Development of High Yielding Rice Varieties Tolerant to Phosphorus Deficiency

Bacterial leaf blight (BLB) is one of the major and oldest diseases of rice. The best cost effective management of this disease is the development of resistant cultivars. Morphological and molecular screening are widely used approach in the recent scenario for identifying BLB resistant cultivar. In present study, two experiments were carried out to identify the BLB resistant rice lines and varieties. An active strain of Xanthomonas oryzae pv. oryaze (Xoo.) BXO-09 was used for the inoculation experiments. Then, morphological rating was done to find out the resistant rice lines and varieties whereas three RFLP primers (RG136, RG556 and pTA248) were used for identifying the BLB resistant genes. Through morphological analysis, the rice line RC251 was recorded as susceptible where the rest of the rice lines resulted moderately susceptible or moderately resistant. Among the rice varieties, BR-26, BRRI Dhan31, IRBB5, IRBB21, IRBB60, IRBB65, and Kumragur were recorded as resistant where BR-11, Binadhan-8, and Binadhan-10 were found highly susceptible to BLB. In case of RFLP marker based analysis, a specific type of banding pattern was observed for IRBB5 for RG556 primer which indicated the presence of xa5 gene. For RG136 primer 8 kb single band was formed for different lines and varieties whereas only IRBB60 showed 2 fragments of 8 kb and 5 kb which also indicated the presence of xa13 gene. Finally, DNA amplification of 27 rice lines and varieties using pTA248 primer showed the band at 4 kb position for the BLB resistant lines and varieties and 3.7 kb position for the susceptible lines and varieties. The findings of morpho-molecular characterization information could be useful to the breeders for further planning of developing BLB resistant cultivars.

The study was conducted to determine the effects of cultivars susceptibility to infection with the pathogenic isolates on the pathogenicity of rice kernel smut fungus (Tilletia barclayana). Rice (Oryza sativa L.) cultivars vary in susceptibility to kernel smut disease. The susceptibility of 18 commercial rice cultivars to T. barclayana was evaluated. Moreover, pathogenicity of 46 isolates of T. barclayana which had been isolated from six governorates in Egypt was studied using Giza 178 rice cultivar and Hybrid 1. The activities of certain oxidative enzymes, e.g. peroxidase (POX) and polyphenoloxidase (PPO) and total protein were determined in healthy and inoculated cultivars. Intron-exon splice junctions (ISJ) protocol was used to study the relationship among rice cultivars differing in their susceptibility to infection with the pathogen. Results showed that Giza 178 rice cultivar and Hybrid 1 were the most susceptible cultivars for rice kernel smut disease. Isolate no. 35 from the pathogenic fungus was the most aggressive isolate. Additionally, an increment in the defense-related enzymes and total protein was observed in rice cultivars as a result of inoculation with T. barclayana. ISJ technique showed the relationship between the studied rice cultivars and lines upon susceptibility to T. barclayana. It can also differentiate between the isolated T. barclayana isolates upon virulence on the studied rice cultivars and lines. Key words: Rice kernel smut disease, intron-exon splice junctions, rice, enzymes activity.

Salinity affects all growth stages of rice in varying degrees starting from germination up to maturation. The present study was conducted to screen the commonly cultivated rice varieties in salinity affected areas in Sri Lanka against salt stress. Screening of 21 improved rice varieties and check variety Pokkali was performed at seed germination, seedling and maturity stages in petri dishes, in a hydroponic system and in soil filled pots, respectively. Rice varieties were tested for ability to sustain seed viability, growth performance of seedling and plant survival, growth performance and grain yield reduction at maturity under salt stress. At germination stage, Bg 406 and Pokkali were identified as highly tolerant rice varieties whereas, At 402 showed the highest tolerance level followed by Pokkali, Bg 369 and At 354 at seedling stage. Based on the mean separation on survival of plants per pot at 12 dS/m and 8 dS/m, three groups (highly tolerant, tolerant and susceptible) could be identified. Percentage reduction increased with increasing salt levels for most of the parameters tested (PH, PL, RDW, SDW, PWT, PNO and YLD). Based on the phenotypic observations Pokkali was identified as high salinity tolerant variety whereas Bg 369, At 354, At 402 were identified as salinity tolerant varieties at maturity stage.

Numerous variables, such as drought period, growth stage, and varieties, influence rice growth and yield in response to drought. This study was conducted to determine the effect of drought periods on the growth and yields of several rice lines and varieties as well as to select drought-tolerant lines. Using a split-plot design with three replications, the pot experiment was carried out in the greenhouse from December 2015 to April 2016 at the Sukamandi Experimental Site of Indonesian Center for Rice Research (BB Padi). Drought periods were treated as the main-plot, while the rice lines/varieties were treated as sub-plots. The main-plot consists of four levels: control, drought at the maximum tillering stage, drought at the primordia stage, and drought at the grain filling stage. The rice lines used are expand lines of rainfed lowland rice and upland rice from the BB Padi breeding program. The results showed that of the 36 rice lines and 6 varieties tested, drought periods during maximum tillering and primordia affected plant height, while the tiller number was not affected by all drought periods. From the yield characters, drought periods increased unfilled grain percentage and decreased 1000 grains weight and also grain weight per plant. Jatiluhur is consistently tolerant and has the highest yield. There are 8 rice lines with consistent tolerance and not significantly different yields with Jatiluhur: B13650E-TB-80-2, B14168E-MR-6, B14168E-MR-10, B14168E-MR-11, B14168E-MR-12, B14168E-MR-13, B12480D-MR-7-1-1, and B12056F-TB-1-29-1. Keywords: Drought periods, Rice lines, Growth, Yield

Comparative analysis on grain quality and yield of different panicle weight indica-japonica hybrid rice (Oryza sativa L.) cultivars

Chapter 4 - The significance of nutrient interactions for crop yield and nutrient use efficiency

ABSTRACTPerennial fruits crops by the virtue of their nutritional qualities have already emerged as a major alternative, cutting short the menacing load on the consumption of traditional monotonous cereal/tuber crop-based diet. A nutrient management-based production system of perennial fruit crops is inherently complex to understand due to large variation in nutrient use efficiency (NUE). The current state of diagnosis of nutrient constraints in the current season-standing crop has minimum efficacy. Therefore, the development of production-linked nutrient norms using crop-specific index plant parts needs a thorough revisit at the orchard level using conventional basin irrigation versus fertigation. The application of hyperspectral analysis as proximal sensing of nutrient stress has started imparting precision to nutrient constraint diagnosis. On the other hand, the biggest constraint in making soil test ratings more purposeful is the non-redressal of spatial variation in soil fertility in the form of soil fertility analogs vis-a-vis fruit crops. The conjoint use of geoinformatics and Nutrient Experts as decision support tool(s) accommodating site-specific nutrient management strategy, newer concept of fertigation such as open-field hydroponics and variable-rate application as possible improvements in NUE collectively using a logical relationship between canopy volume and nutrient requirement, and exploiting further the nutrient–harmone and nutrient–microbe (in the consortium mode) synergies have yielded a definite edge over conventional methods of nutrient management options in fruit crops.

Rice is a key crop, and metal pollution is an important factor affecting rice yield and quality. Excavating the QTLs related to the accumulation of rice grain metal content, and analyzing its candidate genes, and then improving the ability of rice to withstand metal ion stress through genetic breeding can effectively reduce the caused by metal pollution in soil. In this study, a japonica rice variety Nekken was used as the female parent, and an indica rice variety HZ was used as the male parent. After F1 generation was obtained by cross-breeding, successive selfings were performed for 120 recombinant inbred lines (RIL population) for experimental materials. Cultured under the same and suitable conditions, routine management, then we measured the metal ion content in rice grains of each line at the maturity stage. A genetic map was constructed using the RIL population to map the QTLs resistant to metal ion stress in rice. As a result, a total of 9 QTLs related to metal ion content were detected. It contains 1 multi-effect QTL related to Cu and Hg; 3 QTLs related to As; 2 QTLs related to Fe, one of which has a LOD value as high as 5.53; 2 QTLs related to Zn accumulation, The LOD of one of them is as high as 7.29. Quantitative analysis of candidate genes related to resistance to metal ion stress in these QTL intervals found that the expression levels of the four genes LOC_Os01g14440 , LOC_Os01g18584 , LOC_Os01g20160 , LOC_Os04g34600 were significantly different between parents, Combining the results of the accumulated data of parental concentrations of different metal ions, we speculated that the high expression of LOC_Os01g14440 , LOC_Os01g18584 , and LOC_Os01g20160 may greatly improve the absorption capacity and the tolerance of rice to Zn stress, while the high expression of LOC_Os04g34600 may increase the absorption capacity and the tolerance of rice to Fe stress. Through the excavation and analysis of this QTL, it was found that these genes may affect the ability of rice to withstand metal ion stress, creating conditions for further breeding and screening of rice varieties resistant to metal ion stress.

Hybrid rice (Oryza sativa L.) varieties usually need more N application to produce a higher grain yield and exhibit lower N use efficiency (NUE) than inbreds. However, little information is available about the mechanism underlying an indica–japonica rice variety with high yield and high NUE under low N rates. This study investigated this issue. The indica–japonica hybrid rice variety Yongyou 2640 (Y‐2640) and the japonica inbred rice variety Lianjing 7 (L‐7) were grown in a paddy field at N rates of 0 and 200 kg N ha−1. The results showed that the grain yield and internal NUE (grain yield/total N uptake of plants) of Y‐2640 were 16–23% and 9–10%, respectively, higher than those of L‐7. A higher grain yield for Y‐2640 was mainly attributed to the greater spikelet number per unit area that resulted from greater root oxidation activity at panicle initiation and its higher crop growth rate and net assimilation rate before heading. A higher leaf area index and greater root length, root, and shoot biomass were the important agronomic traits of Y‐2640. Higher cytokinin content and the expression of genes involved in the amino acid transporters OsAAP1 and OsLHT1 in the roots and leaves, a higher photosynthetic NUE, and a greater N harvest index were the main physiological traits of Y‐2640. The results suggest that improved agronomic and physiological performance accounts for the high yield and high NUE for the indica–japonica hybrid rice variety.

Phosphorus (P) deficiency of soils is a major yield-limiting factor in rice production. Increasing the P-deficiency tolerance of rice cultivars may represent a more cost-effective solution than relying on fertilizer application. The objective of this study was to identify putative QTLs for P-deficiency tolerance in rice, using 98 backcross inbred lines derived from a japonica×indica cross and genotyped at 245 RFLP marker loci. Lines were grown on P-deficient soil and P uptake, internal P-use efficiency, dry weight, and tiller number were determined. Three QTLs were identified for dry weight and four QTLs for P uptake, together explaining 45.4% and 54.5% of the variation for the respective traits. Peaks for both traits were in good agreement which was to be expected considering the tight correlation of r=0.96 between dry weight and P uptake. For both traits the QTL linked to marker C443 on chromosome 12 had a major effect. Two of the three QTLs detected for internal P-use efficiency, including the major one on chromosome 12, coincided with QTLs for P uptake; however, whereas indica alleles increased P uptake they reduced P-use efficiency. We concluded that this was not due to the tight linkage of two genes in repulsion but rather due to an indirect effect of P uptake on P-use efficiency. Most lines with high use efficiency were characterized by very low P uptake and dry weight and apparently experienced extreme P-deficiency stress. Their higher P-use efficiency was thus the result of highly sub-optimal tissue-P concentrations and did not represent a positive adaptation to low P availability. The number of tillers produced under P deficiency is viewed as an indirect indicator of P-deficiency tolerance in rice. In addition to the major QTL on chromosome 12 already identified for all other traits, two QTLs on chromosome 4 and 12 were identified for tiller number. Their position, however, coincided with QTLs for tiller number reported elsewhere under P-sufficient conditions and therefore appear to be not related to P-deficiency tolerance. In this study P-deficiency tolerance was mainly caused by differences in P uptake and not in P-use efficiency. Using a trait indirectly related to P-deficiency tolerance such as tiller number, we detected a major QTL but none of the minor QTLs detected for P uptake or dry weight.

Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid

In plants, cellular lipid peroxidation is enhanced under low nitrogen (LN) stress; this increases the lipid-derived reactive carbonyl species (RCS) levels. The cellular toxicity of RCS can be reduced by various RCS-scavenging enzymes. However, the roles of these enzymes in alleviating oxidative stress and improving nutrient use efficiency (NUE) under nutrient stress remain unknown. Here, we overexpressed maize endogenous NADPH-dependent 2-alkenal reductase (ZmAER) in maize; it significantly increased the tolerance of transgenic plants (OX-AER) to LN stress. Under LN condition, the biomass, nitrogen accumulation, NUE, and leaf photosynthesis of the OX-AER plants were significantly higher than those of the wild-type (WT) plants. The leaf and root malondialdehyde and H2 O2 levels in the transgenic plants were significantly lower than those in WT. The expression of antioxidant enzyme-related genes ZmCAT3, ZmPOD5 and ZmPOD13 was significantly higher in the transgenic lines than in WT. Under LN stress, the nitrate reductase activity in the OX-AER leaves was significantly increased compared with that in the WT leaves. Furthermore, under LN stress, ZmNRT1.1 and ZmNRT2.5 expression was upregulated in the OX-AER plants compared with that in WT. Overall, up-regulated ZmAER expression could enhance maize's tolerance to LN stress by alleviating oxidative stress and improve NUE.

Phosphate availability is a major factor limiting tillering, grain filling vis-á-vis productivity of rice. Rice is often cultivated in soil like red and lateritic or acid, with low soluble phosphate content. To identify the best genotype suitable for these types of soils, P acquisition efficiency was estimated from 108 genotypes. Gobindabhog, Tulaipanji, Radhunipagal and Raghusail accumulated almost equal amounts of phosphate even when they were grown on P-sufficient soil. Here, we have reported the presence as well as the expression of a previously characterized rice gene, phosphate starvation tolerance locus (PSTOL1) in a set of selected genotypes. Two of four genotypes did not show any detectable expression but carried the gene. One mega cultivar, Swarna did not possess this gene but showed high P-deficiency tolerance ability. Increase of root biomass, not length, in P-limiting situations might be considered as one of the selecting criteria at the seedling stage. Neither the presence of PSTOL1 gene nor its closely-linked SSR RM1261, showed any association with P-deficiency tolerance among the 108 genotypes. Not only this, but the presence of PSTOL1 in recombinant inbred line (RIL) developed from a cross between Gobindabhog and Satabdi, also did not show any linkage with P-deficiency tolerance ability. Thus, before considering PSTOL1 gene in MAB, its expression and role in P-deficiency tolerance in the donor parent must be ascertained.

Abstract. Subekti NA, Sembiring H, Erythrina, Nugraha D, Priatmojo B, Nafisah. 2020. Yield of different rice cultivars at two levels of soil salinity under seawater intrusion in West Java, Indonesia. Biodiversitas 21: 14-20. A tendency to use saline water in rice production is rising in recent years, but the adaptation of variety under saline conditions is still questionable. The aim of the study was to evaluate the response of several rice cultivars on the growth and yield of rice under seawater intrusion in West Java. Two salt-tolerant cultivars (Inpari 34 and Inpari 35), two promising lines (PL-1 and PL-2) and two modern cultivars (Inpari 30 (Ciherang sub1) and Sidenuk) were evaluated in two soil salinity levels. In each farmer's field a Randomized Complete Block Design was applied with three replications per treatment. Results showed that Sidenuk and Inpari 30 produced same yield compared to tolerant varieties and promising lines during dry season under moderate soil salinity. There were not much different among the cultivars tested in terms of plant height and tiller number as well as the biomass and harvest index. However, under high soil salinity seed germination, plant height, number of tillers per plant, above-ground biomass, spikelet number, percent of sterile florets and productivity were significantly affected. Saline tolerant varieties Inpari 34 and Inpari 35 showed their superiority compared to non-tolerant varieties. Both varieties produced 40% higher yield than Inpari 30 (Ciherang sub 1) and Sidenuk.

Reducing water requirements and lowering environmental footprints require attention to minimize risks to food security. The present study was conducted with the aim to identify appropriate root traits enhancing rice grain yield under alternate wetting and drying conditions (AWD) and identify stable, high-yielding genotypes better suited to the AWD across variable ecosystems. Advanced breeding lines, popular rice varieties and drought-tolerant lines were evaluated in a series of 23 experiments conducted in the Philippines, India, Bangladesh, Nepal and Cambodia in 2015 and 2016. A large variation in grain yield under AWD conditions enabled the selection of high-yielding and stable genotypes across locations, seasons and years. Water savings of 5.7–23.4% were achieved without significant yield penalty across different ecosystems. The mean grain yield of genotypes across locations ranged from 3.5 to 5.6 t/ha and the mean environment grain yields ranged from 3.7 (Cambodia) to 6.6 (India) t/ha. The best-fitting Finlay-Wilkinson regression model identified eight stable genotypes with mean grain yield of more than 5.0 t/ha across locations. Multidimensional preference analysis represented the strong association of root traits (nodal root number, root dry weight at 22 and 30 days after transplanting) with grain yield. The genotype IR14L253 outperformed in terms of root traits and high mean grain yield across seasons and six locations. The 1.0 t/ha yield advantage of IR14L253 over the popular cultivar IR64 under AWD shall encourage farmers to cultivate IR14L253 and also adopt AWD. The results suggest an important role of root architectural traits in term of more number of nodal roots and root dry weight at 10–20 cm depth on 22–30 days after transplanting (DAT) in providing yield stability and preventing yield reduction under AWD compared to continuous flooded conditions. Genotypes possessing increased number of nodal roots provided higher yield over IR64 as well as no yield reduction under AWD compared to flooded irrigation. The identification of appropriate root architecture traits at specific depth and specific growth stage shall help breeding programs develop better rice varieties for AWD conditions.