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    28 July 2018, Volume 25 Issue 4 Previous Issue    Next Issue

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    Orginal Article
    Identification and Characterization of Drought Stress- Responsive Novel microRNAs in Dongxiang Wild Rice
    Fantao Zhang, Yuan Luo, Meng Zhang, Yi Zhou, Hongping Chen, Biaolin Hu, Jiankun Xie
    2018, 25(4): 175-184.  DOI: 10.1016/j.rsci.2018.06.001
    Abstract ( )   HTML ( )   PDF (838KB) ( )  

    MicroRNAs (miRNAs) are non-coding small RNAs, which play important regulatory roles in response to biotic and abiotic stresses. Dongxiang wild rice (Oryza rufipogon, DXWR) can survive in extreme drought environment, but its molecular mechanism of drought resistance is still largely unknown. To further explore miRNA regulatory mechanisms involved in drought resistance, we identified 138 novel miRNAs in DXWR using small RNA sequencing and bioinformatics approaches, and found that the expression levels of 67 novel miRNAs were significantly affected by drought stress. In total, 200 candidate target genes were predicted and annotated for the drought stress-responsive novel miRNAs. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways suggested that most of the target genes were related to metabolism. Stem-loop quantitative real-time PCR (qRT-PCR) results exhibited high concordance with sequencing data, which confirmed that miRNA expression patterns based on small RNA sequencing in the present study were reliable. Meanwhile, qRT-PCR validated the inverse expression patterns between several miRNAs and their target genes. These results will enhance our understanding of miRNA regulatory mechanisms in response to drought stress in DXWR, and can serve as an important reference for the protection and utilization of this valuable genetic resource.

    Antioxidant Protection Mechanisms Reveal Significant Response in Drought-Induced Oxidative Stress in Some Traditional Rice of Assam, India
    Nahar Shamsun, R. Vemireddy Lakshminarayana, Sahoo Lingaraj, Tanti Bhaben
    2018, 25(4): 185-196.  DOI: 10.1016/j.rsci.2018.06.002
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    Drought tolerance levels and antioxidant protection mechanisms were evaluated for 21 traditional rice varieties of Assam, India, along with Sahbhagi Dhan (drought tolerant) and IR64 (drought sensitive) as controls. Drought was imposed in hydroponic culture with polyethylene glycol 6000 (PEG6000) that was initially standardized with different concentrations. All the rice varieties showed apparent decreases in growth characteristics under drought stress (initially at 15% for 7 d followed by 20% PEG6000 for 7 d in Yoshida medium). On the basis of standard evaluation score (SES), eight rice varieties showed high drought tolerance which were carried forward for further biochemical analyses. Based on different morpho- physiological parameters, SN03 (Bora), SN04 (Prosad Bhog), SN05 (Kola Joha), SN06 (Helash Bora), SN08 (Salihoi Bao), SN12 (Kola Amona), SN20 (Ronga Bora) and SN21 (Sok-Bonglong) were identified as promising drought tolerant varieties. The non-enzymatic antioxidants activities viz., glutathione, ascorbate and enzymatic antioxidant activities such as superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPX), ascorbate peroxidase (APX), glutathione reductase (GR) in shoots and roots of all the selected varieties revealed significant level of protection mechanisms as compared with controls. Enhancement in activities of the overall antioxidant enzymes including SOD, GPX, CAT, GR and APX under drought stress reflects their role in the adaptation process under water stress.

    QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations
    P. M. Swamy B., Kaladhar K., Anuradha K., K. Batchu Anil, Longvah T., Sarla N.
    2018, 25(4): 197-207.  DOI: 10.1016/j.rsci.2018.06.003
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    Identification of quantitative trait loci (QTLs) for grain mineral elements can assist in faster and more precise development of micronutrient dense rice varieties through marker-assisted breeding. In the present study, QTLs were mapped for Fe and Zn concentrations in two BC2F3 mapping populations derived from the crosses of O. sativa cv Swarna with two different accessions of O. nivara. In all, 10 and 8 QTLs were identified for grain Fe and Zn concentrations in population 1, and 7 and 5 QTLs were identified in population 2, respectively. Eighty percent of the QTLs detected in both populations were derived from O. nivara. Five QTLs for Fe and three QTLs for Zn explained more than 15% phenotypic variance either in interval or composite interval mapping. The locations of O. nivara derived QTLs such as qFe2.1, qFe3.1, qFe8.2 and qZn12.1 were consistently identified in both the populations. Epistatic interaction was observed only between RM106 and RM6 on chromosome 2 and between RM22 and RM7 on chromosome 3 for Fe concentration in population 1. Sixteen candidate genes for metal homeostasis were found to co-locate with 10 QTLs for Fe and Zn concentrations in both the populations. Most of the Fe and Zn QTLs were found to co-locate with QTLs for grain yield and grain quality traits. Some of the major effect QTLs identified can be used to improve rice grain Fe and Zn concentrations.

    Genome-Wide Survey and Expression Analysis of P1B-ATPases in Rice, Maize and Sorghum
    Zhiguo E, Tingting Li, Chen Chen, Lei Wang
    2018, 25(4): 208-217.  DOI: 10.1016/j.rsci.2018.06.004
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    P1B-type ATPase ion pumps that transport heavy metal ions across cellular membranes are essential for plant growth and development. To date, a genomic comparison overview of the family in rice, maize and sorghum is not yet available. In this study, a total of 31 heavy metal P1B-type ATPase (HMA) genes were identified, including 9 in rice, 11 each from maize and sorghum. They were classified into two distinct subfamilies based on their sequence composition and phylogenetic relationship. Four pairs of HMA genes were expanded via gene duplication with tandemly duplicated. Comprehensive analyses were performed to investigate the expression profiles of HMA genes in various tissues by using quantitative real-time PCR. Some HMA members exhibited abundant and tissue-specific expression patterns. Moreover, most of the genes were found to be differentially expressed under the Cu/Cd treatment. This study will facilitate further studies on P1B-type ATPase family and provide valuable hints for the functional validation in rice, maize and sorghum.

    Effects of Heat Stress at Vegetative and Reproductive Stages on Spikelet Fertility
    Cheabu Sulaiman, Moung-ngam Peerapon, Arikit Siwaret, Vanavichit Apichart, Malumpong Chanate
    2018, 25(4): 218-226.  DOI: 10.1016/j.rsci.2018.06.005
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    Seed-setting rate, yield components and grain quality traits of 169 accessions from an exotic rice germplasm were tested under high temperatures from 40 ºC to 45 ºC for 6 h during the daytime at the vegetative and reproductive stages, respectively. The results showed that heat stress significantly decreased the seed-setting rate of all the accessions, but the heat stress effects varied among accessions. Based on the decreases in seed-setting rate at high temperatures, N22 was the most tolerant, followed by AUS17, M9962, SONALEE and AUS16. Moreover, the reductions in seed-setting rate and yield under heat stress were more serious at the vegetative stage (45 d before heading) than at the booting stage (15 d before heading). In addition, heat stress also affected grain quality, especially by conferring chalkiness to most of the accessions, but SONALEE did not change much. The heat-tolerant accessions identified here and the phenotype protocols developed could be used in future genetic studies and breeding programmes focused on heat tolerance.

    Transcript Profiling Reveals Abscisic Acid, Salicylic Acid and Jasmonic-Isoleucine Pathways Involved in High Regenerative Capacities of Immature Embryos Compared with Mature Seeds in japonica Rice
    Kaizhuan Xiao, Xiaohui Mao, Yingheng Wang, Jinlan Wang, Yidong Wei, Qiuhua Cai, Hua’an Xie, Jianfu Zhang
    2018, 25(4): 227-234.  DOI: 10.1016/j.rsci.2018.06.006
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    Induced pluripotent cell mass plays a role in genetic transformation mediated by Agrobacterium. Mature seeds are more recalcitrant to the induction of suitable calli than immature embryos in rice, but the exact molecular mechanisms involved remain elusive. In this study, the morphological structure of calli induced from mature seeds and immature embryos were observed under a scanning electron microscope using a paraffin embedded technique. Meanwhile, a total of 2 173 up- and down-regulated genes were identified in calli induced from mature seeds and immature embryos by RNA-seq technique and furtherly confirmed by quantitative real-time PCR. The results revealed the remarkable morphological differences in calli induced from mature seeds and immature embryos, and plant hormone signal transduction and hormone biosynthesis pathways, such as abscisic acid, salicylic acid and jasmonic-isoleucine, were found to play roles in somatic embryogenesis. This study provided comprehensive gene expression sets for mature seeds and immature embryos that were served as an important platform resource for further functional studies in plant embryogenesis.