10% of the phenotypic variation in the RIL population, whereas 70.2% (33/47) explained

快速检测秸秆-煤混燃物对生物质混燃发电中补贴政策的制定具有重要意义。该研究采用可见/近红外光谱法定性判别秸秆、煤和秸秆-煤混燃物，定量分析秸秆-煤混燃物中秸秆含量。收集并制备秸秆样品80个（粒径小于80 mm）、煤样品9个（粒径小于10 mm），制备秸秆质量分数为70%～99%的秸秆-煤混燃物样品120个（混燃物1）、秸秆分数含量为1%～30%的秸秆-煤混燃物样品120个（混燃物2）。使用FOSS NIRS DS 2500型光谱仪获取样品光谱。分别使用偏最小二乘判别法（PLS-DA）建立定性分析模型，使用改进的偏最小二乘法（MPLS）建立定量分析模型。结果显示，在秸秆和混燃物1之间进行判别，使用1100～2 500 nm谱区，正确判别率为90.00%；在煤和混燃物2之间进行判别，使用400～2 500 nm谱区，正确判别率为71.88%；定量分析混燃物1和混燃物2中秸秆含量，相对分析误差分别为2.32（400～2 500 nm谱区）和1.48（400～1 100 nm谱区）。研究结果表明，1 100～2 500 nm谱区较适合秸秆和混燃物1之间的判别，该谱区同样适合定量分析混燃物1中秸秆含量。400～1 100 nm谱区较适合煤和混燃物2之间的判别，该谱区同样适合定量分析混燃物2中秸秆含量。可见/近红外光谱结合化学计量学是快速定性和定量分析大粒度秸秆-煤混燃物的可行方法。

以非转基因玉米种子为材料,比较了常用的3种植物基因组DNA提取试剂盒及改良的CTAB法,通过琼脂糖凝胶电泳、紫外分光光度及实时荧光PCR扩增检测,对提取得到的基因组DNA的纯度、得率及4种提取方法的重复性、提取时间进行分析;比较紫外分光光度法、Qubit荧光法、Pico Green荧光分光光度法,以实时荧光定量PCR检测结果为参照,对3种DNA浓度测定方法的准确性进行分析。结果显示,磁珠法(Promega)最适合应用于快速、简便、高效检测中的植物基因组DNA提取,能有效获得纯度高、完整性好的基因组DNA,并且磁珠法提取效率高,重复性好,提取时间短;在基因组DNA浓度测定中,紫外分光光度法、Qubit荧光法、Pico Green荧光分光光度法的相对误差分别为99.8%、49.8%和28.9%,表明Pico Green荧光分光光度法测定DNA浓度的准确度最高。

MOTIVATION: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. RESULTS: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. AVAILABILITY: http://maq.sourceforge.net.

Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.

Oilseed crops are used to produce vegetable oil. Sesame (Sesamum indicum), an oilseed crop grown worldwide, has high oil content and a small diploid genome, but the genetic basis of oil production and quality is unclear. Here we sequence 705 diverse sesame varieties to construct a haplotype map of the sesame genome and de novo assemble two representative varieties to identify sequence variations. We investigate 56 agronomic traits in four environments and identify 549 associated loci. Examination of the major loci identifies 46 candidate causative genes, including genes related to oil content, fatty acid biosynthesis and yield. Several of the candidate genes for oil content encode enzymes involved in oil metabolism. Two major genes associated with lignification and black pigmentation in the seed coat are also associated with large variation in oil content. These findings may inform breeding and improvement strategies for a broad range of oilseed crops.

UNLABELLED: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface. AVAILABILITY: http://www.broad.mit.edu/mpg/haploview/ CONTACT: jcbarret@broad.mit.edu

High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a 'variants reduction' protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires approximately 4 min to perform gene-based annotation and approximately 15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/.

Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.

The cell wall is the major limiting factor for plant growth. Wall extension is thought to result from the loosening of its structure. However, it is not known how this is coordinated with wall synthesis. We have identified two novel allelic cellulose-deficient dwarf mutants, kobito1-1 and kobito1-2 (kob1-1 and kob1-2). The cellulose deficiency was confirmed by the direct observation of microfibrils in most recent wall layers of elongating root cells. In contrast to the wild type, which showed transversely oriented parallel microfibrils, kob1 microfibrils were randomized and occluded by a layer of pectic material. No such changes were observed in another dwarf mutant, pom1, suggesting that the cellulose defect in kob1 is not an indirect result of the reduced cell elongation. Interestingly, in the meristematic zone of kob1 roots, microfibrils appeared unaltered compared with the wild type, suggesting a role for KOB1 preferentially in rapidly elongating cells. KOB1 was cloned and encodes a novel, highly conserved, plant-specific protein that is plasma membrane bound, as shown with a green fluorescent protein-KOB1 fusion protein. KOB1 mRNA was present in all organs investigated, and its overexpression did not cause visible phenotypic changes. KOB1 may be part of the cellulose synthesis machinery in elongating cells, or it may play a role in the coordination between cell elongation and cellulose synthesis.

Xyloglucan is the major hemicellulosic polysaccharide in the primary cell walls of most vascular dicotyledonous plants and has important structural and physiological functions in plant growth and development. In Arabidopsis (Arabidopsis thaliana), the 1,4-beta-glucan synthase, Cellulose Synthase-Like C4 (CSLC4), and three xylosyltransferases, XXT1, XXT2, and XXT5, act in the Golgi to form the xylosylated glucan backbone during xyloglucan biosynthesis. However, the functional organization of these enzymes in the Golgi membrane is currently unknown. In this study, we used bimolecular fluorescence complementation and in vitro pull-down assays to investigate the supramolecular organization of the CSLC4, XXT1, XXT2, and XXT5 proteins in Arabidopsis protoplasts. Quantification of bimolecular fluorescence complementation fluorescence by flow cytometry allowed us to perform competition assays that demonstrated the high probability of protein-protein complex formation in vivo and revealed differences in the abilities of these proteins to form multiprotein complexes. Results of in vitro pull-down assays using recombinant proteins confirmed that the physical interactions among XXTs occur through their catalytic domains. Additionally, coimmunoprecipitation of XXT2YFP and XXT5HA proteins from Arabidopsis protoplasts indicated that while the formation of the XXT2-XXT2 homocomplex involves disulfide bonds, the formation of the XXT2-XXT5 heterocomplex does not involve covalent interactions. The combined data allow us to propose that the proteins involved in xyloglucan biosynthesis function in a multiprotein complex composed of at least two homocomplexes, CSLC4-CSLC4 and XXT2-XXT2, and three heterocomplexes, XXT2-XXT5, XXT1-XXT2, and XXT5-CSLC4.

Root hairs are important for nutrient uptake, anchorage, and plant-microbe interactions. From a population of rice (Oryza sativa) mutagenized by ethyl methanesulfonate (EMS), a short root hair2 (srh2) mutant was identified. In hydroponic culture, srh2 seedlings were significantly reduced in root hair length. Bubble-like extrusions and irregular epidermal cells were observed at the tips of srh2 root hairs when grown under acidic conditions, suggesting the possible reduction of the tensile strength of the cell wall in this mutant. Map-based cloning identified a mutation in the gene encoding xyloglucan (XyG) 6-xylosyltransferase (OsXXT1). OsXXT1 displays more than 70% amino acid sequence identity with the previously characterized Arabidopsis thaliana XYG XYLOSYL TRANSFERASE 1 (AtXXT1) and XYG XYLOSYL TRANSFERASE 2 (AtXXT2), which catalyse the transfer of xylose onto beta-1,4-glucan chains. Furthermore, expression of the full-length coding sequence of OsXXT1 could complement the root hair defect, and slow growth and XyG synthesis in the Arabidopsis xxt1 xxt2 double mutant. Transgenic plants expressing the beta-glucuronidase (GUS) reporter under the control of the OsXXT1 promoter displayed GUS expression in multiple tissues, most prominently in root epidermal cells. These results demonstrate the importance of OsXXT1 in maintaining cell wall structure and tensile strength in rice, a typical grass species that contains relatively low XyG content in cell walls.

AbstractThe high degree of structural complexity of plant cell wall polysaccharides has led to suggestions that some components might function as latent signal molecules that are released during pathogen infections and elicit defensive responses by the plant. However, there has been a paucity of genetic evidence supporting the idea that variation in cell wall composition plays a role in the outcome of host–pathogen interactions. Recently, several genetic studies have provided new lines of evidence implicating cell wall polysaccharides as factors in host–pathogen interactions.]]>

We investigated the relationship between the expression of lipoxygenase (LOX) genes and the systemin-dependent wound response in tomato (Lycopersicon esculentum) leaves. A polymerase chain reaction-based approach was used to isolate two tomato Lox cDNAs, called TomLoxC and TomLoxD. Both TomLOXC and TomLOXD amino acid sequences possess an N-terminal extension of about 60 residues that were shown by in vitro uptake to function as transit peptides, targeting these proteins into the chloroplast. Within 30 to 50 min following wounding or systemin or methyl jasmonate treatments, the TomLoxD mRNA level increased and reached a maximum between 1 and 2 h. TomLoxC mRNA was not detectable in leaves and was not found following wounding, but it was found in ripening fruits, indicating that the two tomato Lox genes are regulated in different tissues by different processes. The results suggest that the TomLoxD gene is up-regulated in leaves in response to wounding and encodes a chloroplast LOX that may play a role as a component of the octadecanoid defense-signaling pathway.

植物蛋白酶抑制素是植物重要的防御物质之一，一般是分子量较小的多肽或蛋白质，能够与昆虫消化道内的蛋白酶形成复合物，阻断或削弱蛋白酶对食物中蛋白的水解，使昆虫厌食或消化不良而致死。植物蛋白酶抑制素在植物体内一般是诱导表达的，昆虫取食危害后，导致某些植物在伤口产生一种寡聚糖信息素-蛋白酶抑制素诱导因子，蛋白酶抑制素诱导因子诱导叶片局部产生植物蛋白酶抑制素，并刺激产生信号物质系统肽，通过十八烷酸途径在一系列酶的作用下产生茉莉酸，茉莉酸与受体结合，活化植物蛋白酶抑制素基因。昆虫在长期取食植物蛋白酶抑制素后会在生理及行为上产生适应性而导致不敏感，适应方式主要包括：(1)改变肠道蛋白酶对蛋白酶抑制素的敏感性；(2) 水解蛋白酶抑制素；(3)过量取食及干扰产生蛋白酶抑制素的信号通道。由于昆虫能够对植物蛋白酶抑制素产生适应，因此合理利用植物蛋白酶抑制素的抗虫作用显得十分重要。

Plants, as sessile organisms, employ multiple mechanisms to adapt to the seasonal and daily temperature fluctuations associated with their habitats. Here, we provide genetic and physiological evidence that the FtsH11 protease of Arabidopsis contributes to the overall tolerance of the plant to elevated temperatures. To identify the various mechanisms of thermotolerance in plants, we isolated a series of Arabidopsis thaliana thermo-sensitive mutants (atts) that fail to acquire thermotolerance after pre-conditioning at 38 degrees C. Two allelic mutants, atts244 and atts405, were found to be both highly susceptible to moderately elevated temperatures and defective in acquired thermotolerance. The growth and development of the mutant plants at all stages examined were arrested after exposure to temperatures above 30 degrees C, which are permissive conditions for wild-type plants. The affected gene in atts244 was identified through map-based cloning and encodes a chloroplast targeted FtsH protease, FtsH11. The Arabidopsis genome contains 12 predicted FtsH protease genes, with all previously characterized FtsH genes playing roles in the alleviation of light stress through the degradation of unassembled thylakoid membrane proteins and photodamaged photosystem II D1 protein. Photosynthetic capability, as measured by chlorophyll content (chl a/b ratios) and PSII quantum yield, is greatly reduced in the leaves of FtsH11 mutants when exposed to the moderately high temperature of 30 degrees C. Under high light conditions, however, FtsH11 mutants and wild-type plants showed no significant difference in photosynthesis capacity. Our results support a direct role for the A. thaliana FtsH11-encoded protease in thermotolerance, a function previously reported for bacterial and yeast FtsH proteases but not for those from plants.