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10 May 2016, Volume 30 Issue 3 Previous Issue    Next Issue
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Bioinformatic and Expression Analysis of Rice Ubiquitin-conjugating Enzyme Gene Family Xin LIU, Heng ZHANG, Hu-fei KAN, Li-shuai ZHOU, Hao HUANG, Lin-lin SONG, Huan-chen ZHAI, Jun ZHANG, Guo-dong LU 2016, 30(3): 223-231.  DOI: 10.16819/j.1001-7216.2016.5177 Abstract ( )   HTML ( )   PDF (2244KB) ( )   The ubiquitin / proteasome system plays an important role in plant growth and development, morphogenesis and disease resistance. Recent studies have shown that some pathogens can mimic the host plant ubiquitin / proteasome system components to achieve their own purposes. Ubiquitin-conjugating enzyme is the second enzyme in the ubiquitination process and is indispensable for the plant ubiquitin/proteasome system. Previous studies showed that there are 48 predicted ubiquitin-conjugating enzyme genes in rice genome. In order to preliminarily elucidate the functions of rice ubiquitin-conjugating enzyme genes in plant disease resistance, bioinformatic, RNA-seq and qRT-PCR methods were used to analyze characteristics and expression patterns of rice ubiquitin-conjugating enzyme gene family. Phylogenetic tree analyses indicate that the 48 rice ubiquitin-conjugating enzyme genes can be divided into 3 groups, 7 sub-groups in total. Protein domain analysis showed that ubiquitin-conjugating enzyme genes mainly consist of a big ubiquitin-conjugating enzyme catalytic domain. Expression analysis in silico suggested that most of the rice ubiquitin-conjugating enzymes can be induced by blast fungus infection. Plant cis-acting elements analysis indicated that four pathogen resistance cis-acting elements and one hypersensitivity reaction cis-acting element have high distribution in the promoter region of the 48 rice ubiquitin-conjugating enzyme genes. RNA-seq data from compatible and incompatible monogenic rice after rice blast fungus infection showed that 44 rice ubiquitin-conjugating enzyme genes were expressed at 36 hours after treatment, among which more than 50% were highly expressed genes. qRT-PCR analysis showed that expression of some ubiquitin-conjugating enzyme genes can be induced by the inoculation of rice blast fungus both in compatible and incompatible monogenic rice. However, in incompatible rice the expression of rice ubiquitin-conjugating enzyme genes tends to be inhibited after rice blast fungus inoculation.

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Genetic Analysis and Gene Mapping of a Heading-delayed Mutant dth9 in Rice (Oryza sativa L.) Wei-jun YE, Shi-kai HU, Li-wen WU, Long-biao GUO, Qian QIAN 2016, 30(3): 232-238.  DOI: 10.16819/j.1001-7216.2016.5156 Abstract ( )   HTML ( )   PDF (885KB) ( )   A heading-delayed mutant, dth9 (days to heading 9)was identified from an ethyl methylsulfonate (EMS)-induced 93-11 mutant library. The heading date of dth9 delayed about 50 days compared to the wild-type and there was no significant difference in other agronomic traits. Genetic analysis showed that the phenotype of dth9 was controlled by a single recessive nuclear gene. To map this gene, two F2 populations were generated by crossing the dth9 mutant with Nipponbare or Wuyunjing 7 as mapping populations. By using SSR markers and eight new designed InDel markers, DTH9 was narrowed to a 240kb interval between the markers D9-9 and D9-17 near the centromere of chromosome 9, there were no reports about genes associated with heading date in this interval. In addition, the expression levels of genes related to heading date were significantly decreased in dth9 by quantitative real-time PCR analysis.

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Characterization and Gene Mapping of Lesion Mimic Mutant wy3 in Rice Hong-Gen ZHANG, Mao-yu WANG, Li-jia ZHANG, Ya HU, Jia-qi MA, Yi-fan ZHANG, Shu-zhu TANG, Guo-hua LIANG, Ming-hong GU 2016, 30(3): 239-246.  DOI: 10.16819/j.1001-7216.2016.5176 Abstract ( )   HTML ( )   PDF (1494KB) ( )   A lesion mimic mutant wy3 was obtained from the progeny of a japonica variety Wuyujing 3 by natural mutation. The lesions were first observed on the leaves at the seedling stage, then spread gradually to the whole leaf at the initial tillering stage. Compared with the wild type(WT), the plant height, the number of effective tiller, panicle length, grain number per panicle and seed setting rate of wy3 were reduced significantly. The shading assay showed that the lesions on leaves of wy3 were induced by natural light. Compared with the wild type, the photosynthetic pigment and the net photosynthetic rate of wy3 were significantly reduced, but the SOD activity, POD activity, CAT activity and MDA content of wy3 were significantly higher than those of WT. Trypan blue staining experiments showed that there were a large number of dead cells in the mutant lesion. Genetic analysis suggested that the phenotype of wy3 was controlled by a single recessive nuclear locus, and the target gene was mapped between markers W2-17 and W2-18 with the physical distance of 28 kb on chromosome 2. Sequence analysis revealed that the mutated gene in wy3 had a single nucleotide deletion at the 375th in CDS of LOC_Os02g02000, resulting in a premature termination of translation of the target gene, which is an new allele of OsHPL3.

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QTL Analysis for Heading Date in Rice (Oryza sativa L.) Under Different Temperatures and Light Intensities Jun WANG, Jin-yan ZHU, Yong ZHOU, Jie YANG, Fang-jun FAN, Wen-qi LI, Fang-quan WANG, Wei-gong ZHONG, Guo-hua LIANG 2016, 30(3): 247-255.  DOI: 10.16819/j.1001-7216.2016.5172 Abstract ( )   HTML ( )   PDF (1693KB) ( )   QTLs for heading date were identified with 85 rice chromosome single segment substitution lines (CSSSLs) derived from Nipponbare as donor parent in the background of Guanglu’ai 4, for means comparisons between CSSSLs and the recipient parent Guanglu’ai 4 by one-way analysis of variance and Dunnett’s test. A total of 40 QTLs for heading date were identified on all 12 chromosomes under two different temperatures and light intensities with a significance of P≤0.001. Twenty-one QTLs for heading date were mapped in the two environments, 15 QTLs only in Nanjing, and four only in Sanya. Thirty-six QTLs were mapped in Nanjing, the additive effects of which ranged from 2.8 d to 15.7 d, the additive effect percentages from 3.8% to 21.1%; 25 QTLs were mapped in Sanya, the additive effect of which ranged from 1.8 to 12.1 d, the additive effect percentages from 1.7% to 11.3%. The results are important for the QTLs cloning and breeding of new high-quality rice variety in different environments.

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Development and Identification of Insect Resistant Transgenic Rice with Cry30Fa1 Gene Hai-peng WANG, Xiao-xi HUANG, Yue-yang LIANG, Jun ZHU, Cui-xia ZHANG, Xiu-mei WANG, Chang-wei GONG, Ai-ping ZHENG, Qi-ming DENG, Shuang-cheng LI, Ling-xia WANG, Ping LI, Shi-quan WANG 2016, 30(3): 256-264.  DOI: 10.16819/j.1001-7216.2016.5190 Abstract ( )   HTML ( )   PDF (2421KB) ( )   Modified Cry30Fa1, a Bacillus thuringiensis (Bt) gene encoding a high-efficiency insecticidal protein to the brown planthopper(BPH),was introduced into Shuhui 818(R818) by Agrobacterium-mediated genetic transformation and 46 transgene lines were obtained. We confirmed the valid transformation by RT-qRCR and Western blot at transcriptional level and translational level, and fixed the stable expression Cry30Fa1 in homozygosis. The classical pedigree breeding methods were also used to select the important agronomic traits in transgenic lines. Furthermore, we evaluated the resistance to BPH of different lines in growth chamber and field, and found that the R818-Cry30Fal displayed higher resistance than untransformed R818 in seedling stage. We also observed the reduced population of BPH feeding the transgenic lines, suggesting that the transformed Cry30Fa1 enhanced resistibility to BPH in rice. We cultivated new BT protein transgenic rice restorer line R818-Cry30Fal, which may provide new BPH resistance material to three line hybrid rice breeding and enrich BPH resistance germplasm resources in rice.

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Sequence Variation of Functional Fragment in Pita Gene for Rice Blast Resistance in Yunnan Rice Landraces Ji-qiong MA, Yi YANG, Yi-ding SUN, Yan-yan WANG, Ming-hui XU 2016, 30(3): 265-272.  DOI: 10.16819/j.1001-7216.2016.5188 Abstract ( )   HTML ( )   PDF (517KB) ( )   Identification and analysis of the variations of rice blast resistance gene sequence is the basis to dig into the genetic resources of the rice blast resistance. In this paper, 609 bases in the second code functional region of the rice blast resistance gene Pita were analyzed using 218 rice landraces from 56 counties of Yunnan Province. A total of 18 nucleotide variations were found in the sequence and the ORFs of 218 rice accessions were grouped into 46 haplotypes and 28 proteins types. Pita-H1 (17.89%), Pita-H2(29.82%) and Pita-H6(20.18%) were high-frequency types in Yunnan, while other types were at low frequency (0.46%-3.67%). So the advantage haplotypes in Yunnan were Pita-H1, Pita-H2 and Pita-H6 (totally 67.89%). A total of 61 rice landraces carrying the resistance gene Pita, the base functional site 2752 was G with the rate of 27.98%. The sequence of Pita in 39 resistance varieties was identical with the sequence obtained from the Vietnamese resistance variety Tetep. The distribution of resistance gene Pita in rice subspecies or ecotypes was unbalanced. The distribution frequency of indica was 35.06%, japonica 24.11%, rice 31.03%, upland rice 21.92%, no-glutinous rice 30.77%, glutinous rice 18.37%. The distribution of blast resistance gene Pita in Yunnan Province featured wide distribution and small concentration. Pita gene was detected in 36 counties of Yunnan Province. The distribution frequency in southern Yunnan was higher than other area. Moreover, some counties were of high distribution frequency. The resistance gene Pita was not detected in seven rice varieties growing over 2200 m elevation.

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Effects of Nitrogen Application on Accumulation and Translocation of Non-structural Carbohydrates in Internodes and Sheaths of Rice Jun-feng PAN, Bo WANG, Ke-hui CUI, Jian-liang HUANG, Li-xiao NIE 2016, 30(3): 273-282.  DOI: 10.16819/j.1001-7216.2016.5128 Abstract ( )   HTML ( )   PDF (1151KB) ( )   Two indica rice varieties, Liangyoupeijiu (LYP9) and Yangdao 6 (YD6), were grown in pots under low (N1) and high (N2) nitrogen application rates. The accumulation and translocation of non-structural carbohydrates (NSC) in the top-most three internodes and leaf sheaths of main stems and its contributions to grain yield were investigated. 1) Compared with N2 treatment, N1 treatment enhanced NSC translocation of the second and third internodes and sheaths in LYP9 during the early grain filling stage, and also increased the apparent transferred mass of NSC (ATMNSC) of the three internodes from the top and sheaths in YD6 and the third internode from the top and sheath in LYP9, respectively. However, N1 treatment had no obvious effect on ATMNSC of the top first and second internodes and sheaths in LYP9. Noticeably, N1 treatment increased the apparent contributions of NSC to grain yield (ACNSC) of the three internodes and sheaths in both two varieties. 2) Except the top-most third sheath in LYP9, the ATMNSC and ACNSC of sheaths were higher than those of internodes in both two varieties under N1 and N2 treatments. 3) Under N1 and N2 treatments, ATMNSC and ACNSC of the top-most second and third internodes and sheaths, and total ATMNSC and ACNSC of the three internodes and sheaths in LYP9 were higher than those in YD6, respectively. 4) Under N1 treatment, the top-most second and third internodes and sheaths totally contributed 92% and 91% of total ATMNSC and ACNSCof the three internodes and sheaths in LYP9, and 75% and 76% in YD6. Under N2 treatment,the top-most second and third internodes and sheaths totally contributed 90% and 91% in LYP9, and no NSC translocation from the top-most second and third internodes and totally accounted for 77% of total ACNSC. Our results indicated that ATMNSC of the three internodes and sheaths showed genotypic variation and depended on internode/sheath, and was affected by N application rate. Optimizing N fertilizer application and selecting suitable rice variety might enhance pre-anthesis NSC accumulation and post-anthesis NSC translocation, which could further increase rice yield potential and nitrogen use efficiency, especially stability of grain yield under adverse environments and nitrogen fertilizer-reducing practice.

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Relation of Plant Type Traits with Yield and Quality in the RIL Population Derived from Cross Between Chinese Rice Variety and Japanese Rice Variety Hai XU, Yan-long GONG, Yuan-ye XIA, Zhi-min DU, Zhi-qiang YAN, Hua-jie WANG, Wen-fu CHEN, Zheng-jin XU 2016, 30(3): 283-290.  DOI: 10.16819/j.1001-7216.2016.5174 Abstract ( )   HTML ( )   PDF (523KB) ( )   The F9 recombinant inbreed lines population (RIL population) derived from the cross between Liaojing 5, the most representative rice variety with erect panicle type in the northeast of China, and Akita Komachi, the famous rice varieties with curved panicle type and good quality in Japan, were constructed through single seed descent method to study the variation of plant type traits and their relation with rice yield and quality in the hybrid progenies of cross between typical Chinese rice variety and Japanese rice variety. The results showed that segregation and recombination occurred in plant-type, yield and quality traits in the RIL population. Plant height, the length of top third and fourth internodes and the leaf angle and yield were significantly positively correlated. The higher the plant height, the greater the degree of curve of the panicle, and the narrower the three top leaves, the better processing quality and appearance quality. The correlation between taste value and the vast majority of plant type traits was not significant, and only the width of top third leaf, the number of secondary rachis branches and grain density were negatively significantly correlated with taste value. Further analysis of the relation between grain yield and quality revealed that higher yield led to higher head milled rice rate, but worse taste. The plant type traits and yield and quality characters were closely related, despite the yield and taste value were difficult to unity, a tiny fraction of lines with high yield and good taste could be found in the RIL population. The lines with high yield and good taste mainly featured long panicle and top internode.

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Effects of MeJA on the Physiological Characteristics of japonica Rice Wuyunjing 24 and Ningjing 3 During Early Grain Filling Stage Under Heat Stress Xia LIU, She TANG, Zhi DOU, Gang-hua LI, Zheng-hui LIU, Shao-hua WANG, Cheng-qiang DING, Yan-feng DING 2016, 30(3): 291-303.  DOI: 10.16819/j.1001-7216.2016.5063 Abstract ( )   HTML ( )   PDF (2833KB) ( )   Methyl jasmonate (MeJA) was used on the conventional japonica rice varieties Wuyunjing 24 and Ningjing 3 to study its effects on rice physiological characteristics under high temperature stress during early grain filling stage. The results indicated that MeJA could increase the accumulation of soluble sugar in rice leaf and keep the osmotic balances. Furthermore, MeJA increased the stomatal conductance (Gs) and transpiration rate (Tr), which accordingly reduced the temperature of leaf and panicle and further effectively alleviated the high temperature damages. Exogenous MeJA reduced the heat damages to the photosynthetic system, thereby leading to the increased PSⅡ maximum quantum yield (Fv /Fm), photochemical efficiency (ΦPSⅡ), photosynthetic electron transport rate (ETR), energy ratio of photochemical reactions (Pr) and net photosynthetic rate(Pn). Increased grain weight and seed setting rate were found in those MeJA treated rice plants and antioxidant enzyme activity analysis showed that when exposed to high temperature for 12 days, superoxide dismutase(SOD) and peroxidase(POD) antioxidant enzyme activities of Wuyunjing 24 were decreased, while SOD and POD activities of Ningjing 3 in late stage of high-temperature treatment were greatly increased compared to the CK. The results indicated that MeJA enhanced the activities of SOD and POD and reduced the accumulation of malonaldehyde(MDA), which ultimately increased the membrane stability. In conclusion, exogenous MeJA could reduce the rice canopy temperature and effectively relieve heat stress injury to plant physiological characteristics. Furthermore, exogenous MeJA could promote recovery function during recovery stage and finally mitigate yield losses.

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Expression Characteristics and Sequence Variation Analysis of Glutamine Synthetase Gene in Grain of japonica Rice with Transgressive Variation Zhen-hua XU, Ying QU, Hai-ying LIU, Li-nan ZHU, Zhong-chen ZHANG, Zheng-xun JIN 2016, 30(3): 304-312.  DOI: 10.16819/j.1001-7216.2016.5150 Abstract ( )   HTML ( )   PDF (2045KB) ( )   The transgressive variants derived from rice varieties with significant difference in grain protein content were used to investigate the expression level and structure of glutamine synthetase gene(GS), activity of glutamine synthetase and protein accumulation characteristics during grain filling. The results showed that transgressive variants could be obtained through successive directive selection of grain protein content, because the grain protein content was closely related to corresponding genotype. During grain filling, the activity of glutamine synthetase followed a single-peak curve, highly correlated with grain protein content and significantly differed between parents and progenies. GS1.3 and GS2 genes, in transgressive variants and their parents with different protein content, exhibited similar transcription trend during grain filling, that is, the transcription level increased 15-20 days before heading and then decreased gradually. Moreover, the grain protein content was closely related to GS1.3 and GS2 expression levels. The varieties with higher GS transcription level showed higher protein content compared with their parents. In addition, although GS1.3 and GS2 gene sequences showed high conservation, the gene sequence and protein sequence of GS1.3 and GS2 were not completely identical in different varieties, and there are some single nuclear polymorphisms. Random base variation as well as changes in codon and amino acids might occur because inter-variety sexual hybridization causes base substitution during segregation and stability.

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Effects of Cold Stress During Booting Stage on Dry Matter Production of Rice in Cold Region Shi-qiang WANG, Hai-hong ZHAO, Chang-liang XIAO, Li-ming ZHAO, Chun-mei GU, Yong-guang NA, Bao-sheng XIE, Shi-hua CHENG 2016, 30(3): 313-322.  DOI: 10.16819/j.1001-7216.2016.5187 Abstract ( )   HTML ( )   PDF (850KB) ( )   To reveal the effects of chilling at the booting stage on rice dry matter production, 30 main rice cultivars (lines) in Heilongjiang Province were selected and subjected to chilling stress (17°C cold water irrigation) for 20 days. The results showed that the filled grain number per hill, seed setting rate, 1000-grain weight, and grain yield of all cultivars decreased under cold water irrigation at booting stage. The materials were classified as grades 1, 3, 5, 7 and 9 according to relative seed setting rate. Most of them belonged to grades 7 and 9, accounting for 30% of the total, while the fewest cultivars belonged to grade 1, occupying 10%. The cold water stress decreased dry matter accumulation from heading to maturity and its ratio, crop growth rate, net assimilation rate, filled grain number per square centimeter leaf area, harvest index, leaf area index, leaf basic angle of flag leaf, drooping angle of flag leaf, drooping angle of second leaf from top, drooping angle of third leaf from top. However, the cold water stress increased the ratio of leaf area of top three leaves. The correlation analysis results showed that the relative seed setting rate was significantly positively correlated with the cold water response indices(CRI) of harvest index after heading(r=0.96**), grain yield(r=0.91**),filled grain number per square centimeter leaf area(r=0.84**), and dry matter accumulation(r=0.48**); this rate was also positively correlated with the CRI of crop growth rate(r=0.44*), net assimilation rate(r=0.44*), and ratio of dry matter accumulation from heading to maturity(r=0.43*). In conclusion, the reduction of rice dry matter production under cold water stress during early grain filling largely varied with rice cultivar. The cold tolerant germplasm was insensitive to cold water stress in dry matter accumulation, ratio of dry matter accumulation from heading to maturity, crop growth rate, net assimilation, filled grain number per square centimeter leaf area, harvest index after heading, which might be attributed to its important morphological specificity and physiological mechanism in maintaining grain yield under cold water stress at the booting stage.

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Changes in Safe Production Dates and Heat-light Resources of Double Cropping Rice in Jiangxi Province in Recent 30 Years Wei-sheng LÜ, Yong-jun ZENG, Qing-hua SHI, Xiao-hua PAN, Shan HUANG, Qing-yin SHANG, Xue-ming TAN, Mu-ying LI, Shui-xiu HU, Yan-hua ZENG 2016, 30(3): 323-334.  DOI: 10.16819/j.1001-7216.2016.5157 Abstract ( )   HTML ( )   PDF (939KB) ( )   Ascertaining the change rules of safe production dates and heat-light resources of rice is an important basis for high use efficiency of heat-light resources, and high and stable production. In this study, the daily mean temperatures and sunshine hours during the past 30 years (1984—2013) provided by 15 meteorological stations in different ecological regions in Jiangxi Province (Northern Jiangxi, Central Jiangxi and Southern Jiangxi) were analyzed. According to the critical temperature indices for rice safe production dates, the change rules of safe production dates and heat-light resources of double rice with 50% and 80% guarantee rates were provided. The results showed that the safe production dates and heat-light resources changed obviously between the first 15 years(1984—1998) and the second 15 years(1999—2013), and there were certain differences among different regions. Compared with the first 15-year period, the safe sowing dates of early rice seedlings with film-mulching in the second 15-year period were ten-day ahead of time(with the tendency of -4.16 d 10a-1, the same as below), and those of direct seedling shifted to four days earlier(-3.17 d 10a-1); the safe transplanting dates were two-day ahead of time(-2.21 d 10a-1). For late rice, the safe maturity dates were delayed by eight days (3.56 d 10a-1), while those of full heading delayed unobviously. The safe production season for the early rice with film-mulching and direct seedling extended by eighteen (7.72 d 10a-1) and eleven (6.73 d 10a-1) days, respectively. During the safe production season, daily mean temperature increased obviously, accumulated temperature added remarkably, and sunshine hours changed unobviously.Monitoring data showed that, practical production dates were different from the safe production dates, though the practical production dates were adjusted correspondingly in recent years. So the safe production dates under 80% guarantee rate over the past 30 years were obtained by each meteorological stations, which can be referred in production arrangement, planting patterns and varieties collocation for double rice in the regions nearby. Finally, according to the trends of climate changes, the possible adaptive strategies of agronomic measures were discussed.