Alterations of mitochondrial protein assembly and jasmonic acid biosynthesis pathway in Honglian (HL)-type cytoplasmic male sterility rice.

It has been suggested that the mitochondrial chimeric gene orfH79 is the cause for abortion of microspores in Honglian cytoplasmic male sterile rice, yet little is known regarding its mechanism of action. In this study, we used a mass spectrometry-based quantitative proteomics strategy to compare the mitochondrial proteome between the sterile line Yuetai A and its fertile near-isogenic line Yuetai B. We discovered a reduced quantity of specific proteins in mitochondrial complexes in Yuetai A compared with Yuetai B, indicating a defect in mitochondrial complex assembly in the sterile line. Western blotting showed that ORFH79 protein and ATP1 protein, an F(1) sector component of complex V, are both associated with large protein complexes of similar size. Respiratory complex activity assays and transmission electron microscopy revealed functional and morphological defects in the mitochondria of Yuetai A when compared with Yuetai B. In addition, we identified one sex determination TASSELSEED2-like protein increased in Yuetai A, leading to the discovery of an aberrant variation of the jasmonic acid pathway during the development of microspores.

WITHDRAWN: Study on tolerance to ischemia-reperfusion injury and protection of ischemic preconditioning of type 1 diabetes rat heart.

The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.biomag.2010.09.004. The duplicate article has therefore been withdrawn.

[Construction of T7 phage display library from the anther of Honglian hybrid line of rice].

Phage display is a powerful method to study protein-protein interactions. In order to study the molecular mechanism of cytoplasmic male sterility and fertility restoration in Honglian rice, the mRNA was isolated with PolyA Tract mRNA Isolation Kit from the anther of F1 hybrid rice and the double strand (ds) cDNA was synthesized by reverse transcription. Then the directional EcoRI /Hind III linkers were ligated into the ends of ds cDNA and the ds cDNA was further digested with EcoR I and Hind, which resulted in ds cDNA with EcoR I and Hind III ends. The digested ds cDNA fragments longer than 300 bp in length were fractionated with Mini Column, then ligated into the T7 Select 10-3b vertor with EcoR I and Hind III ends. After packaging in vitro, the T7 Select 10-3b vertor was transformed into BL T5403 to construct the T7 phage display library. Analysis showed that the library contained 1.03 x 106 clones per microliter, and approximately 100% of the clones in library was recombinant. The titer of the amplied library was 2.14 x 1012 pfu/mL, and the insert length of the recombinants over 300 bp was about 97%.

[The editing sites in the transcripts of mitochondrial atp6 gene of maize sterile lines and maintainer line].

Using maize (Zea mays L.) cytoplasmic male-sterile lines T Huang Zao Si, C Huang Zao Si, S Huang Zao Si and maintainer line N Huang Zao Si as the plant materials, editing sites in the conservative area of mitochondrial atp6 gene transcripts of the 4 experimental materials' tassels, of which microspores had developed to uni-nucleate stage, were analyzed. The results showed that DNA sequences of the T, C and S male-sterile cytoplasms were completely unanimous, while being compared with the N-cytoplasm, all the sequences were similar except for the 27th and 28th nucleotides. However, the cDNA sequences of each cytoplasm were not always the same. By comparing DNA and cDNA sequences, we found that within the conservative area of atp6 gene transcripts there were 19, 22, 20 and 19 editing sites in the N, T, C and S cytoplasms, respectively. The 4 cytoplasms also shared 18 sites. The majority of the editings occurred at the 1st or the 2nd position of codons, which might alter the amino acid type. Most the shared editings were fully editing, and the 1st and the 19th sites were partially edited in nearly all cytoplasms, except for the 19th sites editing in the N-cytoplasm. The specific editings in each cytoplasm occurred in the form of partially editing. Thus the editing of atp6 gene in maize was not only sequence specific but also affected by cytoplasmic background. Furthermore, plant RNA editing was inclined to improve the predicted protein's hydrophobicity and enhance the conservation among species.

[Distribution and SNPs of the rice CMS-related gene in AA-genome of Oryza species].

The moiety of a chimeric gene in mitochondrial genome, orf79 and orfH79, probably related to BT-type and HL-type CMS of rice respectively, has 98% homology and only 4 nucleotide variation in DNA sequence. Of which, the former comes from Oryza sativa L., and the latter originates from Oryza rufipogon Griff. That means the orf79/ orfH79 may widely exist in Oryza species with AA genome. In order to investigate the distribution and difference of orf79/ orfH79 in the Oryza species, 190 cultivated rice accessions (including O. sativa and O. glaberrima) and 104 accessions of AA-genome Oryza wild species (including O. nivara, O. rufipogon, O. barthii, O. longistaminlata, O. glumaepatula, and O. meridion-alis) were detected with PCR amplification. Of which, 31 accessions mainly from AA-genome Oryza species were found to share the special amplified fragment with the control of Yuetai A and Shijin A. The special amplified fragments were all recovered and sequenced. Phylogenetic analysis based on DNA sequences showed that the 31 accessions were fallen into two groups, correspondingly representing HL-type and BT-type cytoplasm group. Further, the results revealed that the HL-type cytoplasm distributed mainly in annual O. nivara, and the BT-type cytoplasm centered in cultivated varieties or perennial O. rufipogon.

Identification, genetic characterization, GA response and molecular mapping of Sdt97: a dominant mutant gene conferring semi-dwarfism in rice (Oryza sativa L.).

Semi-dwarfism is an important agronomic trait in rice breeding programmes. sd-1, termed the 'Green Revolution gene', confers semi-dwarf stature, increases harvest index, improves lodging resistance, and is associated with increased responsiveness to nitrogen fertilizer. It has contributed substantially to the significant increase in rice production. In this paper, a novel semi-dwarf mutant in rice is reported. Genetic analysis revealed that only a single dominant gene locus non-allelic to sd-1, temporarily designated Sdt97, is involved in the control of semi-dwarfism of the mutant. The semi-dwarfism of the mutant could be partly restored to the tall wild-type by application of exogenous GA3, suggesting that the mutant gene Sdt97 may be involved in the gibberellin (GA) synthesis pathway and not the GA response pathway in rice. A residual heterozygous line (RHL) population derived from a recombinant inbred line (RIL) was developed. Simple sequence repeat (SSR) and bulked segregation analysis (BSA) combined with recessive class analysis (RCA) techniques were used to map Sdt97 to the long arm of chromosome 6 at the interval between two STS markers, N6 and TX5, with a genetic distance of 0.2 cM and 0.8 cM, respectively. A contig map was constructed based on the reference sequence aligned by the Sdt97 linked markers. The physical map of the Sdt97 locus was defined to a 118 kb interval, and 19 candidate genes were detected in the target region. This is the first time that a dominant semi-dwarf gene has been reported in rice. Cloning and functional analysis of gene Sdt97 will help us to learn more about molecular mechanism of rice semi-dwarfism.

[Cytological observation on pollen abortion of genetic male sterile mutant induced by space flight in maize].

In order to understand the cytological mechanism of pollen abortion of genetic male sterile mutant induced by space flight in maize, the sister cross population were used for sterility analysis and cytological observation. Intact anther observation, isolated cells observation and paraffin section were adopted in this research. The results showed that pollen abortion occured mostly in dyad stage of meiosis in genetic male sterile mutant. The dyad were degenerated with abnormal shape. In late anther developing stage, the tapetal cells were giant vacuolated and delayed degeneration. The pollen mother cells (PMC) began to dissolve and degenerate in a few anther before meiosis.

[Improvement of two-dimensional gel electrophoresis of total proteins from rice anthers].

This paper reported an improvement in 2-D gel electrophoresis of the proteome in Honglian cytoplasmic male sterile rice. An IPGphor unit with immobile pH gradient strips was used as the first dimension and SDS-PAGE as the second. The total anther proteins were extracted using TCA/acetone and then were washed 5-6 times with acetone till the proteins were white and clean, and then tributylphosphine and DTT were added into the rehydration buffer to improve the solubility of the proteins. The 2-D gel was stained by both methods of coomassie blue G-250 and silver. Extraction of proteins, pH of the strips and rehydration of the strips were optimized and compared. Higher repeatability and better separating protein pattern could be gained by this technique.

[A novel method of the genome-wide prediction for the target genes and its application].

Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted.

RFLP analysis for mitochondrial genome of CMS-rice.

Restriction fragment length polymorphism (RFLP) was used to analyze mitochondrial (mt) genome of cytoplasmic male sterility (CMS) rice. Differences were observed among mitochondrial genomes of the sterile line (A) and maintain line (B) of nine types of CMS rice; Mitochondrial genomic differences were also detected between A and B in many functional gene regions. Even the materials with the same nucleic background have differences in their mtDNA. This provides molecular evidence for the cytoplasmic heterogeneity and the CMS mechanism research.

[Preliminary proteomics analysis of the total proteins of HL Type cytoplasmic male sterility rice anther].

The proteins of HL type cytoplasmic male sterility rice anther of YTA (CMS) and YTB (maintenance line) were separated by two-dimensional electrophoresis with immobilized ph (3-10 non-linear) gradients as the first dimension and SDS-PAGE as the second. The silver-stained proteins spots were analyzed using Image Master 2D software, there were about 1800 detectable spots on each 2D-gel, and about 85 spots were differential expressed. With direct MALDI-TOF mass spectrometry analysis and protein database searching, 9 protein spots out of 16 were identified. Among those proteins, there were Putative nucleic acid binding protein, glucose-1-phosphate adenylyltransferase (ADP-glucose pyrophosphorylase, AGPase) (EC: 2.7.7.27) large chain, UDP-glucuronic acid decarboxylase, putative calcium-binding protein annexin, putative acetyl-CoA synthetase and putative lipoamide dehydrogenase etc. They were closely associated with metabolism, protein biosynthesis, transcription, signal transduction and so on, all of which are cell activities that are essential to pollen development. Some of the identified proteins, i.e. AGPase, putative lipoamide dehydrogenase and putative acetyl-CoA synthetase were deeply discussed on the relationship to CMS. AGPase catalyzes a very important step in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants: synthesis of the activated glucosyl donor, ADP-glucose, from glucose-1-phosphate and ATP. The lack of the AGPase in male sterile line might directly result in the reduction of starch, and the synthesis of starch was the most important processes during the development of pollen. In present research, the descent or reduction of putative lipoamide dehydrogenase and putative acetyl-CoA synthetase seemed involved in pollen sterility in rice. The degeneration and formation of various tissues during pollen development may impose high demands for energy and key biosynthetic intermediates. Under such conditions, the TCA cycle needs to operate fully, because the TCA cycle is an important source for many intermediates required for biosynthetic pathways, in addition to performing an oxidative, energy-producing role. Thus, it seemed reasonable to infer that the decrease of putative lipoamide dehydrogenase and putative acetyl-CoA synthetase in anther might prevent the conversion of pyruvate into acetyl-CoA, and as a result, the TCA cycle could no longer operate at a sufficient rate to meet all requirements in anther cells, leading to pollen sterility. This study gave new insights into the mechanism of CMS in rice and demonstrated the power of the proteomic approach in plant biology studies.

[The discovery of a specific DNA fragment associated with maize cytoplasmic male sterility and its differential display].

Three pairs of PCR primers were designed according to the mitochondrial DNA sequence. PCR amplification was applied to 3 sets of isonuclear alloplasm materials and 3 sets of isoplasm allonuclear materials. Multiplex PCR and general PCR protocol were adopted with total genomic DNA. As for the primers having detected polymorphsim between male sterility and its maintainers, differential display was conducted with mRNA from different development stage of microspore. The results showed as follows: with total genomic DNA template, primer P1-P2 has amplified a specific fragment only in all the male sterile materials, primer P5-P6 has amplified a specific fragment only in maintainer Huangzaosi, primer P3-P4 has no amplification in all the experiment materials. So primer P1-P2 can be used to distinguish male sterile cytoplasm and normal cytoplasm. RT-PCR was conducted with primer P1-P2 in inbred line huangzaosi and 48-2 with male sterile cytoplasm and normal cytoplasm, mRNA was separately isolated from tetrad stage, uninucleate stage and binucleate stage of microspore development, cDNA was obtained with random hexanucleotide primers. With the cDNA template, specific amplified fragments were also detected by primer P1-P2 in the male sterile materials at different development stage of microspore, but there was no amplification by primer P1-P2 in the 2 maintainer lines. This result indicated that primer P1-P2 can be transcripted at 3 development stages of microspore in all male sterile materials, and same transcript was produced by primer P1-P2 among all male sterile materials include 3 sets of isonuclear alloplasm and 3 sets of isoplasm allonuclear. It was suggested from this experiment that the specific DNA sequence detected by primer P1-P2 in all male sterile material total genomic DNA might be related to the cytoplasmic male sterile character.

[Isolation and analysis of isolation of differentially-methylated fragment CIDM7 in rice induced by cold stress].

By using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites, AFLP analysis is carried out to analyse differences of the methylation state of anonymous CCGG sequences between cold-treated(5 degrees for 2 d) and control 9311(Oryza sativa L.) leaves DNA. Demethylation or De novo methylation induced by cold stress are found in some CCGG sites. Some differentially-methylated encoding sequences are isolated, of which a fragment named CIDM7 (cold-inducing differential methylation) is sequenced and executed BLAST against Nipponbare cDNA data, thus we obtain its full length cDNA of 1422 bp encoding a hypothetical F-box protein(425 aa).CIDM7 is demethylated induced by cold stress. Northern blot analysis confirms that CIDM7 gene expression is up-regulated by cold stress. CIDM7 is single copy and lacated on the Nipponbare chromosome 10 (12.56 Mb-12.57 Mb).

[Genetic polymorphism of bluegrass cultivars detected by RAPDs].

Kentucky bluegrass (Poa pratensis L.) is a hardy, persistent forage and turf grass adapted to a wide range of soils and climates. Its ever-increasing adoption in highly cared-for sports fields has attracted the attention of many seed companies. However in the past, the breeding of elite varieties was often hampered by the extreme complexity of the genome. The polymorphism is important for broading the genetic basis and may be exploited for application of heterosis. The genetic relationship of 16 bluegrass cultivars, including 15 accessions Kentucky bluegrass cultivars and 1 entries Canada bluegrass (Poa compressa L.) cultivar from different breeding company were analyzed using 25 RAPD markers. 25 RAPD primers generated 218 bands, of which 196 bands (89.91%) were polymorphism. It showed that the Canada Bluegrass was separated from other Kentucky Bluegrass and genetic polymorphism in the Kentucky Bluegrass cultivars was low, the genetic similarity among the cultivars fell between 66%-98%. Dendrogram obtained using these molecular markers were partly in agreement with their separated morphologic character. Cultivars from the same company were not clustered in one group.

[RAPD Identification of Three Types of Three-lines Hybrid Rice with Defferent Male Sterile Cytoplasms and Their Parent Lines.].

The RAPD analysis was conducted on genome DNA from 21 sets of rice, including 6 three-line hybrid rice combinations, separately derived from three different kinds of cytoplasmic male sterile (CMS) lines and their related parents. Out of 264 random primers screened first, 25 primers displayed well in polymorphisms. It was shown that only 7 bands amplified respectively from 7 primers were enough to discriminate the different types of CMS, the hybrid combinations and their parents.

Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa).

BACKGROUND AND AIMS: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype x environmental temperature interactions for seedling vigour QTL. METHODS: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25 degrees C, 20 degrees C and 15 degrees C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. KEY RESULTS: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82%) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20 degrees C and 25 degrees C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. CONCLUSIONS: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.

Identification of chromosome regions associated with seedling vigor in rice.

Seedling vigor is important for optimum stand establishment in rice cropping. In this paper,a set of 264 F12 recombinant inbred lines (RILs) derived by single seed descent from a cross between Lemont (japonica) and Teqing (indica) was phenotyped for three seedling vigor related traits, including seed germination rate (GR), seedling shoot length and dry weight by the rolled paper towel tests. The phenotype data and a linkage map consisting of 198 DNA markers were combined to map quantitative trait loci (QTL) for seedling vigor by using a computer program QTLMapper1.0. A total of 13 putative main-effect QTL were detected. All of these QTL had much smaller effects on the traits with a mean R2 of 6.2%, ranging from 2.9% to 12.7%. As for digenic interaction, 18 pairs of epistatic loci with R2 > or = 5% were resolved with a mean R2 of 6.9% ,ranging from 5.1% to 11.8%, which was slightly larger than that of the main-effect QTL identified for the traits. The majority of the main-effect and epistatic loci detected for seedling vigor related traits were clustered in a few chromosome regions. Together, seven such chromosome regions (CRs), each with three or more seedling vigor main-effect and epistatic loci, were found to be highly associated with seedling vigor. These CRs can be classified into three types, i.e. M-CRs, E-CRs and ME-CRs. For some CRs just like CR(SV-6), the QTL within one CR were found to interact simultaneously with QTL within more than one other CRs to affect different seedling vigor related traits. The above results revealed that seedling vigor in rice is controlled by many loci, most of which have relatively small effects. Comparatively, epistasis as a genetic factor would be more important than main-effects of QTL for seedling vigor in rice. Nevertheless, the effects of the QTL are still large enough to be detected and in fact several chromosome regions were found to be highly associated with seedling vigor in very different populations as compared with previous studies. Molecular tagging of favorable alleles and marker-aided selection strategy may, therefore, be a promising approach to the improvement of rice seedling vigor.

[Genomic context of nucleus influences mitochondrial gene expression of HL-type rice].

In eukaryotic cells, the role of mitochondria is to generate both ATP and carbon skeletons for biosynthetic purposes. Meanwhile, the mitochondrial genes, in plant, are also involved in the development of anther. The presence of genetic information within mitochondria and nucleus make intracellular cooperation necessary. In this paper, a new RAPD method is used to analyze the expression differences of rice mitochondrial gene with the change of nuclear background. Many different fragments are obtained from hybrids, but not from sterile line or remainder line. According to the results, it is concluded that there are extensive effects of nuclear background on mitochondrial gene expression.

Transgenic tobacco plants overexpressing cotton glutathione S-transferase (GST) show enhanced resistance to methyl viologen.

A GST (EC 2.5.1.18) gene (Gst-cr 1) from cotton was introduced into Nicotiana tabacum by Agrobacterium tumefaciens-mediated transformation. Transgenic tobacco plants overexpressing Gst-cr1 were normal in growth and mature compared with control, but had much higher levels of GST and GPx activities and showed an enhanced resistance to oxidative stress induced by a low concentration of methyl viologen (MV). Six antioxidant enzymes, glutathione S-transferase, glutathione peroxidase (EC 1.11.1.9), superoxide dismutase (EC 1.15.1.1), peroxidase (EC 1.11.1.7), catalase (EC 1.11.1.6), and ascorbate peroxidase (EC 1.11.1.11) were monitored in transgenic lines and non-transgenic control during MV treatments. When they were treated with 0.03 mmol/L of MV, both transgenic lines and control showed a rapid increase in the activities of GST, GPx, SOD, POD, APx, while the activity of CAT seemed to be irregular. The percent of the increase in SOD and POD activities was much higher in control than in transgenic plants. When treated with 0.05 mmol/L of MV, both control and transgenic plants were severely damaged, and the activities of the six enzymes decreased sharply.

Characterization of QTLs for harvest index and source-sink characters in a DH population of rice (Oryza sativa L.).

A DH population containing 81 DH lines from an indica-japonica cross of rice and an RFLP linkage map consisting of 232 markers were used to map quantitative trait loci(QTLs) for harvest index, biomass, grain yield, sink capacity and plant height by a computer program QTLMapper1.0 based on mixed linear models. A total of 21 significant main-effect QTLs and 9 pairs of epistatic loci were detected. Of these, three detected QTLs for grain yield collectively accounted for 42% of the phenotypic variation with a LOD of 7.10. These three grain yield QTLs were corresponded either to QTLs for harvest index or QTLs for biomass in both locations and directions of additive effects, which sheds light on the genetic basis of the formula 'grain yield = biomass x harvest index'. Four detected QTLs for harvest index collectively explained 46% of the total phenotypic variation and four QTLs for biomass jointly accounted for 64% of the trait variation. No coincidence of harvest index QTLs with any biomass QTLs was found, therefore indicating the possibility of pyramiding favorable alleles for both traits through gene recombination so as to obtain a genotype possessing both high harvest index and heavy plant biomass. Five QTLs for plant height were detected that cumulatively explained 64% of the phenotypic variation with a LOD of 11.62. Among these, three with smaller effects respectively co-located with some of the QTLs for biomass, sink capacity and/or grain yield, but not with any of harvest index QTLs, thus suggesting that plant height was to some extent directly associated with 'source' and 'sink' but not with 'transportation' of the 'source-transportation-sink' concept, at least in this genetic background and environment. In view of a somewhat low resolution of the genetic map used in the study and the fact that when plant height QTLs co-located with those for yield and/or yield related traits, these co-located QTLs were all in the same directions of additive effects, it is more likely that these QTLs co-located in a same chromosomal region might be a single QTL which have effects on multiple traits. If this is true, the above observation have led us to assume that QTLs which have pleotropic effects on yield and/or yield related traits and plant height are very different from those which had relatively large effects only on plant height. The former contribute strongly to yield and/or yield related traits but weakly to plant height while the later contribute mainly to plant height. Obviously, due to that an increase of plant height is always coupled with an increase in lodging susceptibility, discriminating between above two types of QTLs is critical in breaking the traits' undesired association in breeding for improved yield potential of rice. In addition, based on the co-location analysis of main-effect QTLs for the studied traits, five genomic regions were found to be highly associated with harvest index, biomass, sink capacity and grain yield.