Limiting Rice Production Research Articles

English

Salinity stress, drought and the lack of water supply are major constraints limiting rice productivity in rainfed lowland of the Sine Saloum region. To alleviate these constraints, several actions have been undertaken including construction of anti-salt dykes and using of salt tolerant varieties. The objectives of this study were: (a) analyze the hydraulic operation of these lowlands and salinity rate during wet season. (b) To test, the response of new salt-tolerant varieties, with different fertilizers and to identify the best suitable. Trials were conducted in two sites. The level of groundwater and salinity were measured during two wet seasons in two sites. At least 100 mm of rainfall are required to decrease salinity (EC) below 3 dS / m on a leveled land, before sowing. Before sowing, the management of water flow at the anti-salt dam must take into account not only the leaching of salt, but also the groundwater recharge. It is this groundwater that will allow rice to reach maturity, at the end of rains by mitigating late season drought. In both sites, D14 and IR70870-B-P-2-2 were the most biomass productive varieties. Among the eleven rice varieties tested, five have performed well with the average grain yields of 4 t.ha-1.   Key words: Rainfall, groundwater, sea water, new salt-tolerant varieties, lowland.

Yield Traits and Water Productivity Responses among Rice Varieties (Oryza sativa L.) Grown in A Fadama Ecosystem in Akure, Southwestern Nigeria

Drought is the most important factor limiting rice productivity under rainfed system of the humid tropics. Field experiments were conducted to determine the effects of soil water management strategies (growth on residual soil moisture at the vegetative stage supplemented with irrigation at the reproductive stage and growth under full irrigation throughout) on water use, yield and yield components of four varieties of rice grown in the dry season in an inland valley swamp (fadama). The four selected varieties were two upland (Ekpoma local and upland Nerica 4) and two lowland (lowland Nerica 1 and 2). The first planting (December, 2010) adequacy of soil moisture from planting to date of first flowering was assumed, thereafter irrigation was imposed during reproductive growth. In the second sowing (Janaury, 2011), rice plants were drip-irrigated from Original Research Article Agele et al.; AJEA, 5(5): 435-449, 2015; Article no.AJEA.2015.043 436 planting to seed harvest. The results indicated that differences between the December and January sowing dates were found significant for most of the traits measured (root and shoot weight, leaf area, plant height, number of tillers, weights of panicle and 100-seed and harvest index). Total seed yield and harvest indices (3.19 t ha:10.1) were higher in January over December (1.24 t.ha: 6.3) sowing in addition to higher water use efficiencies (0.053 and 0.031 t.ha -1 .mm -1 ). The seed yield reduction was associated with reductions in plant height (103.4:76.8 cm), leaf area (51.9: 76.1 m 2 ) and shoot weight (103.7: 76.8 g) across all tested lines. Seasonal soil moisture storage ranged from 186 to 223 mm for the respective first (December) and second (January) sowing dates. The two best lines (Upland cultivars: Ekpoma and Nerica 4), had similar yield performance when grown under irrigation from planting to maturity (harvest) but differed significantly in their trait combinations. Over other varieties, upland Ekpoma and Nerica 4 exhibited superior ability to produce tillers, panicle and seed weights in both first and second sowing dates. Functional relationships between some weather variables and growth and yield characteristics of rice which gave high regression coefficients (R 2 ) showed that, the differences in shoot biomass and seed yield production between the sowing dates were explained by a combination of weather parameters. The evaluated varietal yield potential and related traits measured under variable soil moisture regimes were discussed in relation to genotypic adaptation (drought tolerance) among the tested rice varieties. It is concluded that, in a cultivar, higher yield potential may be related to ability to tolerate multiple and concurrent abiotic stresses of soil and air moisture deficit and temperature stresses.

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia.

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.

Genetic analysis of salt tolerance at seedling and reproductive stages in rice (Oryza sativa)

AbstractSalinity is a major abiotic stress that limits rice production across rice areas as high‐yielding modern rice varieties are generally sensitive to salt stress. The study was conducted to deduce heritability and combining ability estimates of rice for various morphological and physiological traits using a 7 × 7 full‐diallel‐cross analysis at seedling and reproductive stages. The salinity stress treatment was 12 dS m−1 at the seedling stage and 8 dS m−1 at the reproductive stage. Diallel analysis revealed high for salinity tolerance scores and shoot height, moderate for shoot dry weight and root dry weight and low for Na+ and K+ concentrations and K+/Na+ ratio. The low‐to‐moderate narrow‐sense heritability for number of panicles, number of fertile spikelets, grain weight, spikelet fertility and K+/Na+ ratio suggests a large breeding population and delayed selection for tolerance until later generations. Significant maternal effects indicate that selection of the female parent is very important for desired trait development. The results of this study confirmed that salinity tolerance at the seedling and reproductive stages is regulated by a different set of genes that could be pyramided using different donors to enhance the level of tolerance.

A simple assessment on spatial variability of rice yield and selected soil chemical properties of paddy fields in South China

Data related to the spatial variability of properties of paddy soil is critical for improving rice productivity and designing sustainable farming techniques. However, a systematic assessment focusing on the spatial variability of low-yield paddy soil has not been conducted in South China. In this context, 560 soil samples were collected across South China and analyzed for nine common chemical properties. Rice yield data was obtained by surveying farmers during soil sampling. Soil parameters and rice yield varied considerably throughout the study area and their coefficients of variation ranged from 17.3% to 74.2%. Experimental semivariograms were developed and a moderate spatial dependence was observed for all selected parameters. Distribution maps, derived by kriging interpolation, illustrated that these paddy fields were characterized by high concentrations of soil organic matter (SOM), total N (TN), available N (AN) and available Zn (AZn); pH values decreased widely comparing with the data reported by the National Soil Survey, especially in southeast China; the areas with low soil P concentrations (<10mgkg−1) were mainly located in southwest China; cation exchange capacity (CEC), available K (AK) and available Si (ASi) had similar trends in spatial distributions with high concentrations in southeast China and low concentrations in southwest. Notably, paddy fields in southeast China were typically deficient in AK due to their concentrations, all of which are almost less than 100mgkg−1. Correlation analysis revealed that rice yield was significantly positively correlated with pH, CEC, AK and ASi, while negatively correlated with AN and AZn. Low pH, AK, CEC and ASi levels may be the most important constraints limiting rice productivity and fertilizers with N and Zn may be over-used and must be applied appropriately. The soil quality index (SQI) was also calculated using the analyzed chemical properties and a significant correlation was observed between SQI and rice yield, supporting earlier findings that good soil chemical health is essential for optimum sustained crop production. The remarkable variations of SQI and rice yield indicated that the potential for increasing rice productivity is a real prospect. Therefore, regional planning fertilization should pay more attention to the spatial variability of soil chemical properties to avoid economic losses and environmental pollution, and especially to the limited nutrients.

Transcriptome profiling confirmed correlations between symptoms and transcriptional changes in RDV infected rice and revealed nucleolus as a possible target of RDV manipulation.

BackgroundRice dwarf virus (RDV) is the causal agent of rice dwarf disease, which limits rice production in many areas of south East Asia. Transcriptional changes of rice in response to RDV infection have been characterized by Shimizu et al. and Satoh et al.. Both studies found induction of defense related genes and correlations between transcriptional changes and symptom development in RDV-infected rice. However, the same rice cultivar, namely Nipponbare belonging to the Japonic subspecies of rice was used in both studies.MethodsGene expression changes of the indica subspecies of rice, namely Oryza sativa L. ssp. indica cv Yixiang2292 that show moderate resistance to RDV, in response to RDV infection were characterized using an Affymetrix Rice Genome Array. Differentially expressed genes (DEGs) were classified according to their Gene Ontology (GO) annotation. The effects of transient expression of Pns11 in Nicotiana benthaminana on the expression of nucleolar genes were studied using real-time PCR (RT-PCR).Results856 genes involved in defense or other physiological processes were identified to be DEGs, most of which showed up-regulation. Ribosome- and nucleolus related genes were significantly enriched in the DEGs. Representative genes related to nucleolar function exhibited altered expression in N. benthaminana plants transiently expressing Pns11 of RDV.ConclusionsInduction of defense related genes is common for rice infected with RDV. There is a co-relation between symptom severity and transcriptional alteration in RDV infected rice. Besides ribosome, RDV may also target nucleolus to manipulate the translation machinery of rice. Given the tight links between nucleolus and ribosome, it is intriguing to speculate that RDV may enhance expression of ribosomal genes by targeting nucleolus through Pns11.

Comparative Analysis of Two Emerging Rice Seed Bacterial Pathogens

Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that, although both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and U.S. strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. Whereas previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane-sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality, although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.

Distinction and characterisation of salinity tolerant and sensitive rice cultivars as probed by the chlorophyll fluorescence characteristics and growth parameters.

Soil salinity is a major abiotic stress that limits rice productivity worldwide. The problem is intense - particularly in areas with extremely dry and hot climatic conditions. Designing an effective phenotyping strategy requires thorough understanding of plant survival under stress. The investigation was conducted using 12 rice cultivars differing in salinity tolerance. Among these cultivars, seedling survival on day 10 of salt treatment (12dSm-1) was above 85% during wet season and 75% during dry season in FL478, AC39416, Pokkali and Kamini. Highly salt-tolerant cultivars maintained greater proportion of green leaf and chlorophyll content under salt stress. Unlike sensitive cultivars, tolerant cultivars taken up less Na+ and more K+, resulting in lower Na+:K+ ratio in leaf and sheath. Normalised chlorophyll a fluorescence data revealed that the Fv/Fm and PIABS values decreased on days 3 and 7, respectively, of salt stress in susceptible rice cultivar. Salinity factor index (SFI) calculated by giving different weights to relative PIABS values after variable days of salinity stress clearly distinguished the level of tolerance among rice cultivars. The SFI can be used for grouping of moderately to highly salt-tolerant cultivars based on their tolerance level. We conclude that maintenance of greater proportion of green leaf, and restricted transport of Na+ to sheath and leaf helps the plant to counteract adverse effects of salinity on rice growth.

Characterization of a Nagina22 rice mutant for heat tolerance and mapping of yield traits

BackgroundHeat is one of the major factors that considerably limit rice production. Nagina 22 (N22) is a deep-rooted, drought and heat tolerant aus rice cultivar. This study reports the characterization of a previously isolated dark green leaf mutant N22-H-dgl219 (NH219) which showed reduced accumulation of reactive oxygen species in leaf under 40°C heat conditions.The mutant was characterized for several traits in field under ambient (38°C) and heat stress (44°C) conditions by raising temperature artificially from flowering stage till maturity by covering plants with polythene sheets during dry season 2011. Yield traits were mapped in 70 F2 segregants of IR64 × NH219 and 36 F2 segregants of its reciprocal cross.ResultsLeaf proteome analysis using two-dimensional gel electrophoresis from N22 and NH219 showed distinct constitutive expression of ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) in NH219 under ambient growth condition. Heat stress resulted in reduction of all 11 traits except plant height in both N22 and NH219. The extent of reduction was more in N22 than in NH219. Both pollen viability and spikelet fertility were not reduced significantly in N22 and NH219 but reduced by 20% in IR64.ConclusionNH219 is more tolerant to heat stress than wild type N22 as its percent yield reduction is lesser than N22. Single marker analysis showed significant association of RM1089 with number of tillers and yield per plant, RM423 with leaf senescence, RM584 with leaf width and RM229 with yield per plant.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-36) contains supplementary material, which is available to authorized users.

High Night Temperature and Abscisic Acid Affect Rice Productivity through Altered Photosynthesis, Respiration and Spikelet Fertility

ABSTRACTHigh night temperature (HNT) is among the important abiotic stresses limiting rice production. The impacts of abscisic acid (ABA) on higher plants have been the subject of many studies. However, little or no work has been performed on rice responses to ABA under HNT‐stress conditions. This study determined the effects of ABA on rice leaf photosynthetic rate (PN), photochemistry, respiration, and physiology under HNT. Plants were grown under ambient night temperature (ANT; 25°C) or HNT (30°C) with or without ABA (100 ppm) application from the boot stage of rice plants until harvest. The HNT decreased rice yield (11%), which was associated with decreasing PN (5%), pollen viability (11%), and spikelet fertility (5%) and increasing respiration rate (44%). In addition, HNT decreased grain width (4%) and increased grain chalkiness (65%), thereby decreasing grain quality. The ABA‐treated plants showed increased yield (15%) as a result of increased PN (6%) and spikelet fertility (6%) and decreased respiration (33%), under HNT. The increased PN under HNT as a result of ABA application is associated with increased stomatal conductance (22%) and decreased nonphotochemical quenching (NPQ; 29%). In addition, ABA‐treated plants grown under ANT also showed increased yield (9%) as a result of increased PN (7%) and spikelet fertility (7%) and decreased respiration (16%). The increased PN under ANT as a result of ABA application was due to increased quantum yield (8%) and electron transport rate (8%). This study shows that exogenous application of ABA has the potential to increase rice yields under HNT.

Temporal profiling of primary metabolites under chilling stress and its association with seedling chilling tolerance of rice (Oryza sativa L.)

BackgroundChilling stress is a major factor limiting rice production. Rice genotypes differ greatly in their seedling chilling tolerance (CT), which is known to involve differential expression of large numbers of genes and proteins. To further understand the metabolomic responses of rice to chilling stress, profiles of the 106 primary metabolites of a CT japonica variety, Lijiangxintuanhegu (LTH) and a chilling sensitive indica line, IR29, were investigated under a time-series of chilling stress and non-stress control conditions at the seedling stage.ResultsWe identified 106 primary metabolites that were temporally and genotype-dependently regulated in LTH and IR29 under the time-series chilling stress and subsequent recovery. Three major groups of primary metabolites, amino acids (AAs), organic acids (OAs) and sugars, showed distinct change patterns in both genotypes in response to the chilling stress: a more general accumulation of most AAs, more dramatic decreased levels of most OAs, and greatly reduced levels for most sugars at early time points of stress but increased levels of specific sugars at the later time points of stress. Compared to IR29, LTH had more metabolites showing chilling induced changes, greater levels of these metabolomic changes and a greater ability to recover after stress, implying that LTH used a positive energy-saving strategy against chilling stress. During subsequent recovery, more metabolites were significantly and exclusively up-regulated in LTH, indicating their positive role in chilling tolerance. A comparative analysis of these metabolites data and differentially expressed genes data allowed identification of 7 AAs and related genes that were both chilling responsive and contributed greatly to the CT of LTH.ConclusionsThe metabolomic responses of rice to chilling stress at the seedling stage were dynamic and involved large numbers of the metabolites. The chilling induced changes of three major groups of metabolites, AAs, OAs and sugars, in rice were well coordinated. The high level seedling CT of LTH was apparently attributed to its increased levels of most AAs and reduced energy consumption that resulted in increased glycolysis and strong resilience on recovery. The results of this study extend our understanding of molecular mechanisms of chilling stress tolerance in rice.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-23) contains supplementary material, which is available to authorized users.

Identification of Indian rice germplasm lines with bacterial leaf blight (BLB) resistance genes

Bacterial leaf blight of rice, caused by Xanthomonas oryzae pv. oryzae is one of the major constraints limiting rice production and productivity in South East Asia, particularly in Japan, Philippines, Indonesia, China and India. No effective chemical control for the disease is available. It is therefore, important to identify lines resistant to blight, which can then be used as parental lines in breeding programmes. Gene-linked and gene-based molecular markers and well defined donors are available for most of these genes. In the present study, a total of 386 Indian rice germplasm lines including commercially cultivated Indian rice varieties were screened for the presence of four bacterial blight resistance genes i.e. Xa4, xa5, xa13 and Xa21. The rationale behind the study was to identify new hitherto unreported, rice lines carrying BLB resistance genes and studying the allelic distribution of these genes in the germplasm.

Proteomic analysis of rice anthers under salt stress

Salinity is a major factor that limits rice production worldwide. Rice is considered generally to be sensitive to salt stress during the reproductive stage. To determine the molecular mechanisms of salt tolerance at the reproductive stage, anther proteomic patterns for two contrasting rice genotypes IR64 (salt sensitive) and Cheriviruppu (salt tolerant) under salt stress were compared. Plants were grown in a greenhouse and salt stress (100mM NaCl) was imposed at the booting stage. Anther samples were collected from control and salt-treated plants at the anthesis stage. The Na(+)/K(+) ratio in IR64 anthers under salt stress was >1.7 times greater than that under control conditions, whereas no significant change was observed in Cheriviruppu. We also observed an 83% reduction in IR64 pollen viability, whereas this reduction was only 23% in Cheriviruppu. Of 454 protein spots detected reproducibly on two-dimensional electrophoresis gels, 38 showed significant changes in at least one genotype in response to stress. Using Mass spectrometry (MALDI TOF/TOF) analysis, we identified 18 protein spots that were involved in several processes that might increase plant adaptation to salt stress, such as carbohydrate/energy metabolism, anther wall remodelling and metabolism, and protein synthesis and assembly. Three isoforms of fructokinase-2 were upregulated only in Cheriviruppu under salt stress. This upregulation might result in increased starch content in pollen, which would support pollen growth and development under salt stress. The results also suggested that anther and pollen wall remodelling/metabolism proteins contribute to the tolerance of rice to salt stress.

Zinc nutrition in rice production systems: a review

Zinc (Zn) deficiency is one of the important abiotic factors limiting rice productivity worldwide and also a widespread nutritional disorder affecting human health. Given that rice is a staple for populations in many countries, studies of Zn dynamics and management in rice soils is of great importance. Changing climate is forcing the growers to switch from conventional rice transplanting in flooded soils to water-saving cultivation, including aerobic rice culture and alternate wetting and drying system. As soil properties are changed with altered soil and water management, which is likely to affect Zn solubility and plant availability and should be considered before Zn management in rice. In this review, we critically appraise the role of Zn in plant biology and its dynamics in soil and rice production systems. Strategies and options to improve Zn uptake and partitioning efficiency in rice by using agronomic, breeding and biotechnological tools are also discussed. Although soil application of inorganic Zn fertilizers is widely used, organic and chelated sources are better from economic and environmental perspectives. Use of other methods of Zn application (such as seed treatment, foliar application etc., in association with mycorrhizal fungi) may improve Zn-use efficiency in rice. Conventional breeding together with modern genomic and biotechnological tools may result in development of Zn-efficient rice genotypes that should be used in conjunction with judicious fertilization to optimize rice yield and grain Zn content.

Water resources management: case study of Sharkia governorate, Egypt

Ministry of water resources and irrigation in Egypt is currently implementing projects that expand new cultivated area, and accordingly the supplies of Nile River to the Nile Delta will be negatively affected. So, Enormous interest toward water resources management has been taken in the Egyptian water sector. Conveyance infrastructure and irrigation technology has been gradually improved to ensure efficient distribution and utilization of scarce water resources. The present study is focused on the optimum utilization of water resources in Sharkia governorate, Egypt. Operational and planning distribution model is implemented on the selected case study (Sharkia governorate) to develop appropriate water plan. The gross revenue of all crops is correlated to surface water discharge, ground water discharge, surface water salinity, and ground water salinity. In addition, the effect of varying both surface and groundwater quantities and qualities on the gross revenue has been investigated. Moreover, the effect of limiting rice production on the gross revenue is allocated.

Mapping QTLs for Plant Phenology and Production Traits Using Indica Rice (Oryza sativa L.) Lines Adapted to Rainfed Environment

Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204-RM197-RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585-RM204-RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585-RM204-RM197-RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement.

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.

Identification of QTLs for Drought-Related Traits in Alien Introgression Lines Derived from Crosses of Rice (Oryza sativa cv. IR64) × O. glaberrima under Lowland Moisture Stress

Drought is a major abiotic stress that limits rice productivity in rain-fed and upland ecosystems. African rice, Oryza glaberrima, has low yields but is tolerant to drought and other stresses. We evaluated 513 BC2F3 progenies from alien introgression lines (AILs) that were derived from crosses of Oryza sativa (IR64) × O. glaberrima. They were assessed for yield and other traits when grown under drought at two locations. Such conditions reduced grain production by 59% compared with the recurrent parent (IR64). However, 33 AILs had higher yields, thus demonstrating their potential as genetic material for transferring drought-related traits from O. glaberrima to O. sativa. A set of 200 AILs was selectively genotyped with 173 simple sequence repeat and sequenced tagged site markers. Molecular analysis showed that a mean of 4.5% of the O. glaberrima genome was introgressed in BC2F3 AILs. Our analysis revealed 33 quantitative trait loci (QTLs; including 10 novel) for different traits. O. glaberrima contributed 50% of the alleles to those newly identified QTLs, with one for grain yield per plant (ypp9.1) being new. A QTL at RM208 on chromosome 2 positively affected yield under stress, accounting for 22% of the genetic variation. Our identification of drought-related QTLs for yield and yield components will be useful to future research efforts in marker-assisted selection.

Simultaneously improving yield under drought stress and non-stress conditions: a case study of rice (Oryza sativa L.)

Drought is the most important factor limiting rice productivity in the rainfed areas of Asia. In this study, 48 pyramiding lines (PLs) and their recurrent parent, IR64, were evaluated over two years for their yield performances and related traits under severe drought stress at the reproductive stage (RS), the vegetative stage (VS) and irrigated control in order to understand the relationship between drought tolerance (DT) and yield potential (YP) in rice and their underlying mechanisms. When compared with IR64, all PLs had significantly improved DT to RS and 36 PLs also had significantly improved DT to VS. In addition, 17 PLs had higher YP than IR64 and the remaining 31 PLs had a similar YP IR64 under irrigated conditions. Detailed characterization of the PLs revealed three possible mechanisms that functioned together to contribute to their improved DT. The most important mechanism was dehydration avoidance (DA), characterized by significantly higher growth rate and biomass of all PLs than IR64 under stress and no reduction in biomass under control conditions. The second mechanism was efficient partitioning, characterized by improved harvest index in all PLs compared with IR64, resulting primarily from heavier grain weight and/or higher spikelet fertility under control conditions, which was the major constituent of the improved YP in the 17 best performing PLs. Drought escape (DE) by accelerated heading under drought was the third mechanism that contributed to DT of the PLs to RS. The considerable variation in the measured traits among the PLs with similar levels of DT and YP implies the complex genetic control of the mechanisms for DT/YP and offers opportunities to improve DT and YP further by fine-tuning of a small number of QTLs segregating among the PLs using MAS. Finally, our results indicate that selection for yield plus some secondary traits under appropriate type(s) of stress and non-stress conditions similar to the target environments are critically important for improving both DT and YP in rice.

Effective strategy for pyramiding three bacterial blight resistance genes into fine grain rice cultivar, Samba Mahsuri, using sequence tagged site markers

Bacterial leaf blight (BB) of rice is a major disease limiting rice production in several rice growing regions of the world. The pathogen, Xanthomonas oryzae pv oryzae, causing the disease is highly virulent to rice crops and is capable of evolving new races. Breeding efforts to incorporate single BB resistant gene often leads to resistance breakdown within a short period. To overcome such breakdown of resistance and develop germplasm with durable disease resistance, we have introgressed three bacterial blight resistance genes, xa5, xa13, and Xa21 into a fine grain rice variety, Samba Mahsuri, using sequence tagged site (STS) markers linked to these genes. Since the efficiency of the STS markers linked to recessive genes to detect homozygotes is less than 100%, we adopted four different pyramiding schemes to minimize loss of recessive resistance genes in advanced backcross generations. Pyramiding scheme A in which a two-gene Samba Mahsuri pyramid line containing Xa21 and xa5 genes was crossed with the Samba Mahsuri line having xa13 gene alone was found to be most effective in preventing the loss of an important recessive gene xa13. We further demonstrated that there was no yield penalty due to pyramiding of multiple genes into the elite indica rice variety.