Rice Variety IR64 Research Articles

Overexpression of Orysa;KRP4 drastically reduces grain filling in rice.

Excess of KRP4 in the developing kernels in rice causes poor filling of the grains possibly through inhibition of CDKA;2 and CDKB;1 activity mediated by its interaction with CDKF;3. The potential yield of the rice varieties producing compact and heavy panicles bearing numerous spikelets is compromised because a high percentage of spikelets remain poorly filled, reportedly because of a high expression of KRPs that causes suppression of endosperm cell proliferation. To test the stated negative relationship between KRP expression and grain filling, Orysa;KRP4 was overexpressed under the control of seed-specific glutelin promoter in IR-64 rice variety that shows good grain filling. The transgenic lines showed more than 15-fold increase in expression of KRP4 in the spikelets concomitant with nearly 50% reduction in grain filling compared with the wild type without producing any significant changes on the other yield-related parameters like panicle length and the spikelets numbers that were respectively 30.23 ± 0.89cm and 229.25 ± 33.72 per panicle in the wild type, suggesting a highly organ-targeted effect of the genetic transformation. Yeast two-hybrid test revealed CDKF;3 as the interacting partner of KRP4, and CDKF;3 was found to interact with CDKA;2, CDKB;1 and CDKD;1. Significant decrease in grain filling in the transgenic lines compared with the wild type due to overexpression of KRP4 could be because of suppression of the activity of CDKB;1 and CDKA;2 by inhibition of their phosphorylation directly by CDKF;3, or mediated through inhibition of phosphorylation of CDKD;1 by CDKF;3. The study thus indicated that suppression of expression of KRP(s) by genetic manipulation of their promoters could be an important way of improving the yield of the rice varieties bearing compact and heavy panicles.

Vis/NIR and FTIR spectroscopy supported by machine learning techniques to distinguish pure from impure Iranian rice varieties

Vis/NIR and FTIR spectroscopy supported by machine learning techniques to distinguish pure from impure Iranian rice varieties

Identifying the authenticity and geographical origin of rice by analyzing hyperspectral images using unsupervised clustering algorithms

The present study evaluated the capability of the hyperspectral imaging system (HSI) as a rapid and non-destructive technique to identify the authenticity and origin of three Iranian rice varieties (Shiroudi, Khazar, and Hashemi) from three main origins. Captured raw spectral data were pre-processed using de-trending (DT), multiplicative scatter correction (MSC), and standard normal variant (SNV), and then were fed to principal component analysis (PCA) for the visual discrimination of the samples and data reduction. Next, since in real applications, the system might face unknown rice samples with unknown patterns, three unsupervised algorithms, self-organizing map (SOM), automatic clustering by artificial bee colony (ABC), and k-means algorithms were applied for clustering the samples in their original group. Results illustrated that SOM and k-means clustering algorithms led to the reliable grouping of the rice varieties. The models indicated that the high-yielding rice (Shiroudi and Hashemi) from two different origins with similar weather conditions were distinguished close to each other and completely separated from the third variety (Khazar). However, the automatic clustering method separated the varieties with less accuracy than the other two methods. Finally, the HSI system coupled with unsupervised algorithms provided satisfactory results and could be used as a reliable, out-lab, and fast method for ‎authenticating rice‎ varieties from different geographical origins.

Stomatal Development and Gene Expression in Rice Florets.

Stomata play a fundamental role in modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well studied, little attention has been paid to the development or function of floral stomata. Here, we characterize in detail the spatial distribution and development of the floral stomata of the indica rice variety IR64. We show that stomatal complexes are present at low density on specific areas of the lemma, palea and anthers and are morphologically different compared to stomata found on leaves. We reveal that in the bract-like organs, stomatal development follows the same cell lineage transitions as in rice leaves and demonstrate that the overexpression of the stomatal development regulators OsEPFL9-1 and OsEPF1 leads to dramatic changes in stomatal density in rice floral organs, producing lemma with approximately twice as many stomata (OsEPFL9-1_oe) or lemma where stomata are practically absent (OsEPF1_oe). Transcriptomic analysis of developing florets also indicates that the cellular transitions during the development of floral stomata are regulated by the same genetic network used in rice leaves. Finally, although we were unable to detect an impact on plant reproduction linked to changes in the density of floral stomata, we report alterations in global gene expression in lines overexpressing OsEPF1 and discuss how our results reflect on the possible role(s) of floral stomata.

Resistance gene expression in selected Indonesian pigmented rice varieties against infection by Xanthomonas oryzae pv. oryzae

Rice (Oryza sativa L.) production is limited by bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo). For decades, researchers have attempted to control this disease by growing plants with blight‐resistant Xa genes. Genetic resources often vary between rice varieties, and there is little information about the genetic resources of the pigmented rice varieties widely grown in Indonesia and their resistance genes against Xoo. The purpose of this study was to determine the expression of Xa genes in pigmented rice such as Inpari 24 and Cempo Merah (red‐pigmented) along with Hitam Bantul (black‐pigmented) and white rice varieties IR64 and Ciherang, and to evaluate their resistance to BLB. All varieties carried the Xa4, Xa10 and xa13 genes but varied in the Xa1, Xa7 and Xa21 genes. The rice varieties expressed some of these genes only after inoculation with Xoo. Disease assessment categorised the three different pigmented rice varieties as resistant (Ciherang, Cempo Merah and Hitam Bantul), while IR64 (white) and Inpari 24 (red) were moderately resistant. There was no specific pattern of Xa genes possession, quality of expression or resistance level to X. oryzae pv. oryzae. Therefore, when breeding plants, the selection of parental variety must be considered in terms of the possession and expression of Xa genes such as Xa10 as a molecular marker for resistance.

Quality control, classification, and authentication of Iranian rice varieties using FT-IR spectroscopy and sparse chemometric methods

The authentication and classification of rice varieties have attracted much attention in food industry, in recent years. In this study, FTIR spectroscopy and sparse chemometric methods were used for discriminating different classes of Iranian rice samples and detecting adulteration in high-quality products. The sparse version of the linear discriminant analysis (sLDA) was used for developing interpretable classification models and detecting adulteration in rice samples. More than 400 samples from eight different classes of the most favorable Iranian rice varieties were used for developing sparse models. The performance of the sLDA model was compared with common chemometric methods, and the results revealed the superiority of the sLDA in terms of interpretability and prediction accuracy. Moreover, sparse multivariate regression methods including least absolute shrinkage and selection operator (lasso), ridge, and elastic net were used for quantitative analysis and fast assessment of rice adulteration. The overall accuracy for sLDA was 0.967 and the ranges of coefficient of determination (R2) for lasso models were 0.879–0.948, for the test sets. The results showed that the sparse chemometric methods combined with FTIR spectroscopy can be successfully applied as robust and interpretable tools for classification and adulteration detection of rice samples in food industry.

TAL Effectors with Avirulence Activity in African Strains of Xanthomonas oryzae pv. oryzae

BackgroundXanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating disease of rice. Among the type-3 effectors secreted by Xoo to support pathogen virulence, the Transcription Activator-Like Effector (TALE) family plays a critical role. Some TALEs are major virulence factors that activate susceptibility (S) genes, overexpression of which contributes to disease development. Host incompatibility can result from TALE-induced expression of so-called executor (E) genes leading to a strong and rapid resistance response that blocks disease development. In that context, the TALE functions as an avirulence (Avr) factor. To date no such avirulence factors have been identified in African strains of Xoo.ResultsWith respect to the importance of TALEs in the Rice-Xoo pathosystem, we aimed at identifying those that may act as Avr factor within African Xoo. We screened 86 rice accessions, and identified 12 that were resistant to two African strains while being susceptible to a well-studied Asian strain. In a gain of function approach based on the introduction of each of the nine tal genes of the avirulent African strain MAI1 into the virulent Asian strain PXO99A, four were found to trigger resistance on specific rice accessions. Loss-of-function mutational analysis further demonstrated the avr activity of two of them, talD and talI, on the rice varieties IR64 and CT13432 respectively. Further analysis of TalI demonstrated the requirement of its activation domain for triggering resistance in CT13432. Resistance in 9 of the 12 rice accessions that were resistant against African Xoo specifically, including CT13432, could be suppressed or largely suppressed by trans-expression of the truncTALE tal2h, similarly to resistance conferred by the Xa1 gene which recognizes TALEs generally independently of their activation domain.ConclusionWe identified and characterized TalD and TalI as two African Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against African Xoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on an Xa1-like gene or allele.

Growth and nutrition of rice seedlings when phosphorus or silicon was applied to a soil heavily contaminated with both arsenic and cadmium

There is a lack of affordable and effective strategies to mitigate multiple heavy metal contamination in lowland rice production. We tested phosphorus (P) or silicon (Si) addition to a soil contaminated with both arsenic (As) and cadmium (Cd) for their mitigation potential in rice seedlings. Rice variety IR64 was grown in pots with either P (0, 2.5, 5, 10, 20 (recommended rate), 40 and 80 mg P kg−1 soil), or Si (0, 0.15, 0.3, 0.6, 1.2 and 2.4 g Si kg−1 soil) addition until the end of tillering phase (nine weeks). Over this period, growth of rice was enhanced by up to 35% with the addition of P until the recommended rate, whereas growth was reduced beyond 0.3 g Si kg−1 application. Photosynthetic rate and maximum PSII quantum yield of the youngest fully expanded leaves were similar among P and Si treatments. Phosphorus addition increased shoot [As] and decreased shoot [Cd] by up to 59% and 63%, respectively, and both effects were visible only after plants reached P sufficiency. Silicon addition from 0 to 2.4 mg Si kg−1 soil increased shoot [As] by up to 28% and decreased [Cd] by up to 25%. Accumulation of As and Cd in the leaves from top to bottom of the canopy increased by factors of 10 and 7.6, respectively. Therefore, P or Si application cannot generally be recommended as remedy for rice production on multiple heavy metal contaminated soil. However, rice plants have efficient mechanisms to translocate As and Cd to mature leaves.

Evaluating the implementation of fertilizer-based decision support systems to increase yield productivity and efficiency of irrigated rice farming in West Java

Nutrient management and fertilizer application are paramount elements for increasing rice productivity. However, most of farmers are still applying fertilizer in an improper way and hence economic benefit of the yield remain low. The objective of this study was to examine various fertilizer recommendations and hence the best and efficient dose of fertilizer can be obtain to increase growth and yield of rice. This experiment was conducted in farmers irrigated lowland Sukabumi, West Java in dry season 2019. The material used was high yielding IR-64 rice variety subjected to six fertilizer recommendation, namely urea only (A), LKP (B), factory’s recommendation (C), PUTS, (D), KATAM (E) and farmer’s practice (F). This experiment was arranged in randomized block design (RBD) with four replications. The quantitative morphological and physiological traits and financial analysis were observed. The result showed that fertilizer significantly affected morphological, physiological parameters and grain yield of rice. PUTS and KATAM (9,7t/ha) treatments had higher grain yield compared to other treatments. Fertilizer by farmer’s practice tended lower in morphological, physiological and grain yield responses compared to other fertilizer recommendation. Similar pattern showed for yield components such as panicle number, grains number and % empty grain were also affected by fertilizer recommendation. Based on the financial analysis that treatment with LKP fertilizer recommendation had higher profit (75.61%) compared with farmer’s practice. That treatment can reduce fertilizer costs by 61.57%, can increase revenue by 14.04% and give a profit of Rp. 5,580,969,-.

Alleviation of Submergence Stress in Rice Seedlings by Plant Growth-Promoting Rhizobacteria With ACC Deaminase Activity

Submergence stress slows seed germination, imposes fatalities, and delays seedling establishment in rice. Seeds of submergence susceptible rice variety IR 42 were inoculated with four 1-aminocyclopropane-1-carboxylic acid (ACC) utilizing isolates viz., Bacillus sp. (AR-ACC1), Microbacterium sp. (AR-ACC2), Methylophaga sp. (AR-ACC3), and Paenibacillus sp. (ANR-ACC3) and subjected to submergence stress under controlled conditions for 7 days. Seeds treated with Microbacterium sp. AR-ACC2, Paenibacillus sp. ANR-ACC3, and Methylophaga sp. AR-ACC3 significantly enhanced the germination percentage (GP), seedling vigor index (SVI), and other growth parameters like root and shoot length and total chlorophyll contents, when compared with nonbacterized seeds submerged similarly. However, the values were statistically at par when control seeds were treated with l-α-(2-aminoethoxyvinyl) glycine hydrochloride (AVG), a known inhibitor of ethylene production. Results suggest that stress ethylene production was significantly reduced by around 85% in seedlings treated with Microbacterium sp. AR-ACC2 as compared with untreated control seeds under submergence. Paenibacillus sp. ANR-ACC3 and Methylophaga sp. AR-ACC3 were the next effective strains. Ethylene synthesis in seedlings was statistically at par with seeds treated with AVG suggesting ACC deaminase can effectively reduce ethylene levels in plants subjected to submergence. Bacillus sp. (AR-ACC1) was neither able to significantly promote seedling growth parameters nor inhibit ethylene production as compared with control seeds. Results suggest that flooded soil planted to rice harbor microorganisms with plant growth-promoting properties that can be used effectively to alleviate submergence stresses in susceptible rice varieties under field conditions.

Chemical intervention for enhancing growth and reducing grain arsenic accumulation in rice.

Arsenic (As) is a ubiquitous environmental carcinogen that enters the human food chain mainly through rice grains. In the present study, we evaluated the potential of thiourea (TU; non-physiological reactive oxygen species scavenger) in mitigating the negative effects of arsenic (As) stress in indica rice variety IR64, with the overall aim to reduce grain As accumulation. At seedling stage, As+TU treatment induced the formation of more numerous and longer crown roots compared with As alone. The As accumulation in main root, crown root, lower leaf and upper leaf was significantly reduced to 0.1-, 0.14-, 0.16-, 0.14-fold, respectively in As+TU treated seedlings compared with those of As alone. This reduced As accumulation was also coincided with light-dependent suppression in the expression levels of aquaporins and photosynthesis-related genes in As+TU treated roots. In addition, the foliar-supplemented TU under As-stress maintained reducing redox conditions which decreased the rate of As accumulation in flag leaves and, eventually grain As by 0.53-fold compared with those of As treatment. The agronomic feasibility of TU was validated under naturally As contaminated sites of Nadia (West Bengal, India). The tiller numbers and crop productivity (kg seed/ha) of TU-sprayed plants were increased by 1.5- and 1.18-fold, respectively; while, grain As accumulation was reduced by 0.36-fold compared with those of water-sprayed control. Thus, this study established TU application as a sustainable solution for cultivating rice in As-contaminated field conditions.

Thiourea and hydrogen peroxide priming improved K+ retention and source-sink relationship for mitigating salt stress in rice

Plant bioregulators (PBRs) represent low-cost chemicals for boosting plant defense, especially under stress conditions. In the present study, redox based PBRs such as thiourea (TU; a non-physiological thiol-based ROS scavenger) and hydrogen peroxide (H2O2; a prevalent biological ROS) were assessed for their ability to mitigate NaCl stress in rice variety IR 64. Despite their contrasting redox chemistry, TU or H2O2 supplementation under NaCl [NaCl + TU (NT) or NaCl + H2O2 (NH)] generated a reducing redox environment in planta, which improved the plant growth compared with those of NaCl alone treatment. This was concomitant with better K+ retention and upregulated expression of NaCl defense related genes including HAK21, LEA1, TSPO and EN20 in both NT and NH treated seedlings. Under field conditions, foliar applications of TU and H2O2, at vegetative growth, pre-flowering and grain filling stages, increased growth and yield attributes under both control and NaCl stress conditions. Principal component analysis revealed glutathione reductase dependent reduced ROS accumulation in source (flag leaves) and sucrose synthase mediated sucrose catabolism in sink (developing inflorescence), as the key variables associated with NT and NH mediated effects, respectively. In addition, photosystem-II efficiency, K+ retention and source-sink relationship were also improved in TU and H2O2 treated plants. Taken together, our study highlights that reducing redox environment acts as a central regulator of plant’s tolerance responses to salt stress. In addition, TU and H2O2 are proposed as potential redox-based PBRs for boosting rice productivity under the realistic field conditions.

Herbivore induced plant volatiles of paddy and their influence in the attraction of mirids Cyrtorhinus lividipennis reuter

In the present study, a popular rice variety IR 20 was selected to characterize volatile profile change due to the two major insect pest infestation (Brown plant hopper Nilaparvata lugens and Yellow stem borer Scirpophaga incertulas). Volatile collection was made using air entrainment method and were characterized using GCMS (Gas Chromatography Mass Spectrometry). Collected volatiles were checked for their attraction towards the predator of Brown plant hopper (BPH), Mirids Cyrtorhinus lividipennis (Reuter) using Y arm olfactometer. Terpenoids were identified as the major compounds differentiating from the healthy plants. Significant attraction was observed in the predators towards BPH infested volatiles. The results of the study suggested its usage for the management of the pest under field conditions.

PENGARUH INSEKTISIDA NABATI KAMANDRAH DAN AKAR TUBA TERHADAP WERENG BATANG COKLAT

[THE INFLUENCE OF BOTANICAL INSECTICIDES BASED ON CROTON OIL AND DERRIS ROOT AGAINST BROWN PLANTHOPPER]. Brown planthopper (BPH) (Nilaparvata lugens Stall) is a serious pest in rice. Using synthetic insecticide to control BPH is harmful for human health and can caused environmental pollution. The objective of this research is to find out ecofriendly insecticide to control BPH. Research has been conducted at Entomological laboratory, Indonesian Spice and Medicinal Crops Research Institute (ISMECRI), Bogor. It was designed with CRD, 16 treatments and 3 replications. Treatments consisted of botanical insecticides based on Croton tiglium and Derris elliptica. Each material was extracted by water, methanol, and xylene, and then tested by individually and combination, so there were 15 formulas and 1 control treatment (water). Third nymph BPH and IR64 rice variety were used in this research. Research was done in two methods, i.e. contact application and residual application. The result shows that there are 11 formulas which are prospective to be further developed i.e aqueous extraction (6 formulas) and combination extraction (aqueous with xylene and methanol (5 formulas). The aqueous extraction maybe the most prospective formulation since the technique could easily be adopted by farmers. Botanical pesticide based on Croton tiglium and Derris elliptica are very promising, therefore the research should be continued to find out the best formula of botanical insecticides for controlling BPH).

Genetic variation of typhoon-induced spikelet sterility in introgression lines with genetic background of Indica group rice (Oryza sativa L.) variety IR 64

ABSTRACT Wide variations of typhoon-induced spikelet sterility and days to heading (DH) were found among 317 introgression lines (INLs) originating from new-plant-type varieties with a genetic background of Indica Group rice variety IR 64. Sterility was induced by continuous dry winds from the typhoon. The most seriously affected were 194 INLs with DH ranging from 83 to 86 days. Positive correlations with the spikelet sterility score (SSS) were found for culm length (CL), panicle length (PL), and panicle weight (PW). Based on these traits and DH, the 194 INLs were classified into three groups: A1, A2, and B. The means of SSS and four traits (CL, PL, culm and leaf weight (CW), and panicle weight (PW)) were the lowest in group A1, and highest in group B. PN was significantly higher in group B than those in the others. Seven quantitative trait loci (QTL) for SSS were detected on chromosomes (chr.) 1, 2, 4, 7 (two), 8, and 11. Among them, the QTL of chr. 4 was located in the same regions as those of DH, CL, PL, CW, and panicle number (PN). Thus, the region on chr.4 might induce sterility in the INLs by modifying plant architecture, such as large panicles or high plant height with the minor effect of many tillers. The relationships among traits, and the QTLs will be useful information for genetic improvement of tolerance to typhoon damage in rice.

Root knot nematode infections promoted by agricultural practice modifications in Vietnam and the impacts on rice production

A survey conducted on newly cultivated lowland rice fields by direct seeding method in Hai Duong Province, Viet Nam, in March 2017 revealed high devastation of the field. In these fields, farmers used an annual crop rotation cycle of rice-scallion-rice. Investigations on the devastated fields revealed that the chemical and physical soil properties were appropriate for rice cultivation. On the other hand, observations done on the root systems showed that the dead plants have symptomatic root galls suggesting the presence of plant parasitic nematodes. Sequencing of the internal transcribed spacer (ITS) region of the rDNA genes of the nematodes showed that the root nematodes extracted from the infested fields belonged to Meloidogyne graminicola. The reproductive factor of the isolated M. graminicola population on the IR64 rice variety (Oryza sativa indica) was normal, suggesting that the impact of this plant pest was not due to the emergence of an unusual virulent population. The combination of the three factors (wrong cropping choice for rotation, using rice variety susceptible to M. graminicola and direct seeding) were obviously promoting the nematode infection and its high proliferation in the surveyed fields. Meloidogyne graminicola could parasitize and propagate in scallions of Vietnam. Since this plant is annually cultivated on a paddy field for crop rotation, preventive measures or alternative plant for crop rottion is necessary.

Synergistic inoculation of Azotobacter vinelandii and Serendipita indica augmented rice growth

In the rhizosphere, microbes act as crucial constituent for plant growth and development. The root-endophytic plant growth-promoting fungus-Serendipita indica and nitrogen fixing bacterium Azotobacter vinelandii are well known for plant growth promotion and stress alleviation. Individual inoculation of S. indica or A. vinelandii strain SRIAz3 has already been reported to augment plant growth. Therefore, it would be interesting to investigate the mutual interaction among these two microbes along with their symbiotic influence on growth of rice plant. The present study explores the interaction of S. indica and A. vinelandii strain SRIAz3 under in vitro condition and perceive their cumulative effect on rice growth. Differential growth response of S. indica was observed after inoculation of A. vinelandii strain SRIAz3 on different days. An enhanced S. indica growth in terms of hyphal radius and dry cell weight was found when SRIAz3 was inoculated 7 days after fungal inoculation. Moreover, confocal microscopy analysis revealed that A. vinelandii strain SRIAz3 cell-free supernatant increased S. indica spore germination. The sequential inoculation of A. vinelandii strain SRIAz3 on seventh day after S. indica inoculation in rice variety IR64 demonstrates better growth in terms of root-shoot biomass and chlorophyll content as compared to the non-inoculated and to singly inoculated plants. These findings recommend the sequential inoculation of S. indica followed by A. vinelandii strain SRIAz3 for the enhancement of rice growth.

De novo Genome Assembly of the indica Rice Variety IR64 Using Linked-Read Sequencing and Nanopore Sequencing.

IR64 is a rice variety with high-yield that has been widely cultivated around the world. IR64 has been replaced by modern varieties in most growing areas. Given that modern varieties are mostly progenies or relatives of IR64, genetic analysis of IR64 is valuable for rice functional genomics. However, chromosome-level genome sequences of IR64 have not been available previously. Here, we sequenced the IR64 genome using synthetic long reads obtained by linked-read sequencing and ultra-long reads obtained by nanopore sequencing. We integrated these data and generated the de novo assembly of the IR64 genome of 367 Mb, equivalent to 99% of the estimated size. Continuity of the IR64 genome assembly was improved compared with that of a publicly available IR64 genome assembly generated by short reads only. We annotated 41,458 protein-coding genes, including 657 IR64-specific genes, that are missing in other high-quality rice genome assemblies IRGSP-1.0 of japonica cultivar Nipponbare or R498 of indica cultivar Shuhui498. The IR64 genome assembly will serve as a genome resource for rice functional genomics as well as genomics-driven and/or molecular breeding.

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.

Mapping and characterization of a quantitative trait locus resistance to the brown planthopper in the rice variety IR64

BackgroundRice planthoppers (main brown planthopper, Nilaparvata lugens Stål; BPH) was one of substantial threats to Asia rice production as its serious destruction and difficulties in control under field conditions. Notably, host-plant resistance was proved to be one of the effective ways to manage the pest. And stronger virulence will probably emergence when continuous use of insecticides. Therefore, more resistance genes with different resistance mechanisms were needed to be detected and then applied in the rice breeding practice.ResultsResistance genes in the rice variety IR64 were evaluated considering the seedling bulk test and seedling survival rate. As a result, a locus with a large LOD score of 7.23 was found between markers RM302 and YM35 on chromosome 1. The locus explained 36.9% of phenotypic variation and was tentatively denominated Bph37. Moreover, Bph1 was detected to be harbored by the markers RM28366 and RM463, and had the largest LOD score of 2.08, explaining 7.7% of phenotypic variance in the same mapping population. Finally, the preliminary-near-isogenic-lines (pre-NILs) carrying Bph37 exhibited significant tolerance to the insects. But no antibiotic or antixenotic effects were observed in the resistant plants when infested with the insects.ConclusionsWe mapped one major BPH resistance gene Bph37 in consideration of seedling survival rate and the resistance lines showed tolerance to BPH. The detected gene should be beneficial for understanding the resistance mechanism of rice to BPH and for insect-resistance rice breeding programs.