast resistance genes. The number of alleles per locus ranged from 2 to 5 with an average of 2.9. The polymorphic information content value per locus ranged from 0.059 (RM537) to 0.755 (RM252) with an average of 0.475. Cluster analysis based on 30 simple sequence repeat markers revealed 5 clusters and also indicated the presence of variability within the rice accessions. The drought QTL qDTY2.1 was found in 56.0% of germplasms and qDTY1.1 was detected in only 6.8% of the germplasms. Out of seven rice blast resistance genes screened, only two rice varieties, RCPL-1-82 and Buh Vubuk (Lubuk), were positive for four blast resistance genes while only Releng possessed two blast resistance genes. Among 74 rice germplasms, only three accessions, Releng, RCPL1-82 and Buh Vubuk (Lubuk), possessed both drought-related QTLs and blast resistance genes. Overall, the 74 indigenous rice genotypes showed low level of genetic diversity, which is in contrast to high level of genetic diversity among rice varieties in northeast India, where highlights the good farming practice, conservation of germplasms and the limitation of molecular markers employed in this study. The presence of both drought related QTLs and blast resistance genes in some of the germplasms can be useful in future breeding programmes.     

Increasing Production of Rainfed Lowland Rice in Drought Prone Environments

Summary

Drought is a major production constraint of rainfed lowland rice grown in Thailand and Laos. Adverse soil conditions also reduce yield. In an attempt to increase rainfed lowland rice production in these countries, a major collaborative international project was conducted during a 6-year period in the region. The objectives of the project were to quantify production constraints, determine genotypic variation in yield, and identify an effective breeding strategy. A rice simulation model was developed also and used to investigate the potential impact of strategies for genetic improvement and agronomic management.

Four major physical or biological constraints to higher production levels of rainfed lowland rice were identified, (1) the lack of standing water at the appropriate time of transplanting, (2) severe water stress that often develops at the end of the growing season, (3) low yield potential of the present cultivars, particularly in Thailand, and (4) adverse soil conditions including low pH and low soil fertility. The results of the field experiments and simulation modelling exercises showed that the influence of these constraints can be reduced and yield increased by several methods : in particular, choice of appropriate cultivars and time of sowing to match crop phenology with water availability, application of appropriate fertilizer, adoption of high yielding cultivars, adoption of direct seeding in place of the traditional transplanting system, and reduction of percolation water loss from the paddies.

A technology package currendy being investigated for the rainfed lowland rice is direct seeding early in the season, using cultivars that flower by the end of the rainy season, with application of organic or chemical fertilizer. The appropriate cultivars are early flowering and short-intermediate statured, possess high yield potential and ability to maintain favourable plant water status at flowering, and have the ability to establish well and compete against weed under direct seeding.     

Enhancing Salt Tolerance in Crops Through Molecular Breeding: A New Strategy

SUMMARY

Salinity limits crop production in many rainfed ecosystems and is an increasing problem in irrigated areas. Developing and developed countries alike need more efficient methods of enhancing salt tolerance in crops. The traditional breeding approach consists of (i) screening germplasm collections for donors of salt tolerance, (ii) crossing a donor with an elite line and advancing the F₁ hybrid to about the F₇ or F₈ generation while selecting for elite traits, and concurrently (iii) selecting for salt tolerance starting at about the F₄ generation. The low efficiency of this pedigree approach is due principally to the difficulty of recovering elite genotypes with salt tolerance traits, the genetic complexity of salt tolerance, and the strength of genotype × environment interactions (GEI). Advances in genomics are making possible an alternative approach in which a pre-breeding phase is used to pyramid several known genes and finely mapped major QTLs for complementary aspects of salt tolerance. The known genes can include transgenes modified by deliberate mutation or promoter switching. DNA-based selection protocols that are used to pyramid these genes are again employed during the breeding phase to transfer the entire set of genes for salt tolerance into any elite line by backcrossing. Breeding efficiency is increased because (i) elite traits are more easily recovered by backcrossing than by the pedigree approach, (ii) the genetic complexity of salt tolerance is reduced to a small set of well-defined genes and loci of large effect, (iii) the confounding effects of GEI are eliminated from the breeding phase, and (iv) the investment in gene discovery and QTL mapping can be recouped by transferring the same set of genes to a range of recipient lines that require salt tolerance. Efficiency will increase over time as more genes are added to the gene set and as QTL are replaced by the corresponding gene. Here we summarize the scientific advances underlying this new strategy, which should be applicable to other complex traits such as drought tolerance, durable resistance to pests and diseases, yield potential and product quality.     

Drought Tolerance in Rice: Focus on Recent Mechanisms and Approaches

Drought stress is a serious limiting factor to rice production,which results in huge economic losses.It is becoming a more serious issue with respect to the global climate change.Keeping in view of the current and forecasted global food demand,it has become essential to enhance the crop productivity on the drought-prone rainfed lands with priority.In order to achieve the production target from rainfed areas,there is a requirement of rice varieties with drought tolerance,and genetic improvement for drought tolerant should be a high priority theme of research in the future.Breeding for drought tolerant rice varieties is a thought-provoking task because of the complex nature and multigenic control of drought tolerant traits would be a major bottleneck for the current research.A great progress has been made during last two decades in our understanding of the mechanisms involved in adaptation and tolerance to drought stress in rice.In this review,we highlighted the recent progresses in physiological,biochemical and molecular adaptation of rice to drought tolerance.A brief discussion on the molecular genetics and breeding approaches for drought tolerance in rice will be focused for the future crop improvement program for development of drought tolerant rice varieties.     

Molecular Breeding for Rainfed Lowland Rice in the Mekong Region

Abstract

In the past 20 years, the rice-breeding program in Thailand had little success in developing new cultivars to replace Kao Dawk Mali 105 (KDML105) and Kao Khor 6 (RD6) for the rainfed lowland rice environments. The main reason for the poor adoption of new cultivars by farmers is the susceptibility to diseases and unacceptable grain qualities. The conventional breeding program also takes at least 15 years from initial crossing to the release of new cultivars. A new breeding strategy can be established to shorten the period for cultivar improvement by using marker-assisted selection (MAS), rapid generations advance (RGA), and early generation testing in multi-locations for grain yield and qualities. Four generation of MAS backcross breeding were conducted to transfer genes and QTL for bacterial blight resistance (BLB), submergence tolerance (SUB), brown plant hopper resistance (BPH) and blast resistance (BL) into KDML105. Selected backcross lines, introgressed with target gene/QTL, were tolerant to SUB and resistant to BLB, BPH and BL. The agronomic performance and grain quality of these lines were as good as or better than KDML105.     

Evaluation of Agronomic Traits in Chromosome Segment Substitution Lines of KDML105 Containing Drought Tolerance QTL under Drought Stress

Drought is a major abiotic constraint to rice production in rainfed lowland and insufficiently irrigated areas.The improvement of drought tolerant varieties is one of the strategies to reduce the negative effects of drought.Quantitative trait loci(QTLs) for primary and secondary traits related to drought tolerance(DT) on chromosomes 1,3,4,8 and 9 that determined from double haploid lines derived from a cross between CT9993 and IR62266 were introgressed and dissected into small pieces in the genetic background of Khao Dawk Mali 105(KDML105) to develop chromosome segment substitution line(CSSL) population.The CSSLs were evaluated at the reproductive stage for their agronomic performance and yield components under drought stress,and results were compared with irrigated condition.The flowering of CSSL lines was 6 to 7 d earlier than KDML105.The mean values of grain yields in the CSSLs were higher than KDML105 under drought and irrigated conditions.At irrigated condition,the grain yields of introgression lines carrying DT-QTLs from chromosomes 4 and 8 were higher than that of KDML105,whereas other traits showed little difference with KDML105.Analysis indicated that grain yield has positive correlation with plant height,tiller and panicle number per plant,and total grain weight per plant under drought stress while negatively correlated with days to flowering.As mentioned above,CSSLs showing good adaptation under drought stress can be used as genetic materials to improve drought tolerance in Thai rainfed lowland rice breeding program,and as materials to dissect genes underlying drought tolerance.     

Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.     

Growth and Yield of New Rice for Africa (NERICAs) under Different Ecosystems and Nitrogen Levels

Abstract

Scarcity of water and N fertilizer are major constraints to rice production, particularly in developing countries where rainfed upland condition dominates. Improvement of genetic adaptability to inadequate water and N fertilizer is one option to maintain productivity in these regions. NERICAs are expected to yield higher under low input conditions, but growth and yield responses of the cultivars to different ecosystems and N levels remain unknown. The objectives of this study were to characterize the growth and yield performance of NERICAs, in comparison with selected Japanese rice cultivars. The two NERICAs (NERICA 1 and NERICA 5), two Japanese upland cultivars (Toyohatamochi and Yumenohatamochi), and a Japanese lowland cultivar Hitomebore were grown under two ecosystems (irrigated lowland (IL) and rainfed upland (RU)) with two N levels (high (H) and low (L)) for two years. The cultivar difference in the aboveground dry weight and grain yield was the largest in the in RU × L plot, where the values of NERICAs were similar to those in the other plots, but the values of other cultivars were substantially reduced. Regardless of cultivar, N contents of the plants at maturity correlated significantly with the aboveground dry weight at maturity, spikelet number and grain yield per area. These results indicate that NERICAs, compared with the selected Japanese upland cultivars that were bred for drought tolerance, have a higher ability to absorb N under upland conditions, which may contribute to higher biomass production and sink formation, resulting in increased gain yield.     

Application of Molecular Markers in Breeding for Nitrogen Use Efficiency

Summary

Nitrogen use efficiency (NUE) is defined as dry matter yield produced per unit of N supplied and available in the soil. NUE is approximately 33% for cereal production worldwide. Increased cereal NUE must accompany increased yield needed to feed the growing world population. Consequently, continued efforts are needed to include plant selection under low N input which is not often considered a priority by plant breeders. Molecular markers have accelerated plant breeding in a number of areas including biotic (disease and insect) resistance and abiotic (drought, low nitrogen fertilization and frost) tolerance. Marker-based technology has already provided scientists with a powerful approach for identifying and mapping quantitative trait loci (QTL) and would lead to the development of a better understanding of genetic phenomena. Two main NUE studies have been discussed. The first study identified QTL for NUE in maize involved the grain yield and secondary morphological traits of interest, such as plant height, ear leaf area, ears per plant and kernels per ear. This was compared with second study of QTL for yield and its components with genes encoding cytolistic gult-amine synthestase and leaf N0₃ ^- content. These secondary traits were correlated with yield and demonstrated segregation with high heritability under low nitrogen conditions. Marker assisted selection (MAS) should be able to offer significant advantages in cases where phenotypic screening is particularly expensive or difficult, including breeding projects involving multiple genes, recessive genes, late expression of the trait of interest, seasonal considerations, or geographical considerations. In addition to reducing costs of conventional breeding, MAS also has the potential to generate time savings. Possibly, the greatest contribution of QTL mapping to plant breeding will be the basic understanding of the genetic architecture of quantitative traits, thereby relating specific genetic loci with the biological mechanisms associated with desirable phenotypes.     

Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields

Root growth at soil depths below 30 cm may provide access to critical soil water reserves during drought in rainfed lowland rice. In this study, the OryzaSNP panel, a set of 20 lines representing genetic diversity in rice used for the discovery of DNA sequence polymorphisms, was evaluated for root characteristics in the field over three seasons varying in drought severity. Root length density (RLD) at a depth of 30–45 cm varied up to 74–92% among genotypes under drought stress (2008–2009 dry seasons), ranging from 0.024 to 0.23 cm cm⁻³ in 2008 and from 0.19 to 0.81 cm cm⁻³ in 2009. Real-time monitoring of soil moisture profiles revealed significant differences among genotypes, and these differences were correlated with RLD at those soil depths. Among the lines evaluated, the Aus isozyme group, particularly the genotype Dular, showed greater drought resistance associated with deep root growth and the highest drought response index (less reduction in yield by drought stress). Since the set of genotypes used in this study has been completely sequenced for SNP markers, the phenotypic information on root growth and drought avoidance responses presented here could be used in initial analysis of the genetic basis of dehydration avoidance traits and in facilitating improvement in drought resistance in rice.     

Yield response of rice (Oryza sativa L.) genotypes to drought under rainfed lowlands: 2. Selection of drought resistant genotypes

Drought frequently reduces grain yield of rainfed lowland rice. A series of experiments were conducted in drought-prone northeast Thailand to study the magnitude and consistency of yield responses of diverse, rainfed lowland rice genotypes to drought stress environments and to examine ways to identify genotypes that confer drought resistance. One hundred and twenty-eight genotypes were grown under non-stress and four different types of drought stress conditions. The relationship of genotypic variation in yield under drought conditions to genetic yield potential, flowering time and flowering delay, and to a drought response index (DRI) that removed the effect of potential yield and flowering time on yield under stress was examined.Drought stress that developed prior to flowering generally delayed the time of flowering of genotypes, and the delay in flowering was negatively associated with grain yield, fertile panicle percentage and filled grain percentage. Genotypes with a longer delay in flowering time had extracted more water during the early drought period, and as a consequence, had higher water deficits. They were consistently associated with a larger yield reduction under drought and in one experiment with a smaller DRI. Genotypes, however, responded differently to the different drought stress conditions and there was no consistency in the DRI estimates for the different genotypes across the drought stress experiments. The results indicate that with the use of irrigated-control and drought test environments, genotypes with drought resistance can be identified by using DRI or delay in flowering. However, selections will differ depending on the type of drought condition. The inconsistency of the estimates in DRI and flowering delay across different drought conditions reflects the nature of the large genotype-by-environment interactions observed for grain yield under various types of drought in rainfed lowland conditions.     

Root plasticity under fluctuating soil moisture stress exhibited by backcross inbred line of a rice variety,Nipponbare carrying introgressed segments from KDML105 and detection of the associated QTLs

In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation (SMF) which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines (BILs) and to identify QTL(s) associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F₂ plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.     

Four Decades of Breeding for Varietal Improvement of Irrigated Lowland Rice in the International Rice Research Institute

Abstract

Since the establishment of the International Rice Research Institute (IRRI) in 1960, IRRI’s breeding effort in varietal improvement for irrigated lowland has passed four decades. Breeding of semi-dwarf rice varieties such as IR8 at IRRI during first decade from 1960 to 1969 resulted in quantum leaps in yield potential, which marked the green revolution in Asia. During the second decade from 1970 to 1979, the primary emphasis of rice improvement has been directed towards incorporation of multiple disease and insect resistance and shortening of growth duration. Grain quality was the main target of crop improvement at IRRI during the third decade from 1980 to 1989. The fourth decade from 1990 to 1999 and beyond was focused again on the improvement of yield potential by developing hybrid rice and new plant type. Up to 1999, 46 indica inbred varieties and 2 indica/indica hybrid rice varieties were developed by IRRI and released in the Philippines for the irrigated lowland rice systems. Large-scale adoption of these improved varieties under modern crop management practices has resulted in a dramatic increase in rice production in major rice-growing countries. The hybrid varieties between indicas increased yield potential by 9% under the tropical conditions. New plant type (NPT) breeding has not yet resulted in an increase in yield potential. The second generation NPT developed by crossing tropical japonica with indica has demonstrated some promising results in terms of improvements in yield potential, disease and insect resistance, and grain quality.     

Genetic Improvement of Rice for Bacterial Blight Resistance: Present Status and Future Prospects

The production and productivity of rice has been challenged due to biotic and abiotic factors. Bacterial blight (BB) disease, caused by Xanthomonas oryzae pv. oryzae, is one of the important biotic stress factors, which reduces rice production by 20%–50%. The deployment of host plant resistance is the most preferred strategy for management of BB disease, and breeding disease resistant varieties remains a very economical and effective option. However, it is difficult to develop rice varieties with durable broad-spectrum resistance against BB using conventional approaches alone. Modern biotechnological tools, particularly the deployment of molecular markers, have facilitated the cloning, characterization and introgression of BB resistance genes into elite varieties. At least 46 BB resistance genes have been identified and mapped from diverse sources till date. Among these, 11 genes have been cloned and characterized. Marker-assisted breeding remains the most efficient approach to improve BB resistance by introducing two or more resistance genes into target varieties. Among the identified genes, xa5, xa13 and Xa21 are being widely used in marker-assisted breeding and more than 70 rice varieties or hybrid rice parental lines have been improved for their BB resistance alone or in combination with genes/QTLs conferring tolerance to other stress. We review the developments related to identification and utilization of various resistance genes to develop BB resistant rice varieties through marker-assisted breeding.     

Identification of Bangladeshi rice varieties resistant to ufra disease caused by the nematode Ditylenchus angustus

The rice stem nematode Ditylenchus angustus causes “Ufra” disease in rice resulting in substantial yield losses. Although it is predominant in deep water rice in South and Southeast Asia, this nematode also infects irrigated and rainfed low land rice. This study evaluated rice genotypes (irrigated, rainfed, deep water and landraces) for resistance to the Bangladeshi population of D. angustus. The experiment was executed using artificial inoculation, in both rainfed and irrigated ecosystems. The rice varieties were first scored at 28 days post inoculation (dpi), and ranked based on the postinfectional reactions and severity of symptoms on a 0–16 rating scale. The susceptibility of the varieties was also evaluated at a later time point, i.e. 55 dpi, based on the percentage of tiller infections, using a disease index scoring system ranging from 0 to 9. Both screening methods showed a similar ranking of the varieties for susceptibility/resistance against this nematode. The experiment was initially conducted in plastic pots, and the promising varieties were analyzed further in field conditions. Out of the 85 varieties, one landrace named ‘Manikpukha’ proved to be highly resistant, while 6 other varieties showed resistance and 13 varieties showed moderately resistant responses under both pot and field conditions. The promising varieties found in the present investigation can be used in rice breeding programs as well as for further detailed studies to develop a sustainable ufra management strategy.     

Hidden diversity for abiotic and biotic stress tolerances in the primary gene pool of rice revealed by a large backcross breeding program

Low and unstable rice productivity in many areas of Asia is associated with many abiotic and biotic stresses such as drought, salinity, anaerobic conditions during germination, submergence, phosphorus and zinc deficiency, etc. To develop rice varieties with tolerance to these stresses, we undertook a large backcross (BC) breeding effort for the last 6 years, using three recurrent elite rice lines and 203 diverse donors, which represent a significant portion of the genetic diversity in the primary gene pool of rice. Significant progress has been made in the BC breeding program, which resulted in development of large numbers of introgression lines with improved tolerance to these stresses. Promising lines have been developed with excellent tolerances (extreme phenotypes) to salinity, submergence and zinc deficiency; resistance to brown plant hopper, ability to germinate under the anaerobic condition and low temperature. Our results indicated that there exist tremendous amounts of ‘hidden’ diversity for abiotic and biotic stress tolerances in the primary gene pool of rice. Furthermore, we demonstrated that despite the complex genetics and diverse physiological mechanisms underlying the abiotic stress tolerances, introgression of genes from a diverse source of donors into elite genetic backgrounds through BC breeding and efficient selection (careful screening under severe stress) is a powerful way to exploit this hidden diversity for improving abiotic stress tolerances of rice. We have developed three large sets of introgression lines, which not only provide an unique platform of breeding materials for developing new rice cultivars with superior yield and stability by trait/gene pyramiding, but also represent unique genetic stocks for a large-scale discovery of genes/alleles underlying the abiotic and biotic stress tolerances of rice using genomic tools.