Genetic variations of glycinin subunit genes among cultivated and wild type soybean species

Glycinin is a predominant storage protein in most soybean accessions. It is a hexamer constituted by five major subunits, which can be classified into two groups. Group I contains G1, G2 and G3, and Group II contains G4 and GS. The genes encoding these subunits have been designated from Gyl to Gy5, respectively. In the present study, Gyl genomic fragments were cloned from wild accessions of subgenera Glycine glycine, Glycine soja and a cultivar of Glycine max. Their sequences and the deduced amino acid sequences were compared. The residues critical for assembling of G1 subunits from the wild perennial accession were conservative. The Gy4 fragments were cloned from two wild perennial accessions and compared with that from subgenus Soja. The intron 3 of Gy4 had abundant variations between the subgenera G. soja and G. glycine as well as within the subgenus G. glycine. Abundant variations existed in the disordered regions 3 and 4 of G4 subunits from two wild perennial accessions. The genomic organization of glycinin genes was analyzed in 19 accessions from subgenera Soja and Glycine. The hybridization patterns were identical among the accessions of subgenus Soja. On the contrary, abundant polymorphisms existed between the accessions from subgenus Glycine. These results indicated that glycinin genes have high degree of conservation within subgenus Soja but more variations within subgenus Glycine.     

The DNA sequence and biological annotation of human chromosome 1

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.     

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles, and these can influence the expression of nearby genes. However, to understand their role in evolution, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations. Transposable elements and short interfering RNAs have been causally linked to DNA methylation. In agreement, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution.     

Genetic variations of glycinin subunit genes among cultivated and wild type soybean species

Glycinin is a predominant storage protein in most soybean accessions. It is a hexamer constituted by five major subunits, which can be classified into two groups. Group I contains G1, G2 and G3, and Group II contains G4 and G5. The genes encoding these subunits have been designated from Gy1 to Gy5 , respectively. In the present study, Gy1 genomic fragments were cloned from wild accessions of subgenera Glycine glycine, Glycine soja and a cultivar of Glycine max . Their sequences and the deduced amino acid sequences were compared. The residues critical for assembling of G1 subunits from the wild perennial accession were conservative. The Gy4 fragments were cloned from two wild perennial accessions and compared with that from subgenus Soja . The intron 3 of Gy4 had abundant variations between the subgenera G. soja and G. glycine as well as within the subgenus G. glycine. Abundant variations existed in the disordered regions 3 and 4 of G4 subunits from two wild perennial accessions. The genomic organization of glycinin genes was analyzed in 19 accessions from subgenera Soja and Glycine . The hybridization patterns were identical among the accessions of subgenus Soja. On the contrary, abundant polymorphisms existed between the accessions from subgenus Glycine . These results indicated that glycinin genes have high degree of conservation within subgenus Soja but more variations within subgenus Glycine .     

黄麻选系材料不同光周期处理下的观察与筛选

观察了10个黄麻圆果种(Corchorus capsularis)和4个黄麻长果种(C.olitorus)选系材料在不同光周期处理下的开花习性.方差分析表明各材料对光周期的反应存在显著差异,在12.5小时光周期下,圆果种材料UO/MC8122和长果种材料IJO/X/087的开花天数明显较长,而且在12.5小时、13.0小时和13.5小时三种光周期处理下的变幅较小.这一结果表明,IJO/MC8122和IJO/X/087可作亲本材料用于黄麻品种改良以选育对日长广适应的新品种.     

Epistasis and balanced polymorphism influencing complex trait variation

Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation. Here, we identified and dissected a one-centimorgan chromosome interval in Arabidopsis thaliana without regard to its effect on growth rate, and examined the signature of historical sequence polymorphism among Arabidopsis accessions. We found that the interval contained two growth rate QTL within 210 kilobases. Both QTL showed epistasis; that is, their phenotypic effects depended on the genetic background. This amount of complexity in such a small area suggests a highly polygenic architecture of quantitative variation, much more than previously documented. One QTL was limited to a single gene. The gene in question displayed a nucleotide signature indicative of balancing selection, and its phenotypic effects are reversed depending on genetic background. If this region typifies many complex trait loci, then non-neutral epistatic polymorphism may be an important contributor to genetic variation in complex traits.     

转录物组学解析植物生长发育的生物钟调控模

基于拟南芥的时间序列的基因组芯片数据,分析了植物生长的昼夜调节模式相关的基因表达规律,发现有2.4%的基因的日振幅达到了显著差异水平.从整体基因转录组水平分析,白天诱导表达的基因主要参与调控植物与环境之间的相互作用,而夜晚表达上调的基因主要参与调节植物的生长发育.此外,植物叶绿素和血红素的生物合成也受到了生物钟的调控.对整个基因组水平上生物钟核心震荡调节子CCA1/LHY和TOC1的共表达基因做了基因组水平上的扫描鉴定,得到了一些新的潜在的生物节律调节因子.这些结果为今后更为系统地完善植物的生物节律的调控网络提供了参考.     

水稻配子体细胞质雄性不育基因orf79/orfH79的变异多态性研究

线粒体基因组异常嵌合基因orf79/orfH79被证实为水稻配子体细胞质雄性不育（cytoplasmic male sterility,CMS）基因。为了调查配子体CMS基因orf79/orfH79在水稻资源中的遗传与变异,来自不同国家的31份水稻材料被用于PCR检测。10份水稻材料被检测出具有配子体CMS基因orf79/orfH79,表明配子体CMS基因orf79/orfH79在水稻资源中具有较高的分布频率（32.2%）。DNA序列分析显示水稻配子体CMS基因orf79/orfH79具有非常保守的遗传特性（98.3%）,只有4个多态性碱基位点被检测出,4个碱基位点的变异导致多肽ORF79/ORFH79三个氨基酸位点的改变。基于orf79/orfH79 DNA序列的聚类分析系显示10份水稻材料被分成了3个类群,表明配子体CMS胞质在水稻资源中存在多种变异模式。研究结果为新水稻CMS胞质的发掘与培育提供重要的理论和实验依据。     

Evolution of genetic mechanisms controlling petal development.

Molecular genetic studies in Arabidopsis thaliana and other higher-eudicot flowering plants have led to the development of the 'ABC' model of the determination of organ identity in flowers, in which three classes of gene, A, B and C, are thought to work together to determine organ identity. According to this model, the B-class genes APETALA3 (AP3) and PISTILLATA (PI) act to specify petal and stamen identity. Here we test whether the roles of these genes are conserved throughout the angiosperms by analysing the expression of AP3 and PI orthologues in the lower eudicot subclass Ranunculidae. We show that, although expression of these orthologues in the stamens is conserved, the expression patterns in the petals differ from those found in the higher eudicots. The differences between these expression patterns suggest that the function of AP3 and PI homologues as B-class organ-identity genes is not rigidly conserved among all angiosperms. These observations have important implications for understanding the evolution of both angiosperm petals and the genetic mechanisms that control the identities of floral organs.     

AhBG1转基因拟南芥的ABA敏感性和抗旱性研究

为探究花生基因AhBG1对拟南芥ABA敏感性和抗旱性的影响,以过表达AhBG1拟南芥为材料,检测其ABA敏感性及脱水处理下ABA质量分数、叶片失水率、干旱存活率及ABA稳态相关基因表达变化.结果表明:AhBG1是编码花生β-葡萄糖苷酶的家族成员,定位于细胞质;与野生型相比,AhBG1过表达拟南芥植株在干旱条件下体内AB...     

Hsp90 as a capacitor of phenotypic variation

Heat-shock protein 90 (Hsp90) chaperones the maturation of many regulatory proteins and, in the fruitfly Drosophila melanogaster, buffers genetic variation in morphogenetic pathways. Levels and patterns of genetic variation differ greatly between obligatorily outbreeding species such as fruitflies and self-fertilizing species such as the plant Arabidopsis thaliana. Also, plant development is more plastic, being coupled to environmental cues. Here we report that, in Arabidopsis accessions and recombinant inbred lines, reducing Hsp90 function produces an array of morphological phenotypes, which are dependent on underlying genetic variation. The strength and breadth of Hsp90's effects on the buffering and release of genetic variation suggests it may have an impact on evolutionary processes. We also show that Hsp90 influences morphogenetic responses to environmental cues and buffers normal development from destabilizing effects of stochastic processes. Manipulating Hsp90's buffering capacity offers a tool for harnessing cryptic genetic variation and for elucidating the interplay between genotypes, environments and stochastic events in the determination of phenotype.     

多基因双T-DNA植物表达载体的构建及拟南芥转化

多基因植物表达载体用于植物遗传转化是培育具有多种优良品质作物的有效策略. 双T-DNA系统是实现筛选完成后选择标记基因删除的一种简便可行的方式. 为培育高度抗逆或去除标记基因的农作物，构建了多基因双T-DNA植物表达载体2T-bbgdD，其中含有一个抗除草剂基因bar, 3个抗逆相关基因(DREB1A, Na+依赖性Pi转运体基因（d5）, betA)和一个报告基因gfp. 利用农杆菌介导法将该载体转入拟南芥，获得了多基因共转化及去除标记基因的转基因拟南芥. 可将此植物表达载体进一步用于作物的遗传转化.     

细胞自噬对拟南芥种子萌发的影响

自噬在植物生长发育过程发挥着至关重要的作用，但是植物中自噬与种子萌发的关系尚不明确。为了探究自噬对种子萌发的影响，通过基因表达检测、蛋白免疫印迹实验和种子萌发速率比较，分析了细胞自噬对拟南芥(Arabidopsis thaliana)种子萌发的影响。研究结果表明细胞自噬在植物种子萌发过程中发挥重要作用:(1)自噬基因的表达在种子萌发过程中明显上调，且ATG8蛋白在种子萌发过程中逐渐积累，表明种子萌发过程中细胞自噬被激活；(2)细胞自噬抑制剂3-methyladenine (3-MA)能够显著地抑制拟南芥野生型种子的萌发，拟南芥自噬突变体种子的萌发速度比野生型种子的慢，表明细胞自噬途径在种子萌发过程中发挥正向调控作用但不是种子萌发所必需的。     

茎瘤芥BjMYB1基因的克隆、表达与遗传转化研究

MYB转录因子广泛地参与了植物细胞分化、细胞周期的调节,激素和环境因子应答等过程。本研究根据茎瘤芥转录组测序筛选获得了一个MYB基因片段。通过RACE的方法,克隆得到了两条长度分别为975bp和864bp的全长序列,分析发现可能为茎瘤芥MYB基因的两种不同选择性拼接形式,并命名为BjMYB1-3和BjMYB1-4。对BjMYB1-3和BjMYB1-4做组织表达分析,发现这两个转录本在茎中特异表达。针对BjMYB1-3和BjMYB1-4的亚细胞定位分析,显示BjMYB1-4定位于细胞核,BjMYB1-3部分定位于细胞核。构建BjMYB-3和BjMYB1-4的超表达载体转化拟南芥,结果显示超表达转化的植株会使拟南芥提前抽薹和开花,说明BjMYB1-3和BjMYB1-4在植株的生长发育过程中起着一定作用,为进一步阐明茎瘤芥BjMYB1基因的功能奠定了基础。     

Plant genetics: increased outcrossing in hothead mutants

Arising from: S. J. Lolle, J. L. Victor, J. M. Young & R. E. Pruitt 434, 505-509 (2005); Lolle et al. reply. Lolle et al. report that loss-of-function alleles of the HOTHEAD (HTH) gene in Arabidopsis thaliana are genetically unstable, giving rise to wild-type revertants. On the basis of the reversion of many other genetic markers in hth plants, they suggested a model in which a cache of extragenomic information could cause genes to revert to the genotype of previous generations. In our attempts to reproduce this phenomenon, we discovered that hth mutants show a marked tendency to outcross (unlike wild-type A. thaliana, which is almost exclusively self-fertilizing). Moreover, when hth plants are grown in isolation, their genetic inheritance is completely stable. These results may provide an alternative explanation for the genome wide non-mendelian inheritance reported by Lolle et al.     

拟南芥BLI基因调控植物衰老的研究

BLISTER(BLI)蛋白是多种应激反应的调节因子,可以促进植物对环境的适应性.BLI蛋白通过抑制IRE 1蛋白以维持植物的正常生长,缺失BLI蛋白的拟南芥植株出现多种发育缺陷表型.文章以拟南芥bli突变体为实验材料,通过细胞生物学及遗传学方法检测其衰老相关表征,发现bli突变体植株早期出现叶片黄化、叶绿素含量下降、...