International journal of plant genomics最新文献

{"title":"Molecular cytogenetic mapping of chromosomal fragments and immunostaining of kinetochore proteins in Beta.","authors":"Daryna Dechyeva,&nbsp;Thomas Schmidt","doi":"10.1155/2009/721091","DOIUrl":"https://doi.org/10.1155/2009/721091","url":null,"abstract":"<p><p>By comparative multicolor FISH, we have physically mapped small chromosome fragments in the sugar beet addition lines PRO1 and PAT2 and analyzed the distribution of repetitive DNA families in species of the section Procumbentes of the genus Beta. Six repetitive probes were applied, including genotype-specific probes-satellites pTS4.1, pTS5, and pRp34 and a dispersed repeat pAp4, the telomere (TTTAGGG)(n), and the conserved 18S-5.8S-25S rRNA genes. Pachytene-FISH analysis of the native centromere organization allowed proposing the origin of PRO1 and PAT2 fragments. Comparative analysis of the repetitive DNA distribution and organization in the wild beet and in the addition lines allowed the development of a physical model of the chromosomal fragments. Immunostaining revealed that the PRO1 chromosome fragment binds alpha-tubulin and the serine 10-phosphorylated histone H3 specific for the active centromere. This is the first experimental detection of the kinetochore proteins in Beta showing their active involvement in chromosome segregation in mitosis.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/721091","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28506480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PROC QTL-A SAS Procedure for Mapping Quantitative Trait Loci.","authors":"Zhiqiu Hu,&nbsp;Shizhong Xu","doi":"10.1155/2009/141234","DOIUrl":"https://doi.org/10.1155/2009/141234","url":null,"abstract":"<p><p>Statistical analysis system (SAS) is the most comprehensive statistical analysis software package in the world. It offers data analysis for almost all experiments under various statistical models. Each analysis is performed using a particular subroutine, called a procedure (PROC). For example, PROC ANOVA performs analysis of variances. PROC QTL is a user-defined SAS procedure for mapping quantitative trait loci (QTL). It allows users to perform QTL mapping for continuous and discrete traits within the SAS platform. Users of PROC QTL are able to take advantage of all existing features offered by the general SAS software, for example, data management and graphical treatment. The current version of PROC QTL can perform QTL mapping for all line crossing experiments using maximum likelihood (ML), least square (LS), iteratively reweighted least square (IRLS), Fisher scoring (FISHER), Bayesian (BAYES), and empirical Bayes (EBAYES) methods.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/141234","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28617115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reproducible RNA preparation from sugarcane and citrus for functional genomic applications.","authors":"Mona B Damaj, Phillip D Beremand, Marco T Buenrostro-Nava, Beth Riedel, Joe J Molina, Siva P Kumpatla, Terry L Thomas, T Erik Mirkov","doi":"10.1155/2009/765367","DOIUrl":"10.1155/2009/765367","url":null,"abstract":"<p><p>High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying molecules can negatively impact the functionality of some plant RNA preparations employed in these procedures. We present a simplified, rapid, and scalable SDS/phenol-based method that provides the high-quantity and -quality RNA required by the newly emerging biotechnology applications. The method is applied to isolating RNA from tissues of two biotechnologically important crop plants, sugarcane and citrus, which provide a challenge due to the presence of fiber, polysaccharides, or secondary metabolites. The RNA isolated by this method is suitable for several downstream applications including northern blot hybridization, microarray analysis, and quantitative RT-PCR. This method has been used in a diverse range of projects ranging from screening plant lines overexpressing mammalian genes to analyzing plant responses to viral infection and defense signaling molecules.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28707556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"QTL mapping of a high protein digestibility trait in Sorghum bicolor.","authors":"Jennifer A Winn,&nbsp;R Esten Mason,&nbsp;Adriana L Robbins,&nbsp;William L Rooney,&nbsp;Dirk B Hays","doi":"10.1155/2009/471853","DOIUrl":"https://doi.org/10.1155/2009/471853","url":null,"abstract":"<p><p>Compared with other cereal grains, Sorghum bicolor shows lower protein digestibility. The low digestibility is thought to result from disulfide cross linking in the beta- and gamma-kafirins. In contrast, the single recessive high digestibility/high lysine content (HD) mutation which confers greater grain digestibility exists in sorghum that is thought to result from reduced accumulation of gamma-kafirin that allows greater access to the high digestible alpha-kafarin fraction. In an effort to both clearly define the molecular basis for the HD trait and develop tools to improve the introgression of this difficult-to-screen trait, this study focuses on mapping the QTLs linked to this trait. While the HD trait has been defined as a single recessive gene, our results uncovered that two major QTLs on chromosome 1 are associated with protein digestibility-one QTL (locus 1 from the HD parent) unfavorably affects digestibility and one QTL (locus 2 from the HD parent) only 20 cM away favorably affects digestibility. A contrast analysis between genotypic groups at these two loci shows that a higher level of protein digestibility may be obtained when this linkage in repulsion is broken and favorable alleles are allowed to recombine.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/471853","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28310875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in maize genomics and their value for enhancing genetic gains from breeding.","authors":"Yunbi Xu, Debra J Skinner, Huixia Wu, Natalia Palacios-Rojas, Jose Luis Araus, Jianbing Yan, Shibin Gao, Marilyn L Warburton, Jonathan H Crouch","doi":"10.1155/2009/957602","DOIUrl":"10.1155/2009/957602","url":null,"abstract":"<p><p>Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28345750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis of starch biosynthesis in the developing grain of hexaploid wheat.","authors":"Boryana S Stamova,&nbsp;Debbie Laudencia-Chingcuanco,&nbsp;Diane M Beckles","doi":"10.1155/2009/407426","DOIUrl":"https://doi.org/10.1155/2009/407426","url":null,"abstract":"<p><p>The expression of genes involved in starch synthesis in wheat was analyzed together with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses obtained from the same biological materials used for profiling of gene expression using DNA microarrays. Multiple expression patterns were detected for the different starch biosynthetic gene isoforms, suggesting their relative importance through caryopsis development. Members of the ADP-glucose pyrophosphorylase, starch synthase, starch branching enzyme, and sucrose synthase gene families showed different expression profiles; expression of some members of these gene families coincided with a period of high accumulation of starch while others did not. A biphasic pattern was observed in the rates of starch and protein accumulation which paralleled changes in global gene expression. Metabolic and regulatory genes that show a pattern of expression similar to starch accumulation and granule size distribution were identified, suggesting their coinvolvement in these biological processes.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/407426","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28772194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterelogous expression of plant genes.","authors":"Filiz Yesilirmak,&nbsp;Zehra Sayers","doi":"10.1155/2009/296482","DOIUrl":"https://doi.org/10.1155/2009/296482","url":null,"abstract":"<p><p>Heterologous expression allows the production of plant proteins in an organism which is simpler than the natural source. This technology is widely used for large-scale purification of plant proteins from microorganisms for biochemical and biophysical analyses. Additionally expression in well-defined model organisms provides insights into the functions of proteins in complex pathways. The present review gives an overview of recombinant plant protein production methods using bacteria, yeast, insect cells, and Xenopus laevis oocytes and discusses the advantages of each system for functional studies and protein characterization.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/296482","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40027599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Nest of LTR Retrotransposons Adjacent the Disease Resistance-Priming Gene NPR1 in Beta vulgaris L. U.S. Hybrid H20.","authors":"David Kuykendall,&nbsp;Jonathan Shao,&nbsp;Kenneth Trimmer","doi":"10.1155/2009/576742","DOIUrl":"https://doi.org/10.1155/2009/576742","url":null,"abstract":"<p><p>A nest of long terminal repeat (LTR) retrotransposons (RTRs), discovered by LTR_STRUC analysis, is near core genes encoding the NPR1 disease resistance-activating factor and a heat-shock-factor-(HSF-) like protein in sugarbeet hybrid US H20. SCHULTE, a 10 833 bp LTR retrotransposon, with 1372 bp LTRs that are 0.7% divergent, has two ORFs with unexpected introns but encoding a reverse transcriptase with rve and Rvt2 domains similar to Ty1/copia-type retrotransposons and a hypothetical protein. SCHULTE produced significant nucleotide BLAST alignments with repeat DNA elements from all four families of plants represented in the TIGR plant repeat database (PRD); the best nucleotide sequence alignment was to ToRTL1 in Lycopersicon esculentum. A second sugarbeet LTR retrotransposon, SCHMIDT, 11 565 bp in length, has 2561 bp LTRs that share 100% identity with each other and share 98-99% nucleotide sequence identity over 10% of their length with DRVs, a family of highly repetitive, relatively small DNA sequences that are widely dispersed over the sugarbeet genome. SCHMIDT encodes a complete gypsy-like polyprotein in a single ORF. Analysis using LTR_STRUC of an in silico deletion of both of the above two LTR retrotransposons found that SCHULTE and SCHMIDT had inserted within an older LTR retrotransposon, resulting in a nest that is only about 10 Kb upstream of NPR1 in sugarbeet hybrid US H20.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/576742","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28129456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery.","authors":"Baozhu Guo, Xiaoping Chen, Yanbin Hong, Xuanqiang Liang, Phat Dang, Tim Brenneman, Corley Holbrook, Albert Culbreath","doi":"10.1155/2009/715605","DOIUrl":"10.1155/2009/715605","url":null,"abstract":"<p><p>Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453.</p>","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28292573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wet laboratory tools widely used in plant genomics.","authors":"Hikmet Budak,&nbsp;Hongbin Zhang,&nbsp;Pushpendra K Gupta,&nbsp;Boulos Chalhoub,&nbsp;Andrew James,&nbsp;Chunji Liu","doi":"10.1155/2009/321975","DOIUrl":"https://doi.org/10.1155/2009/321975","url":null,"abstract":"The availability of laboratory tools is essential for advanced research in all areas of biological sciences. The recent development of genomic tools has made it possible to deeply investigate and to continuously improve agronomically important traits such as crop yield, quality, and biotic and abiotic stress tolerances. Integrating the newly advanced or developed wet laboratory tools that are widely used in modern genomics research and making them readily accessible will be greatly helpful for research of plant genomics and other disciplines of plant biology. Furthermore, the compilation of the tools will also facilitate scientists to advance the existing tools or develop new tools to address complicated or new questions that were previously intractable in plant genomics and biology. \u0000 \u0000In this special issue of the International Journal of Plant Genomics, “Wet lab tools widely used in plant genomics”, we present the current status of widely used genomics tools and update them with their new advances. Articles published in this special issue cover tools for structural, functional, and comparative genomics and proteomics. The issue also summarizes the advances of genome technology in the past decades and synthesizes the current status of knowledge of new tools with an extension of suggestions. By covering up-to-date genomics tools, this special issue provides a reference for studying the structural and functional organization and evolution of plant genomes. We aim that this special issue will become useful material for teaching and research in plant genomics and biology. \u0000 \u0000There are 8 articles in this special issue, starting with articles on tools for studying plant authopagy (Mitou et al.) and microRNA identification (Unver and Budak), cloning of small RNA (Eric et al.), and the use of virus-induced gene silencing techniques (Unver et al.) for functional analysis of genes and QTLs in plants. Included is also a comprehensive article on heterologous gene expression techniques given by Filiz and Sayers. An up-to-date protocol of Agro-mediated gene transfer in cereal crops is presented by Hensel et al. Additionally, Dechyeva and Schmidt reported one of the critical tools, the molecular cytogenetic mapping of chromosomal fragments and immunostaining of kinetochore proteins, which will greatly help cytogeneticists for identifying and tagging genes in plants, thus promoting plant molecular breeding.","PeriodicalId":73471,"journal":{"name":"International journal of plant genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2009/321975","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28736555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}