拟南芥PHD-finger蛋白家族的全基因组分析

PHD—finger蛋白是一类广泛存在于真核生物中,在基因转录和染色质状态调控方面有重要作用的锌指蛋白。目前在动物中对PHD—finger蛋白的结构和功能方面的研究较为广泛和深入,而在植物中仅有少数PHD—finger蛋白的功能被阐明。通过SMART和Pfam等数据库分析,我们发现拟南芥中共有70个PHD-finger蛋白,其中大部分PHD—tinger蛋白的功能未知。本文通过生物信息学分析获得拟南芥PHD-tinger家族较为全面的信息,包括基因结构、染色体定位、基因表达、蛋白结构域、系统进化关系等,为深入研究PHD-finger家族蛋白的结构与功能提供了参考。     

Riboflavin-induced Priming for Pathogen Defense in Arabidopsis thaliana

Riboflavin （vitamin B2） participates in a variety of redox processes that affect plant defense responses. Previously we have shown that riboflavin induces pathogen resistance in the absence of hypersensitive cell death （HCD） in plants. Herein, we report that riboflavin induces priming of defense responses in Arabidopsis thaliana toward infection by virulent Pseudomonas syringae pv. tomato DC3000 （Pst）. Induced resistance was mechanistically connected with the expression of defense response genes and cellular defense events, including H202 burst, HCD, and callose deposition in the plant. Riboflavin treatment and inoculation of plants with Pst were neither active but both synergized to induce defense responses. The priming process needed NPRI （essential regulator of systemic acquired resistance） and maintenance of H202 burst but was independent of salicylic acid, jasmonic acid, ethylene, and abscisic acid. Our results suggest that the role of riboflavin in priming defenses is subject to a signaling process distinct from the known pathways of hormone signal transduction.     

拟南芥BAK1基因转化及防御作用

将拟南芥BAK1基因采用Gateway方法连接到植物表达载体,通过侵花粉管进行转化,从基因和蛋白表达水平检测转化是否成功。以不同BAK1表达水平植株作为试验材料,分析BAK1在芜菁缩叶病毒(Turnip crinkle virus,TCV)-拟南芥(Col-0)亲和互作系统中对植株防御的影响。结果显示,在接种TCV后,BAK1缺陷型植株对TCV较为感病,衰老相关基因表达水平增加,表明BAK1能够增强宿主对病毒的防御作用。     

Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana

Miniature inverted-repeat transposable elements (MITEs) are structurally similar to defective class II elements, but their high copy number and the size and sequence conservation of most MITE families suggest that they can be amplified by a replicative mechanism. Here we present a genome-wide analysis of the Emigrant family of MITEs from Arabidopsis thaliana. In order to be able to detect divergent ancient copies, and low copy number subfamilies with a different internal sequence we have developed a computer program to look for Emigrant elements based solely on the terminal inverted-repeat sequence. We have detected 151 Emigrant elements of different subfamilies. Our results show that different bursts of amplification, probably of few active, or master, elements, have occurred at different times during Arabidopsis evolution. The analysis of the insertion sites of the Emigrant elements shows that recently inserted Emigrant elements tend to be located far from open reading frames, whereas more ancient Emigrant subfamilies are preferentially found associated to genes.     

Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana

The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated—such as the position of a locus within the chromosome, or imperfect repeats—appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing.     

Association of glutathione with flowering in Arabidopsis thaliana

In order to study the relationship between GSH and flowering, wild-type and late-flowering mutant, fca-1, of Arabidopsis thaliana were treated with L-buthionine sulfoximine (BSO), a specific inhibitor of GSH biosynthesis, under long-day conditions. BSO treatment of the fca-1 mutant starting at 17 d after imbibition promoted flowering. However, when the treatment was started at 12 d after imbibition, BSO treatment at 10(-4) M resulted in an inhibition of flowering. This inhibitory effect of BSO on flowering was abolished by GSH treatment at 10(-4) M, although GSH treatment at an increased concentration of 10(-3) M clearly delayed flowering. In contrast, BSO treatment of wild-type plants starting at 12 d after imbibition promoted flowering, whose effect was abolished by GSH application. In the fca-1 mutant, whose endogenous GSH levels were high, chilling treatment lowered the GSH levels and promoted flowering, as was the case in the BSO treatment. An A. thaliana mutant, cad2-1, which has a defect in GSH biosynthesis also exhibited late flowering. The late-flowering phenotype of this mutant tended to be strengthened by BSO and abolished by GSH treatment. These results suggest that flowering is associated with the rate of GSH biosynthesis and/or the levels of GSH in A. thaliana.     

Chromosomal Mapping of Genes in theRBCS Family in Arabidopsis thaliana

In Arabidopsis thaliana, four genes have been identified inthe RBCS gene family, one being assigned to subfamily RBCS-Aand the other three to subfamily RBCS-B (1B, 2B and 3B). Todetermine the chromosomal location ofthese genes, hybridizationanalysis with CIC YAC high-density filters was carried out forthe RBCS-A gene, and CAPS analysis for the three RBCS-B genes,based on the finding that restriction fragment length polymorphismis present in the upstream region of the gene RBCS-3B. The RBCS-Agene was mapped at 100.8 cM from the top of chromosome 1 andthe three RBCS-B genes at 62.70 cM from the top of chromosome5.     

Biochemical Genetics of Plant Secondary Metabolites in Arabidopsis thaliana: The Glucosinolates

Mutants of Arabidopsis thaliana with a glucosinolate content different from wild type were isolated by screening a mutagenized population of plants. Six mutants were detected out of a population of 1200 screened. One of these mutants, TU1, was analyzed in detail. Leaf and seed tissues of line TU1 lack or have reduced amounts of many of the aliphatic glucosinolates found in the wild type due to a recessive allele, gsm1, of a single nuclear gene, GSM1. The seed phenotype is inherited as a maternal effect suggesting that the embryo is dependent on the maternal tissue for its glucosinolates. Experiments involving feeding of (14)C-labeled intermediates suggested that the gsm1 allele results in a metabolic block which decreases the availability of several amino acid substrates required for glucosinolate biosynthesis: 2-amino-6-methylthiohexanoic acid, 2-amino-7-methylthioheptanoic acid, and 2-amino-8-methylthiooctanoic acid. The mutation does not result in any obvious changes in morphology or growth rate. A pathway for the biosynthesis of glucosinolates in A. thaliana is proposed.     

Mapping genes essential for embryo development in Arabidopsis thaliana.

Summary We have previously isolated and characterized over 90 recessive mutants of Arabidopsis thaliana defective in embryo development. These emb mutants have been shown to differ in lethal phase, extent of abnormal development, and response in culture. We demonstrate in this report the value and efficiency of mapping emb genes relative to visible and molecular markers. Sixteen genes essential for embryo development were mapped relative to visible markers by analyzing progeny of selfed F₁ plants. Embryonic lethals are now the most common type of visible marker included on the linkage map of Arabidopsis. Backcrosses were used in several cases to orient genes relative to adjacent markers. Three genes were located to chromosome arms with telotrisomics by screening for a reduction in the percentage of aborted seeds produced by F₁ plants. A restriction fragment length polymorphism (RFLP) mapping strategy that utilizes pooled EMB/EMB F₂ plants was devised to increase the efficiency of mapping embryonic lethals relative to molecular markers. This strategy was tested by demonstrating that the biol locus of Arabidopsis is within 0.5 cM of an existing RFLP marker. Mapping embryonic lethals with both visible and molecular markers may therefore help to identify large numbers of genes with essential functions in Arabidopsis.     

拟南芥网状突变体E-210基因精细定位

通过甲基磺酸乙酯(EMS)诱变与遗传分析,从拟南芥(Arabidopsis thaliana)中筛选到一株隐性单基因控制的网状突变体E-210.该突变体植株生长缓慢,叶脉呈绿色,叶肉呈黄色.通过透射电镜观察,发现野生型植株和突变植株在叶绿体结构上差异不大,猜测该突变体E-210基因与叶绿体的发育可能没有直接关系,而很可能同叶绿素或叶绿体的生物合成有关.通过图位克隆的方法,将该突变体的突变基因定位在第5条染色体上的MRBl7和MBG8-5的分子标记之间,精确到87.130 kb.对MRB17和MBG8-5的分子标记之间的22个基因进行了分析,预测突变体E-210基因可能是At5g54770,编码THI1,即噻唑合成酶.     

QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

Background

Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).

Methodology/Principal Findings

We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F₂ population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.

Conclusions/Significance

The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.