Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation

Oriental ginseng is an important medicinal plant that grows in 2 major forms or ecotypes, wild and domesticated. Each form differs conspicuously in root phenotype, but can be converted from one type to another by habitat. Here we show that the habitat-induced transformation of ginseng root phenotype was accompanied by alteration in cytosine methylation at a large number of 5′-CCGG-3′ sites detected by the methylation-sensitive polymorphism (MSAP) marker. The collective CG and CHG methylation levels of all 4 landraces of the domesticated form were significantly lower than those of the wild form. Interestingly, artificially transplanted ginseng plants recreated in both directions the methylation levels (at least in CHG) of their natural counterparts. The methylation differences between the 2 ginseng ecotypes were validated at 2 isolated MSAP loci bearing homology to a 5S rRNA gene or a copia retrotransposon. Our results implicate a link between epigenetic variation and habitat-induced phenotypic flexibility in Oriental ginseng.     

小麦异源多倍体中亲本基因组相互作用产生快速基因组变异的ISSR标记分析

通过ISSR标记分析,研究了异源多倍体基因组的进化现象.结果表明,基因组组成和普通小麦相同的人工合成异源六倍体小麦,在形成早期发生了迅速、广泛、以非随机性为主的基因组变化,包括遗传变异--主要表现为序列变异和表观遗传变异--主要表现为DNA甲基化变异.而且异源六倍体小麦中来自父本的基因组比来自母本的基因组发生了更多的遗...     

Analysis of DNA methylation variation in wheat genetic background after alien chromatin introduction based on methylation-sensitive amplification polymorphism

During the process of alien germplasm introduced into wheat genome by chromosome engineering, extensive genetic variations of genome structure and gene expression in recipient could be induced. In this study, we performed GISH （genome in situ hybridization） and AFLP （amplified fragment length polymorphism） on wheat-rye chromosome translocation lines and their parents to detect the identity in genomic structure of different translocation lines. The results showed that the genome primary structure variations were not obviously detected in different translocation lines except the same 1RS chromosome translocation. Methylation sensitive amplification polymorphism （MSAP） analyses on genomic DNA showed that the ratios of fully-methylated sites were significantly increased in translocation lines （CN12, 20.15%; CN17, 20.91%; CN18, 22.42%）, but the ratios of hemimethylated sites were significantly lowered （CN12, 21.41%; CN17, 23.43%; CN18, 22.42%）, whereas 16.37% were fully-methylated and 25.44% were hemimethylated in case of their wheat parent. Twenty-nine classes of methylation patterns were identified in a comparative assay of cytosine methylation patterns between wheat-rye translocation lines and their wheat parent, including 13 hypermethylation patterns （33.74%）, 9 demethylation patterns （22.76%） and 7 uncertain patterns （4.07%）. In further sequence analysis, the alterations of methylation pattern affected both repetitive DNA sequences, such as retrotransposons and tandem repetitive sequences, and low-copy DNA.     

F-MSAP： A practical system to detect methylation in chicken genome

By replacing radiation with fluorescent system in the technique of methylation sensitive amplified polymorphism （MSAP） and optimizing reaction conditions, a modified technique to detect DNA methylation called F-MSAP （fluorescent labeled methylation sensitive amplified polymorphism） was developed. In the present study, cytosine methylation patterns of genomic DNA were investigated in two inbred chickens and their F1 hybrids. Three types of methylation patterns were observed in each individual, namely fully methylated, hemi-methylated or not methylated types. The average incidence of methylation was approximately 40%. The percentage that the F1 hybrid individual inherits the methylation for any given sites from either/both parent amounted to 95%, while the percentage of altered methylation patterns in F1 individual was only 5%, including 14 increased and 12 decreased methylation types, demonstrating that F-MSAP was highly efficient for large-scale detection of cytosine methylation in chicken genome. Our technique can be further extended to other animals or plants with complex genome and rich in methylation polymorphism.     

Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice

In higher plant, about 30% cytosines are methy-lated[1], among which about 90% methylated sites lie in CpG dinucleotide and CpNpG trinucleotide[2]. The me-thylated DNA has inducing and epigenetic effects on cell biological procedures such as gene differen…     

Crucial function of histone lysine methylation in plant reproduction

Unlike animals, plants do not set aside germ cells early in development. In angiosperm species, reproduction occurs in the adult plant upon flowering. The multicellular male and female gametophytes differentiate from meiotic products within reproductive floral organs. Double fertilization is another remarkable feature of most angiosperm species. The zygote derived from fertilization of the egg cell by one of the sperm cells and the endosperm from fertilization of the central cell by the second sperm cell develop in a coordinated manner together and enclosed in the sporophytic maternal integuments, forming the seed. Understanding plant reproduction is biologically pertinent and agronomically and ecologically important. Here, we describe the known functions of histone lysine methylations in various steps of reproduction in the reference plant Arabidopsis thaliana. It is emerging that histone lysine methylation is key for understanding epigenetic regulation networks of genome function.     

水稻基因组DNA总甲基化水平测定方法

对高效液相色谱法测定DNA总甲基化水平的关键因素进行研究,即基因组DNA的提取及纯化和高效液相色谱条件的选择。结果表明:CTAB法Ⅰ提取和纯化效果优于CTAB法Ⅱ;较优高效液相色谱条件为:采用Diamonsil C18(2)(250 mm×4.6 mm,5μm)的色谱柱,以甲醇-10 mmol/L磷酸二氢钾(10-90,v/v)为流动相构成,流动相pH为4.7,流速为0.5 mL/min,柱温为30℃,紫外检测器波长为285 nm时,是分离胞嘧啶和5-甲基胞嘧啶的较优条件。以试验优化的DNA提取方法和HPLC色谱条件,基因组DNA水解液的胞嘧啶(C)和5-甲基胞嘧啶(5 mC)可得到较好的分离效果。     

Aberrant DNA methylation in cloned ovine embryos

By using the approach of immunofluorescence staining with an antibody against 5-methylcytosine （5MeC）, the present study detected the DNA methylation patterns of cloned ovine embryos. The embryos derived from in vitro fertilization were also examined for reference purpose. The results showed that： （1） during the preimplantation development, cloned embryos displayed a similar demethylation profile to the fertilized embryos; that is, the methylation level decreased to the lowest at 8-cell stage, and then increased again at morulae stage. However, methylation level was obviously higher in cloned embryos than in stage-matched fertilized embryos, especially at 8-cell stage and afterwards; （2） at blastocyst stage, the methylation pattern in cloned embryos was different from that in fertilized embryos. In cloned blastocyst, inner cell mass （ICM） exhibited a comparable level to trophectoderm cells （TE）, while in in-vitro fertilized blastocyst the methylation level of ICM was lower than that of TE, which is not consistent with that reported by other authors. These results indicate that DNA methylation is abnormally reprogrammed in cloned embryos, implying that aberrant DNA methylation reprogramming may be one of the factors causing cloned embryos developmental failure.     

Detection of DNA methylation changes during seed germination in rapeseed （Brassica napus）

DNA methylation is a common yet important modi- fication of DNA in eukaryotic organisms. DNA methy- lation, especially methylation of cytosine (m5C), have both epigenetic and mutagenic effects on various cellu- lar activities such as differential gene exp…     

聚乙二醇(PEG)胁迫诱导水稻DNA甲基化变异与脯氨酸代谢相关性研究

干旱胁迫经常伴随着植物脯氨酸代谢的变化.为了研究干旱胁迫条件下脯氨酸的累积与DNA甲基化变异之间的相关性,采用聚乙二醇(PEG)模拟天然的干旱胁迫条件,以15%聚乙二醇(PEG)胁迫处理的水稻幼苗为实验材料,利用DNA甲基化敏感扩增多态性技术(MSAP)筛选出1株甲基化变异最大的单株(S0);采用Southern印迹杂交(Southern blot)和实时荧光定量聚合酶链式反应(Realtime-PCR)分别检测S0和S1代(S0自交产生的后代)与脯氨酸代谢相关基因的DNA甲基化变异和基因表达的变化情况,并测定了S0和S1代叶片游离脯氨酸的含量.结果表明:S0代谷氨酸合成途径的相关基因没有发生甲基化,S1代谷氨酸合成途径的Δ1-吡咯啉-5-羧酸合成酶(P5CS)基因在后代(14个单株)全部发生了CHG去甲基化变异,变异率为100%.鸟氨酸合成途径的鸟氨酸转氨酶(δ-OAT)基因在后代中有3个单株发生了去甲基化变异,变异率为21%;Δ1-吡咯琳-5-羧酸脱氢酶(P5CDH)和Δ1-吡咯啉-5-羧酸还原酶(P5CR)基因的甲基化没有明显变异,变异率为0.Realtime-PCR结果表明:S1代P5CS基因表达上调率为100%;δ-OAT和P5CR基因S1代14个单株中有10个单株的表达发生了上调,上调率为71.4%;降解途径中的关键基因P5CDH基因S1代表达下调率7.1%.研究结果表明DNA甲基化变异与基因表达之间可能仅在部分基因上存在一定的关联性.     

青海省春小麦主要农艺性状及育种演化分析

为给青海省现有小麦品种的合理利用提供参考信息,对61份春小麦主要农艺性状进行了考察与分析。结果表明,供试材料穗长平均为10.8 m、千粒重平均为37.9 g、穗粒重平均为2.2 g、稀穗(平均10 cm19.4个)的高杆(平均株高104.6 cm)中熟(平均生育期112.0 d)品种。主成分分析显示的4个主成分(产量因子、穗密度因子、粒数因子、粒重因子)的特征向量累积贡献率达89.37%,可作为亲本选择的依据。聚类分析可将供试材料聚为高产类和密穗类两类,其遗传距离的远近与育种单位和育成地点无必然联系,而引进品种和含有较多地方品种遗传信息的品种与当地育成品种间的遗传距离较远。总体看来,青海省春小麦育种经历了起步、密穗育种、高产育种和品质育种四个阶段,使品种逐步由密穗型向高产型演化,再由高产型向优质型演化,其中,1994年是高产育种的顶峰时期,2001年以后进入品质育种期。     

H_2O_2诱导小麦叶片光合功能衰退的研究

采用不同浓度的H2O2处理小麦,研究H2O2对小麦叶片光合功能的影响.结果表明:1 mmol.L-1H2O2对小麦叶片光合作用基本无影响,10、100、200 mmol.L-1H2O2对小麦离体和连体叶片的光合作用均有不同程度的抑制作用,表现为光合速率、叶绿素含量下降.叶绿体超微结构显示10 mmol.L-1H2O2对其有影响,200 mmol.L-1H2O2处理后基粒明显破坏,类囊体膜无序.核酮糖-1,5-二磷酸羧化酶加氧酶(Rubisco)大小亚基和羧化活性在20 mmol.L-1H2O2逆境下变化小,100 mmol.L-1H2O2处理,Rubisco大小亚基降解明显,羧化活性微弱.说明H2O2诱导小麦叶片光合功能衰退.     

Chromosome sorting and its applications in common wheat (Triticum aestivum) genome sequencing

The large genome size (～17000 Mb) and complicated DNA structures of common wheat (Triticum aestivum) hamper its genome sequencing.By means of flow cytometry,systematic investigations on individual chromosome sorting have been carried out to construct chromosome-specific bacterial artificial chromosome (BAC) libraries since the 1980s.Several wheat chromosome-specific BAC libraries,such as chromosome 3B,three D genome chromosomes (1D,4D and 6D),and the short arm of chromosome 1B,have been developed,and the ph...     

Change of water use efficiency and its relation with root system growth in wheat evolution

Raising crop water use efficiency (WUE) is the physiological basis to implement crop high efficiently using water. The present soil column and field experiments are designed to investigate the change of wheat WUE (Triticum aestivum L.) at whole plant level and root system growth in evolution and the relationship between WUE and its root system growth using 10 wheat evolution genotypes with different ploidy chromosomes sets. Results show that in wheat evolution from 2n→6n, WUE at whole plant level increases with the increase of ploidy chromosomes, and root system growth (root weight, root length) and root/shoot ratio of wheat decrease with the increase of ploidy chromosomes under dry and irrigated conditions. WUE is negatively correlated with root weight and root/shoot ratio of wheat in evolution, significantly. Root system growth has an adverse redundancy for WUE in wheat evolution, and the root redundancy reduces with the increase of ploidy chromosomes, which result in the increase of wheat WUE at whole plant level.     

Development, chromosome location and genetic mapping of EST-SSR markers in wheat

A number of 151695 wheat expression sequence tags （ESTs） that originated from GenBank/dbEST from July 14, 2003 to August 24, 2004 were used to search for simple sequence repeats （SSRs） with motif 2-5 bp, and 2038 simple sequence repeats （EST-SSRs）, which accounted for 1.34% of EST database, were identified. Based on these SSR sequences, 249 EST-SSR primer pairs and 166 amplified clear bands in various wheat cultivars were designed. These EST-SSR markers can be used as new molecular markers in wheat and related species. Using Chinese Spring nulli-tetrasomic lines, 93 EST-SSR primer pairs and 193 EST-SSR loci were located on 19 wheat chromosomes except for 4A and 4B. Forty-three loci were mapped on 11 chromosomes of the genetic framework map previously constructed using recombinant inbred lines.     

Structural and biochemical mechanism responsible for the stay-green phenotype in common wheat

In order to increase the supply of assimilated carbon to grain, a new stay-green wheat cultivar, Chuannong17 (CN17), with delayed leaf senescence, carrying wheat-rye 1RS.1BL translo- cated chromosome was developed. CN17 exhibited distinct differences in net photosynthetic rate (Pn), chlorophyll (Chl) content, malondialdehyde (MDA) content, activity of both superoxide dismutase (SOD) and catalase (CAT) during the grain filling stage, and flag leaf senescence compared with the control. The new cultivar maintained longer and higher photosyn- thetic competence compared with the control, and this aspect correlated with the difference in chloro-plast development. Moreover, the stay-green pheno-type of CN17 was also observed under natural growth conditions. Consequently, the coordination of the physiological, biochemical, and structural aspects in the stay-green cultivar produced higher seed weights and per-plant yield compared with the control cultivar.     

Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.