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    Research Paper
    Molecular Analysis of Rice CIPKs Involved in Both Biotic and Abiotic Stress Responses
    CHEN Xi-feng, GU Zhi-min, LIU Feng, MA Bo-jun, ZHANG Hong-sheng
    2011, 18(1): 1-9 . 
    Abstract ( )   PDF (23694KB) ( )  
    Plant calcineurin B-like (CBL) proteins have been proposed as important Ca2+ sensors and specifically interact with CBL-interacting protein kinases (CIPKs) in plant-specific calcium signaling. Here, we identified and isolated 15 CIPK genes in a japonica rice variety Nipponbare based on the predicted sequences of rice CIPK gene family. Gene structure analysis showed that these 15 genes were divided into intron-less and intron-rich groups, and OsCIPK3 and OsCIPK24 exhibited alternative splicing in their mature process. The phylogenetic analyses indicated that rice CIPKs shared an ancestor with Arabidopsis and poplar CIPKs. Analyses of gene expression showed that these OsCIPK genes were differentially induced by biotic stresses such as bacterial blight and abiotic stresses (heavy metal such as Hg2+, high salinity, cold and ABA). Interestingly, five OsCIPK genes, OsCIPK1, 2, 10, 11 and 12, were transcriptionally up-regulated after bacterial blight infection whereas four OsCIPK genes, OsCIPK2, 10, 11 and 14, were induced by all treatments, indicating that some of OsCIPK genes are involved in multiple stress response pathways in plants. Our finding suggests that CIPKs play a key role in both biotic and abiotic stress responses.
    Resistance of Antimicrobial Peptide Gene Transgenic Rice to Bacterial Blight
    WANG Wei, WU Chao, LIU Mei, LIU Xu-ri, HU Guo-cheng, SI Hua-min, SUN Zong-xiu, LIU Wen-zhen, FU Ya-ping
    2011, 18(1): 10-16 . 
    Abstract ( )   PDF (3505KB) ( )  
    Antimicrobial peptide is a polypeptide with antimicrobial activity. Antimicrobial peptide genes Np3 and Np5 from Chinese shrimp (Fenneropenaeus Chinensis) were integrated into Oryza sativa L. subsp. japonica cv. Aichi ashahi by Agrobacterium mediated transformation system. PCR analysis showed that the positive ratios of Np3 and Np5 were 36% and 45% in T0 generation, respectively. RT-PCR analysis showed that the antimicrobial peptide genes were expressed in T1 generation, and there was no obvious difference in agronomic traits between transgenic plants and non-transgenic plants. Four Np3 and Np5 transgenic lines in T1 generation were inoculated with Xanthomonas oryzae pv. oryzae strain CR4, and all the four transgenic lines had significantly enhanced resistance to bacterial blight caused by the strain CR4. The Np5 transgenic lines also showed higher resistance to bacterial blight caused by strains JS97-2, Zhe 173 and OS-225. It is suggested that transgenic lines with Np5 gene might possess broad spectrum resistance to rice bacterial blight.
    Transgenic Rice Plants Harboring Genomic DNA from Zizania latifolia Confer Bacterial Blight Resistance
    SHEN Wei-wei, SONG Cheng-li, CHEN Jie, FU Ya-ping, WU Jian-li, JIANG Shao-mei
    2011, 18(1): 17-22 . 
    Abstract ( )   PDF (3509KB) ( )  
    Based on the sequence of a resistance gene analog FZ14 derived from Zizania latifolia (Griseb.), a pair of specific PCR primers FZ14P1/FZ14P2 was designed to isolate candidate disease resistance gene. The pooled-PCR approach was adopted using the primer pair to screen a genomic transformation-competent artificial chromosome (TAC) library derived from Z. latifolia. A positive TAC clone (ZR1) was obtained and confirmed by sequence analysis. The results indicated that ZR1 consisted of conserved motifs similar to P-loop (kinase 1a), kinase 2, kinase 3a and GLPL (Gly-Leu-Pro-Leu), suggesting that it could be a portion of NBS-LRR type of resistance gene. Using Agrobacterium-mediated transformation of Nipponbare mature embryo, a total of 48 independent transgenic T0 plants were obtained. Among them, 36 plants were highly resistant to the virulent bacterial blight strain PXO71. The results indicate that ZR1 contains at least one functional bacterial blight resistance gene.
    Mapping QTLs for Drought Tolerance at Seedling Stage in Rice Using Doubled Haploid Population
    XU Qun, YUAN Xiao-ping, YU Han-yong, WANG Yi-ping, TANG Sheng-xiang, WEI Xing-hua
    2011, 18(1): 23-28 . 
    Abstract ( )   PDF (21234KB) ( )  
    QTLs for drought tolerance at the rice seedling stage were analyzed using a doubled haploid (DH) population consisted of 251 lines from the cross between a japonica parent Maybelle and an indica parent Baiyeqiu. A genetic linkage map with 226 SSR marker loci was constructed. Single-locus analysis following composite interval mapping (CIM) detected a total of five QTLs located on five different chromosomes of rice. Four QTLs were also detected following two-locus analysis, resolving two pairs of epistatic QTLs (E-QTLs) with positive and additive genetic effects. The results indicated that the alleles from the parent Baiyeqiu contributed DH population to improve drought tolerance at the seedling stage.
    Effect of H2O2 Pretreatment on Cd Tolerance of Different Rice Cultivars
    BAI Xiao-Juan, LIU Li-Juan, ZHANG Chun-hua, GE Ying, CHENG Wang-da
    2011, 18(1): 29-35 . 
    Abstract ( )   PDF (1085KB) ( )  
    The effect of H2O2 pretreatment on Cd tolerance and translocation of rice seedlings were studied using two rice cultivars (N07-6 and N07-63) differing in Cd tolerance. The contents of malondialdehyde (MDA), reduced glutathione (GSH), non-protein thiols (NPT), phytochelatins (PCs) and the activity of glutathione S-transferase (GST) were compared between the two cultivars exposed to various treatments. The results showed that 50 μmol/L Cd exposure significantly inhibited rice growth, enhanced the production of GSH, NPT, PCs and MDA, and increased the activity of GST, and there were significant differences between the two cultivars. More Cd was transported into the shoot of N07-6. The H2O2 pretreatment alleviated Cd toxicity by further increasing GSH, NPT and PCs contents, as well as the GST activity in roots. The increase degrees of these parameters in N07-63 were higher than those in N07-6, suggesting that the tolerance of N07-63 was enhanced more significantly than N07-6. Hydrogen peroxide reduced Cd translocation to rice shoot but affected the Cd content in root differently. From the above results, it may be speculated that there were remarkable differences in the Cd detoxification and response to the H2O2 pretreatment between the two cultivars.
    Paddy Husk as Support for Solid State Fermentation to Produce Xylanase from Bacillus pumilus
    Ranganathan KAPILAN, Vasanthy ARASARATNAM
    2011, 18(1): 36-45 . 
    Abstract ( )   PDF (2143KB) ( )  
    To optimize culture conditions for xylanase production by solid state fermentation (SSF) using Bacillus pumilus, with paddy husk as support, solid medium contained 200 g of paddy husk with 800 mL of liquid fermentation medium [xylan, 20.0 g/L; peptone, 2.0 g/L; yeast extract, 2.5 g/L; K2HPO4, 2.5 g/L; KH2PO4, 1.0 g/L; NaCl, 0.1 g/L; (NH4)2SO4, 2.0 g/L, CaCl2•2H2O, 0.005 g/L; MgCl2•6H2O, 0.005 g/L; and FeCl3, 0.005 g/L] at pH 9.0 was applied. The highest xylanase activity (142.0 ±0.47 U/g DM] was obtained on the 6th day at 30°C. The optimized paddy husk to liquid fermentation medium ratio was 2:9, and the optimized culture temperature was 40°C. When commercial Birchwood xylan was replaced with different concentrations of corncob, xylanase production was maximized (224.2 U/g DM) in the medium with 150 g/L corncob. Xylanase production was increased by sucrose, fructose and arabinose, whereas reduced by glucose, galactose, lactose and amylose. When organic nitrogen sources were replaced with locally available nitrogen sources such as groundnut powder or sesame seedcake powder or coconut seedcake powder or soy meal powder, the highest xylanase production (290.7 U/g DM) was obtained in the medium with soy meal powder and 16.0 g/L of soy meal powder was the optimum (326.5±0.34 U/g DM). Based on the optimization studies, B. pumilus produced 2.3 times higher xylanase activity. The medium cost was reduced from 2 458.3 to 178.3 SLR/kg and the total activity which could be obtained from 1 kg of the medium was increased from 48 624 to 220 253 Units.
    Strategies on Sample Size Determination and Qualitative and Quantitative Traits Integration to Construct Core Collection of Rice (Oryza sativa)
    LI Xiao-ling, LU Yong-gen, LI Jin-quan, XU Hai-ming, Muhammad Qasim SHAHID
    2011, 18(1): 46-55 . 
    Abstract ( )   PDF (10885KB) ( )  
    The development of a core collection could enhance the utilization of germplasm collections in crop improvement programs and simplify their management. Selection of an appropriate sampling strategy is an important prerequisite to construct a core collection with appropriate size in order to adequately represent the genetic spectrum and maximally capture the genetic diversity in available crop collections. The present study was initiated to construct nested core collections to determine the appropriate sample size to represent the genetic diversity of rice landrace collection based on 15 quantitative traits and 34 qualitative traits of 2 262 rice accessions. The results showed that 50–225 nested core collections, whose sampling rate was 2.2%–9.9%, were sufficient to maintain the maximum genetic diversity of the initial collections. Of these, 150 accessions (6.6%) could capture the maximal genetic diversity of the initial collection. Three data types, i.e. qualitative traits (QT1), quantitative traits (QT2) and integrated qualitative and quantitative traits (QTT), were compared for their efficiency in constructing core collections based on the weighted pair-group average method combined with stepwise clustering and preferred sampling on adjusted Euclidean distances. Every combining scheme constructed eight rice core collections (225, 200, 175, 150, 125, 100, 75 and 50). The results showed that the QTT data was the best in constructing a core collection as indicated by the genetic diversity of core collections. A core collection constructed only on the information of QT1 could not represent the initial collection effectively. QTT should be used together to construct a productive core collection.
    Review or Special Topic
    Advances in Mapping Loci Conferring Resistance to Rice Sheath Blight and Mining Rhizoctonia solani Resistant Resources
    ZENG Yu-xiang, JI Zhi-juan, MA Liang-yong, LI Xi-ming, YANG Chang-deng
    2011, 18(1): 56-66 . 
    Abstract ( )   PDF (733KB) ( )  
    Sheath blight (SB) caused by Rhizoctonia solani is one of the three major diseases of rice, and now has become the most severe disease causing rice yield loss in China. Breeding and use of varieties resistant to SB is crucial in controlling the disease, but the advances achieved have been limited due to the lack of highly SB-resistant rice germplasm. Genetic analysis revealed that the SB resistance in rice was a typical quantitative trait controlled by multi-genes. Although many QTLs conferring resistance to SB have been identified in recent years, most of the QTLs only showed small effects and few of them have been evaluated for utilization potential. Many R. solani-resistant resources have been found in wild rice species, microorganisms and other plant species. It is already known that the SB-resistance could be improved in transgenic rice plants by genetic transformation. This paper reviewed the genetic mapping of loci associated with resistance to rice SB, the evaluation of the potential of resistance QTLs, and the resistant resources found in various organisms besides rice. To develop SB-resistant rice varieties, it is important to develop and explore new resistant rice germplasms, fine map and evaluate resistance QTLs, and also to pay attention to various bio-resources showing resistance to R. solani.
    Short Communication
    Genetic Analysis and Gene Mapping of Short Root Mutant Rice ksr1
    NING Yong-qiang, DING Wo-na, ZHU Shi-hua, YU Hang-wei, YU Hang, LU Kai-xing
    2011, 18(1): 67-70 . 
    Abstract ( )   PDF (10976KB) ( )  
    A short root mutant ksr1 with the Kasalath background was isolated from an EMS-mutagenized population in rice. The root length of 6-day-old ksr1 seedlings was only about 20% of the wild type. Genetic analysis indicated that the short root phenotype of ksr1 was controlled by a recessive mutation in a single nuclear-encoded gene. To map the ksr1 mutation, an F2 population was generated by crossing the ksr1 mutant with Nipponbare. The KSR1 locus was linked to the SSR marker RM1223 on rice chromosome 4. Eight new SSR markers and two InDel markers were developed around this marker. KSR1 gene was further mapped to a 155 kb region, flanked by the InDel marker 4-24725K and the SSR marker RM17182.
    Detection of QTL for Cold Tolerance at Bud Bursting Stage Using Chromosome Segment Substitution Lines in Rice (Oryza sativa)
    LIN Jing, ZHU Wen-yin, ZHANG Ya-dong, ZHU Zhen, ZHAO Ling, CHEN Tao, ZHAO Qing-yong, ZHOU Li-hui, FANG Xian-wen, WANG Yan-ping, WANG Cai-lin
    2011, 18(1): 71-74 . 
    Abstract ( )   PDF (10249KB) ( )  
    The cold tolerance at the bud bursting stage (CTB) was evaluated at 5°C by using a set of 95 chromosome segment substitution lines (CSSLs) derived from an indica rice 9311 and a japonica rice Nipponbare with a genetic background of 9311. The result showed that six CSSLs had slightly stronger effect on CTB than 9311. Total four quantitative trait loci (QTLs) for CTB were preliminary mapped on chromosomes 5 and 7 by substitution mapping. qCTB-5-1, qCTB-5-2 and qCTB-5-3 were mapped in the region of RM267–RM1237, RM2422–RM6054 and RM3321–RM1054, which were 21.3 cM, 27.4 cM and 12.7 cM in genetic distance on rice chromosome 5, respectively. qCTB-7 was mapped in a 6.8-cM region of RM11–RM2752 on rice chromosome 7.
    Genotype × Environment Interaction for Iron Concentration of Rice in Central Java of Indonesia
    Suwarto, Nasrullah
    2011, 18(1): 75-78 . 
    Abstract ( )   PDF (839KB) ( )  
    To explore the effect of genotype and genotype × environment interaction on Fe concentration in rice grains, Fe concentrations of 10 genotypes were analyzed across eight paddy field environments during 2007–2008 using the AMMI-biplot method. Experiments were conducted using a randomized completely block design with three replications in eight environments. Results indicated that environment (E), genotype (G) and genotype × environment interaction (GE) significantly affected Fe concentration in rice grains. Environment explained 74.43 % of total (G+E+GE) variation, whereas G and GE captured 5.60% and 19.67%, respectively. Rice genotype Barumun was desirable in terms of the highest ability and stability for Fe concentration in rice grains. Environment in genotype Cilongok was the best representative of the overall environments and the most powerful to discriminate rice genotypes.