Rice Science

Characterization and Genetic Analysis of Rumpled and Twisted Leaf Mutant (rtl1) in Rice

FANG Yun-xia, SONG Xiu-juan, PENG You-lin, DONG Guo-jun, GUO Long-biao, ZENG Da-li, ZHANG Guang-heng, YAN Hong-lan, QIAN Qian

2011, 18(4): 243-249.

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A rumpled and twisted leaf 1 (rtl1) mutant was generated from a japonica cultivar Nipponbare by ethyl methanesulfonate treatment, which was characterized as rumpled and twisted leaf at the seedling stage. The F2 populations were constructed by crossing with indica cultivars TN1 and Zhefu 802, respectively. Genetic analysis demonstrated that the phenotype was controlled by a single recessive nuclear gene. The closely linked simple sequence repeat (SSR) marker RM1155 was obtained from bulked segregant analysis. Subsequently, sequence tagged site (STS) markers were developed using the published rice genome sequence. Finally, RTL1 was located between an STS marker T1591 and an SSR marker RM1359, at the distances of 0.48 cM and 0.96 cM, respectively. These results will facilitate the cloning of the target gene in further studies.

Prokaryotic Expression of Rice Ospgip1 Gene and Bioinformatic Analysis of Encoded Product

CHEN Xi-jun, LIU Xiao-wei, ZUO Si-min, MA Yu-yin, TONG Yun-hui1 PAN Xue-biao, XU Jing-you

2011, 18(4): 250-256.

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Using the reference sequences of pgip genes in GenBank, a fragment of 930 bp covering the open reading frame (ORF) of rice Ospgip1 (Oryza sativa polygalacturonase-inhibiting protein 1) was amplified. The prokaryotic expression product of the gene inhibited the growth of Rhizoctonia solani, the causal agent of rice sheath blight, and reduced its polygalacturonase activity. Bioinformatic analysis showed that OsPGIP1 is a hydrophobic protein with a molecular weight of 32.8 kDa and an isoelectric point (pI) of 7.26. The protein is mainly located in the cell wall of rice, and its signal peptide cleavage site is located between the 17th and 18th amino acids. There are four cysteines in both the N- and C-termini of the deduced protein, which can form three disulfide bonds (between the 56th and 63rd, the 278th and 298th, and the 300th and 308th amino acids). The protein has a typical leucine-rich repeat (LRR) domain, and its secondary structure comprises α-helices, β-sheets and irregular coils. Compared with polygalacturonase-inhibiting proteins (PGIPs) from other plants, the 7th LRR is absent in OsPGIP1. The nine LRRs could form a cleft that might associate with proteins from pathogenic fungi, such as polygalacturonase.

Quantitative Trait Loci for Yield Traits Located Between Hd3a and Hd1 on the Short Arm of Chromosome 6 in Rice

FAN Ye-yang, CHEN Chen, WU Ji-rong, CHENG Shi-hua, ZHUANG Jie-yun

2011, 18(4): 257-264.

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QTLs for heading date located in the region between Hd3a and Hd1 were detected using an F2:3 population developed from a residual heterozygous line (RHL) identified from the recombinant inbred lines of the indica rice cross Zhenshan 97B/Milyang 46. Linkage in coupling phase between the heading date QTLs and QTLs for yield traits detected in a previous study was found. Four more F2:3 populations were each developed from an RHL, which were homozygous at Hd3a and Hd1 but heterozygous in a portion of the intervals flanked by Hd3a and Hd1. QTLs for grain yield per plant, number of panicles per plant, number of grains per panicle and 1000-grain weight were detected in the heterozygous region. Five sets of near-isogenic lines (NILs) with overlapping heterogenous segments covering the interval RM6119-RM6779 were developed and used to validate and delimitate the QTLs. A QTL having a consistent effect for the number of grains per panicle was located within the interval RM19615-RM19652 that corresponded to a 514.4 kb region on chromosome 6. The same region might have pleiotropic effects on the other three yield traits analyzed, but the effects varied greatly among different populations and across different environments. This study suggests that it is possible to develop a population with little variation on heading date and to identify QTLs for yield traits that might not be associated with heading date by using information of the physical positions of DNA markers and cloned genes.

Mapping and Comparative Analysis of QTL for Rice Plant Height Based on Different Sample Sizes within a Single Line in a RIL Population

LIANG Yong-shu, GAO Zhi-qiang, SHEN Xi-hong, ZHAN Xiao-deng, ZHANG Ying-xin, WU Wei-ming, CAO Li-yong, CHENG Shi-hua

2011, 18(4): 265-272.

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To clarify the most appropriate sample size for obtaining phenotypic data for a single line, we investigated the main-effect QTL (M-QTL) of a quantitative trait plant height (ph) in a recombinant inbred line (RIL) population of rice (derived from the cross between Xieqingzao B and Zhonghui 9308) using five individual plants in 2006 and 2009. Twenty-six ph phenotypic datasets from the completely random combinations of 2, 3, 4, and 5 plants in a single line, and five ph phenotypic datasets from five individual plants were used to detect the QTLs. Fifteen M-QTLs were detected by 1 to 31 datasets. Of these, qph7a was detected repeatedly by all the 31 ph datasets in 2006 and explained 11.67% to 23.93% of phenotypic variation; qph3 was detected repeatedly by all the 31 datasets and explained 5.21% to 7.93% and 11.51% to 24.46% of phenotypic variance in 2006 and 2009, respectively. The results indicate that the M-QTL for a quantitative trait could be detected repeatedly by the phenotypic values from 5 individual plants and 26 sets of completely random combinations of phenotypic data within a single line in an RIL population under different environments. The sample size for a single line of the RIL population did not affect the efficiency for identification of stably expressed M-QTLs.

QTL Detection for Rice Grain Shape Using Chromosome Single Segment Substitution Lines

LI Sheng-qiang, CUI Guo-kun, GUAN Cheng-ran, WANG Jun, LIANG Guo-hua

2011, 18(4): 273-278.

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Rice grain shape is one of the important factors affecting grain quality and yield, but it is liable to be influenced by genetic backgrounds and environments. The chromosome single segment substitution lines (SSSLs) in rice have been considered as ideal populations to identify the quantitative trait loci (QTLs). In this study, 22 QTLs affecting rice grain shape were detected to be distributed on eight chromosomes except chromosomes 6, 9, 11 and 12 by using SSSLs. Among them, seven QTLs conditioned grain length, six conditioned grain width, five affected grain length-width ratio and four controlled grain thickness.

Identification for Heat Tolerance in Backcross Recombinant Lines and Screening of Backcross Introgression Lines with Heat Tolerance at Milky Stage in Rice

LIAO Jiang-lin, ZHANG Hong-yu, SHAO Xue-lian, ZHONG Ping-an, HUANG Ying-jin

2011, 18(4): 279-286.

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The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage. A total of 791 BC1F8 backcross recombinant lines, derived from the cross of Xieqingzao B / N22 // Xieqingzao B, were used as materials. Each rice line was separated evenly into two groups, and the heat tolerance of all rice lines were evaluated at natural high temperature in fields. The rice lines with heat tolerant index higher than 90% or lower than 40% were selected to compare the phenotypic characters and further identify heat tolerance at the early milky stage in a phytotron. Rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were analyzed by 887 simple sequence repeat markers that were evenly distributed on the 12 rice chromosomes. In the result, 12 (6 pairs) rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were obtained. Molecular marker analysis indicated that the genomic polymorphism between 703T and 704S was the smallest in the 6 pairs of rice lines, with only 16 polymorphic sites, including 22 different alleles. The application of these two backcross introgression rice lines for future study on the mechanisms of heat tolerance in rice at the milky stage will be theoretically beneficial in reducing the interference caused by genetic differences from experimental materials.

Genetic Analysis of Heading Date of Japonica Rice Cultivars in Southwest China

ZHOU Zhen-ling, WEI Xiang-jin, JIANG Ling, LIU Kai1 XU Da-yong, ZHAI Hu-qu, WAN Jian-min

2011, 18(4): 287-296.

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Heading dates of 26 native japonica rice cultivars in Southwest China were investigated, and their basic vegetative growth (BVG), photoperiod-sensitivities (PS) and temperature-sensitivities (TS) were analyzed under artificial short-day and natural long-day conditions in Nanjing, as well as artificially high temperature and naturally low temperature conditions in winter in Hainan. The results showed that the PS and TS varied among different cultivars. The BVGs of all the japonica cultivars were well situated, but differed within cultivars. Regression analysis showed a significant correlation between heading date and PS, indicating that PS was the main factor affecting heading date of japonica cultivars in Southwest China. Genetic analyses were conducted on these 26 cultivars using a set of heading date near isogenic lines as test lines. All the japonica cultivars carried the dominant early-heading gene Ef-1or Ef-1t, and most of these cultivars carried the dominant photoperiod sensitivity allele E1 or E1t, the PS of which was slightly weaker than E1. For the Se-1 locus, these cultivars mainly carried recessive photoperiod insensitivity gene Se-1e. In addition, the PS of 22 japonica varieties could be repressed or weakened by the recessive allele hd2, inhibiting the expression of E1 and Se-1. These results indicated that the heading date genotypes determined different PS and well situated BVG in japonica rice cultivars in Southwest China.

Establishment of Agrobacterium tumefaciens-Mediated Transformation System for Rice Sheath Blight Pathogen Rhizoctonia solani AG-1 IA

YANG Ying-qing1, 2, #, YANG Mei1, #, LI Ming-hai1, LI Yong1, HE Xiao-xia1, ZHOU Er-xun

2011, 18(4): 297-303.

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To construct the T-DNA insertional mutagenesis transformation system for rice sheath blight pathogen Rhizoctonia solani AG-1 IA, the virulent isolate GD118 of this pathogen was selected as an initial isolate for transformation. The conditions for transformation of isolate GD118 were optimized in five aspects, i.e. pre-induction time, co-culture time, acetosyringone (AS) concentration at the co-culture phase, co-culture temperature and pH value of induction solid medium (ISM) at the co-culture phase. Finally, a system of Agrobacterium tumefaciens-mediated transformation (ATMT) for R. solani AG-1 IA was established successfully. The optimal conditions for this ATMT system were as follows: the concentration of hygromycin B at 30 μg/mL for transformant screening, 8 h of pre-induction, 20 h of co-culture, 200 μmol/L of AS in ISM, co-culture at 25 °C and pH 5.6 to 5.8 of ISM at the co-culture phase. The transformants still displayed high resistance to hygromycin B after subculture for five generations. A total of 10 randomly selected transformants were used for PCR verification using the specific primers designed for the hph gene, and the results revealed that an expected band of 500 bp was amplified from all of the 10 transformants. Moreover, PCR amplification for these 10 transformants was carried out using specific primers designed for the Vir gene of A. tumefaciens, with four strains of A. tumefaciens as positive controls for eliminating the false-positive caused by the contamination of A. tumefaciens. An expected band of 730 bp was amplified from the four strains of A. tumefaciens, whereas no corresponding DNA band could be amplified from the 10 transformants. The results of the two PCR amplifications clearly showed that T-DNA was indeed inserted into the genome of target isolate GD118.

Effects of Rhizosphere Dissolved Oxygen Content and Nitrogen Form on Root Traits and Nitrogen Accumulation in Rice

ZHAO Feng1, 2, 3, #, XU Chun-mei1, #, ZHANG Wei-jian2, ZHANG Xiu-fu1, LI Feng-bo1, CHEN Jian-ping3, WANG Dan-ying1

2011, 18(4): 304-310.

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Dissolved oxygen and nitrogen form have important effects on rice root growth and nitrogen availability. An indica hybrid rice, Guodao 1, and a conventional japonica rice, Xiushui 09, were cultured in hypoxic nutrient solution with NH4NO3 or (NH4)2SO4 as the nitrogen source for six weeks in pools. A portion of the Guodao 1 seedlings after treatment in the pools for four weeks were transferred to a split-root system at different dissolved oxygen contents and cultured for an additional two weeks. Biomass, root morphological traits and nitrogen accumulation were recorded. Under the low rhizosphere dissolved oxygen content (0–1.0 mg/L), plant biomass was significantly increased under NH4NO3-N supply by about 69% in Guodao 1 and 41% in Xiushui 09 compared with those under NH4+-N alone. Similar results were observed for root number, maximum root length, root dry weight and root activity. Nitrogen accumulations in roots and shoots were increased by 60% and 52% for Guodao 1, and by 41% and 33% for Xiushui 09, respectively, in the NH4NO3-N treatment. In the split-root system, the high rhizosphere dissolved oxygen content (8.0–9.0 mg/L) promoted root growth and development. Root biomass was increased by 21.6%, root number by 27%, maximum root length by 14%, and root volume by 10%. Moreover, nitrogen accumulation in roots was increased by 11% under high rhizosphere oxygen conditions. In conclusion, enhanced dissolved oxygen content and combined ammonium-nitrate nitrogen source have positive effects on root growth and nitrogen accumulation of rice plants.

Assessment of System of Rice Intensification (SRI) and Conventional Practices under Organic and Inorganic Management in Japan

Tejendra CHAPAGAIN, Andrew RISEMAN, Eiji YAMAJI

2011, 18(4): 311-320.

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The System of Rice Intensification (SRI) is a production system that involves the adoption of certain changes in management practices for rice cultivation that create a better growing environment for the crop. This system was compared with conventional practices and assessed under organic and inorganic management. SRI practices showed significant response in root number, effective tillers per hill, days to flowering and Harvest Index. In addition, SRI was found effective in minimizing pest and disease incidence, shortening the crop cycle, and improving plant stand. Grain yield was not different from conventional method. Except for harvest index and plant lodging percentage, there were no significant effects from management treatments. Synergistic responses were noted when SRI practices were combined with organic management for plant height, number of effective tillers per hill, days to flowering and to maturity, improved panicle characteristics, lower plant lodging percentage, and higher harvest index that ultimately led to comparable grain yields. Net returns increased approximately 1.5 times for SRI-organic management regardless of the added labor requirements for weed control. However, comparatively higher grain yield from conventional-inorganic methods underscore the need for further investigations in defining what constitutes an optimum sets of practices for an SRI-organic systems specifically addressing grain yields, and weed management.

Simulating Phenology, Growth and Yield of Transplanted Rice at Different Seedling Ages in Northern Iran Using ORYZA2000

B. Amiri LARIJANI1, Z. T. SARVESTANI1, Gh. NEMATZADEH2, A. M. MANSCHADI3, E. AMIRI4

2011, 18(4): 321-334.

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Rice crop growth and yield in the north Iran are affected by crop duration and phenology. The purpose of this study was to calibrate and validate the ORYZA2000 model under potential production based on experimental data for simulating and quantifying the phenological development, crop duration and yield prediction of rice crop influenced by different seedling ages. In order to calibrate and validate the crop parameters of ORYZA2000 model, a two-year field experiment was conducted under potential growth condition for transplanted lowland rice during the 2008–2009 rice growing seasons, using three rice varieties with three seedling ages (17, 24 and 33 days old). The results showed that the seedling age changed crop duration from 7 to 10 d. The ORYZA2000 model could predict well, but consistently underestimated the length of growing period. The range in normalized root mean square error (RMSEn) values for each phenological stage was between 4% and 6%. From our evaluation, we concluded that ORYZA2000 was sufficiently accurate in simulation of yield, leaf area index (LAI) and biomass of crop organs over time. On average, RMSEn values were 13%?15% for total biomass, 18%?21% for green leaf biomass, 17%?20% for stem biomass, 16%?23% for panicle biomass and 24%?26% for LAI. The RMSEn values for final yield and biomass were 12%?16% and 6%?9%, respectively. Generally, the model simulated LAI, an exceeded measured value for younger seedlings, and best-fit was observed for older seedlings of short-duration varieties. The results revealed that the ORYZA2000 model can be applied as a supportive research tool for selecting the most appropriate strategies for rice yield improvement across the north Iran.

Involvement of Plasma Membrane H+ ATPase in Adaption of Rice to Ammonium Nutrient

ZHU Yi-yong, LIAN Juan, ZENG Hou-qing, Liou GAN, DI Ting-jun, SHEN Qi-rong, XU Guo-hua

2011, 18(4): 335-342.

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The preference of paddy rice for NH4+ rather than NO3ˉ is associated with its tolerance to low pH since a rhizosphere acidification occurs during NH4+ absorption. However, the adaptation of rice root to low pH has not been fully elucidated. The plasma membrane H+-ATPase is a universal electronic H+ pump, which uses ATP as energy source to pump H+ across the plasma membranes into the apoplast. The key function of this enzyme is to keep pH homeostasis of plant cells and generate a H+ electrochemical gradient, thereby providing the driving force for the active influx and efflux of ions and metabolites across the plasma membrane. This study investigated the acclimation of plasma membrane H+-ATPase of rice root to low pH. This mechanism might be partly responsible for the preference of rice plants to NH4+ nutrition. Key words: rice; ammonium nutrient; plasma membrane H+-ATPase

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