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    Review or Special Topic
    Differential Regulatory Mechanisms of CBF Regulon Between Nipponbare (Japonica) and 93-11 (Indica) During Cold Acclimation
    PAN Xiao-wu, LI Yong-chao, LI Xiao-xiang, LIU Wen-qiang, MING Jun, LU Ting-ting, TAN Jiang, SHENG Xin-nian
    2013, 20(3): 165-172.  DOI: 10.1016/S1672-6308(13)60121-3
    Abstract ( )   PDF (577KB) ( )  

    Nine CBF/DREB1 homologous genes in rice were obtained by BLAST search in the NCBI database, which share conserved amino acid sequences with DREB1 protein in Arabidopsis. Three CBF genes organized in tandem, named OsCBF1, OsCBF2 and OsCBF3, showed a transient induction in the process of cold acclimation, much stronger in indica rice 93-11 compared with japonica rice Nipponbare. The candidate downstream genes OsLIP5 and OsLIP9 were induced in 93-11 but not in Nipponbare. The differential expression of CBF regulon might be caused by polymorphisms within promoter sequences between these two rice varieties. These results could be useful for utilization of CBF/DREB1 genes and illustration of differences in chilling tolerance between indica and japonica rice varieties.

    Research Paper
    Purification and Identification of Glutathione S-transferase in Rice Root under Cadmium Stress
    ZHANG Chun-hua1, 2, WU Ze-ying3, JU Ting3, GE Ying2, 3
    2013, 20(3): 173-178.  DOI: 10.1016/S1672-6308(13)60114-6
    Abstract ( )   PDF (334KB) ( )  

    Cadmium (Cd) contamination in paddy soils poses a serious threat to the production and quality of rice. Among various biochemical processes related to Cd detoxification in rice, glutathione S-transferase (GST) plays an important role, catalyzing Cd complexation with glutathione (GSH) and scavenging reactive oxygen species (ROS) in cells. In this study, a hydroponic experiment was conducted to investigate the response of GST isozymes in rice roots upon Cd exposure. Results showed that the GST activity in rice roots was clearly enhanced by 50 μmol/L Cd treatment for 7 d. The GST isozymes were purified by ammonium sulphate precipitation, gel filtration chromatography and affinity chromatography. After being separated by SDS-PAGE and visualized by silver staining, GSTU6 was identified by in-gel digestion, MALDI-TOF-MS analysis and peptide mass fingerprint. The results confirm the vital function of tau class rice GST in Cd detoxification.

    Genetic Analysis and Gene Mapping of Multi-tiller and Dwarf Mutant d63 in Rice
    XUE Jing-jing, WU Shao-hua, ZHANG Hong-yu, XU Pei-zhou, WU Xian-jun
    2013, 20(3): 179-184.  DOI: 10.1016/S1672-6308(13)60130-4
    Abstract ( )   PDF (3241KB) ( )  

    A spontaneous mutation, tentatively named d63, was derived from the twin-seedling progenies of rice crossed by diploid SARIII and Minghui 63. Compared with wild-type plants, the d63 mutant showed multiple abnormal phenotypes, such as dwarfism, more tillers, smaller flag leaf and reduced seed-setting rate and 1000-grain weight. In this study, two F2 populations were developed by crossing between d63 and Nipponbare, d63 and 93-11. Genetic analysis indicated that d63 was controlled by a single recessive gene, which was located on the short arm of chromosome 8, within the genetic distance of 0.40 cM from RM22195. Hence, D63 might be a new gene as there are no dwarf genes reported on the short arm of chromosome 8.

    Screening of Rice Genes Interacting with p5b of Rice Black-Streaked Dwarf Virus
    LU Ying1, 2, YANG Jian 1, ZHANG Heng-mu1, CHEN Jian-ping1
    2013, 20(3): 185-190.  DOI: 10.1016/S1672-6308(13)60128-6
    Abstract ( )   PDF (488KB) ( )  

    Rice black-streaked dwarf virus (RBSDV) is a recognized member of the genus Fijivirus, family Reoviridae. Its genome has ten double-stranded RNA (dsRNA) segments (S1–S10), in which the fifth genome segment (S5) contains two open reading frames (ORFs) with a partially overlapping region. The second ORF of RBSDV S5 encodes a viral nonstructural protein named p5b with unknown function. To reveal the function of p5b, its gene was ligated into the bait plasmid pGBKT7 and an expression library containing rice cDNAs was constructed using plasmid pGADT7 for yeast two-hybrid assay. The bait protein p5b was detected in yeast by western blot, and the result of an auto-activation test showed that p5b could not autonomously activate the expression of reporter genes in yeast. Then the bait protein p5b was used for screening the cDNA expression libraries of rice. Gene fragments of some pivotal enzymes involved in photosynthesis, respiration and other important metabolic processes, were identified to interact with p5b in yeast, suggesting that these interactions may play roles in symptom development in infected plants.

    Development and Application of SCAR Markers for Discriminating Cytoplasmic Male Sterile Lines from Their Cognate Maintainer Lines in Indica Rice
    LU Chao1, LIU Jian1, JIANG Jian-hua1, Caleb Manamik BRERIA1, TAN He-lin1, Masahiko ICHII2, HONG De-lin1
    2013, 20(3): 191-199.  DOI: 10.1016/S1672-6308(13)60122-5
    Abstract ( )   PDF (362KB) ( )  

    The DNA fragments about 1 600 bp were amplified using random amplified polymorphism DNA (RAPD) primer OPA12 with the templates of mitochondrial DNA of Zhenshan 97A and Zhenshan 97B, and were sequenced. The nucleotide sequences and lengths of the fragments from Zhenshan 97A and Zhenshan 97B showed no difference. The precise length of the fragment was 1 588 bp. Sequence characterized amplification region (SCAR) primers were then developed to discriminate the cytoplasmic male sterile (CMS) lines and their maintainer lines. A specific 1 588 bp fragment could be amplified with SCAR primers, CHI19F2/CHI19R2 and CHI20F3/CHI23R3, in the mitochondrial DNA of Zhenshan 97A, but not Zhenshan 97B. Furthermore, the specific fragment could be also amplified from the total DNA from green leaf tissues of Zhenshan 97A with SCAR primers, but not Zhenshan 97B. With the corresponding primers, the specific fragment could also be amplified from the total DNA of green leaves of other two CMS lines with wild abortive type cytoplasm (CMS-WA), namely Zhenpin A and Tianfeng A, but not in their maintainer lines. Moreover, using total DNA as template, each of the four pairs of SCAR primers could also be used to amplify the 1 588 bp fragment in CMS-ID (Indonesia paddy type) line Ⅱ-32A, but not in II-32B, and the specific fragment was amplified from the DNA of both F1 and F2 seedlings of Shanyou 63. The results of detecting the genetic purity of a man-made mixture of the seeds of Zhenshan 97A using CHI20F3/CHI23R3 were completely consistent with the phenotypes. Taken together, these results indicated that the specific 1 588 bp-fragment amplified by CHI20F3/CHI23R3 was the unique amplification products of CMS mitochondrial DNA, and could be used to distinguish CMS-WA and CMS-ID lines from their corresponding maintainer lines at the seedling stage.

    Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice
    JIANG Jian-hua1, 2, CHEN Lan1, LIU Qiang-ming1, HE Ying-jun1, HONG De-lin1
    2013, 20(3): 200-206.  DOI: 10.1016/S1672-6308(13)60126-2
    Abstract ( )   PDF (253KB) ( )  

    To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration (GD) and productive panicle number per plant (PN) were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height (PH) in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat (SSR) marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03?9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.

    Confirmation of Novel Quantitative Trait Loci for Seed Dormancy at Different Ripening Stages in Rice
    Kazuhiro SASAKI1, 2, Yuri KAZAMA1, Youn CHAE1, Tadashi SATO1
    2013, 20(3): 207-212.  DOI: 10.1016/S1672-6308(13)60123-7
    Abstract ( )   PDF (343KB) ( )  

    Seed dormancy contributes resistance to pre-harvest sprouting. Effects on respective quantitative trait loci (QTLs) for dormancy should be assessed by using fresh seeds before germinability altered through storage. We investigated QTLs related to seed dormancy using backcross inbred lines derived from a cross between Nipponbare and Kasalath. Four putative QTLs for seed dormancy were detected immediately after harvest using composite interval mapping. These putative QTLs were mapped near C1488 on chromosome 3 (qSD-3.1), R2171 on chromosome 6 (qSD-6.1), R1245 on chromosome 7 (qSD-7.1) and C488 on chromosome 10 (qSD-10.1). Kasalath alleles promoted dormancy for qSD-3.1, qSD-6.1 and qSD-7.1, and the respective proportions of phenotypic variation explained by each QTL were 12.9%, 9.3% and 8.1%. We evaluated the seed dormancy harvested at different ripening stages during seed development using chromosome segment substitution lines (CSSLs) to confirm gene effects. The germination rates of CSSL27 and CSSL28 substituted with the region including qSD-6.1 were significantly lower than those of Nipponbare and other CSSLs at the late ripening stage. Therefore, qSD-6.1 is considered the most effective novel QTL for pre-harvest sprouting resistance among the QTLs detected in this study.

    Morphological and Anatomical Assessment of KDML 105 (Oryza sativa L. spp. indica) and Its Mutants Induced by Low-Energy Ion Beam
    2013, 20(3): 213-219.  DOI: 10.1016/S1672-6308(13)60129-8
    Abstract ( )   PDF (1358KB) ( )  

    Thai jasmine rice KDML 105 is consumed around the world. BKOS, PKOS and TKOS are new cultivars produced from low-energy ion beam induction in KDML 105. The purpose of this study is to compare the morphology and anatomy between KDML 105 and the three new cultivars. Seeds of the four cultivars were germinated and grown in pots until flowering phase. The plants’ organs were observed and the lengths of culms, ligules, leaves and panicles were measured. Leaf surface area was calculated and numbers of roots, spikelets and tillers were counted. BKOS and PKOS had significantly shorter culms than KDML 105 and TKOS. The largest leaf area was found in KDML 105 followed by TKOS, BKOS and PKOS, respectively. Numbers of roots and tillers in BKOS and TKOS were significantly fewer than those in KDML 105 and PKOS. The number of spikelets per plant in BKOS was the lowest among all cultivars. For anatomical comparison, cross sections of culms and roots were observed. All plants had a similar arrangement of tissues, but the number and size of cells were different. Furthermore, longitudinal sections of culms showed that the lengths of epidermal and parenchyma cells were directly related with the length of the culm. To compare the leaves, both stomata and epidermal cells were counted and the lengths of the guard cells were measured. The lengths of guard cells of BKOS and PKOS were shorter, but the stomatal density and the stomatal index were significantly greater than those of KDML 105. For TKOS, though the length of guard cells was shorter than that in KDML 105, the difference was not significant. However, the stomatal density and stomatal index were significantly higher than those in KDML 105.

    Effects of Nitrogen Fertilizer Level on Chlorophyll Fluorescence Characteristics in Flag Leaf of Super Hybrid Rice at Late Growth Stage
    LONG Ji-rui, MA Guo-hui, WAN Yi-zheng, SONG Chun-fang, SUN Jian, QIN Rui-jun
    2013, 20(3): 220-228.  DOI: 10.1016/S1672-6308(13)60138-9
    Abstract ( )   PDF (491KB) ( )  

    To compare the effects of slow-release nitrogen fertilizer at six different levels on the flag leaf chlorophyll fluorescence characteristics of super hybrid rice, a field fertilization experiment was conducted with super hybrid rice Y Liangyou 1 as a test material. The photosynthetic electron transport rate (ETR), effective quantum yield (EQY), photochemical quenching coefficient (qP), and non-photochemical quenching coefficient (NPQ) of flag leaves were measured at the initial heading, full heading, 10 d after full heading and 20 d after full heading stages. Results showed that the values of ETR, EQY and qP increased with rice development from initial heading to 20 d after full heading, whereas the NPQ decreased. During the measured stages, ETR, EQY and qP increased initially and then decreased as nitrogen application amount increased, but they peaked at different nitrogen fertilizer levels. The maximum ETR and EQY values appeared at the treatment of 135 kg/hm2 N. In conclusion, the optimum nitrogen amount for chlorophyll fluorescence characteristics of super hybrid rice was 135?180 kg/hm2.

    Analysis and Simulation of Plant Type on Canopy Structure and Radiation Transmission in Rice
    HU Ning1, LU Chuan-gen2, YAO Ke-min1, CHEN Jing2, ZHANG Xiao-cui3
    2013, 20(3): 229-237.  DOI: 10.1016/S1672-6308(13)60127-4
    Abstract ( )   PDF (354KB) ( )  

    Three typical hybrid rice cultivars, together with three artificially modified plant types by the application of N fertilizer during the elongation of the two uppermost leaves were used to analyze how the plant type affected the layered leaf area and radiation transmission. Plant type factors, layered leaf area and radiation distribution were measured at the full heading, 10 d and 25 d after full heading stages, respectively. A model for calculating the layered leaf area from plant type factors was established and validated to determine the effects of plant type factors on the layered leaf area for the three hybrids. Furthermore, the relationship between layered leaf area and radiation transmission was established by using the radiation transmission model. The effects of the plant type factors on the radiation transmission for the three hybrids were evaluated by using this model. Finally, a method was established to describe the canopy structure, such as the layered leaf area index and the radiation distribution in the rice canopy. Key words: rice; plant type; layered leaf area index; radiation; simulation model

    Short Communication
    Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings
    WANG Chong-qing1, WANG Tao1, MU Ping2, LI Zi-chao2, YANG Ling1
    2013, 20(3): 238-242.  DOI: 10.1016/S1672-6308(13)60124-9
    Abstract ( )   PDF (234KB) ( )  

    Mercury (Hg) is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth. However, little is known about the molecular genetic basis for root growth under excess Hg2+ stress. To map quantitative trait loci (QTLs) in rice for Hg2+ tolerance, a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution. Relative root length (RRL), percentage of the seminal root length in +HgCl2 to –HgCl2, was used for assessing Hg2+ tolerance. In a dose-response experiment, Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L. Three putative QTLs for RRL were detected on chromosomes 1, 2 and 5, and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance. The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.