9 research outputs found

    MaizeGDB's new data types, resources and activities

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    MaizeGDB is the Maize Genetics and Genomics Database. Available at MaizeGDB are diverse data that support maize research including maps, gene product information, loci and their various alleles, phenotypes (both naturally occurring and as a result of directed mutagenesis), stocks, sequences, molecular markers, references and contact information for maize researchers worldwide. Also available through MaizeGDB are various community support service bulletin boards including the Editorial Board's list of high-impact papers, information about the Annual Maize Genetics Conference and the Jobs board where employment opportunities are posted. Reported here are data updates, improvements to interfaces and changes to standard operating procedures that have been made during the past 2 years. MaizeGDB is freely available and can be accessed online at

    QTL Controlling Masculinization of Ear Tips in a Maize (Zea mays L.) Intraspecific Cross

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    Maize is unique among cereal grasses because of its monoecious flowering habit. Male flowers are normally restricted to the tassel that terminates the primary shoot, whereas female flowers occur as ears at the terminal nodes of lateral branches. We observed Ki14, a tropical maize inbred that produces an ear tipped by a staminate (male) spike under certain environmental conditions, such as long daylengths. Recombinant inbred lines derived from the cross between temperate line B97, which was never observed to produce a staminate ear tip, and Ki14 segregated for the trait under long daylengths. Some progeny lines that had even longer staminate tips than Ki14 were male fertile. We mapped three QTL controlling staminate ear tip using a two-part (binomial plus normal) model. A major QTL on chromosome 3 had a large effect on penetrance of the trait (whether a line would produce staminate ear tips or not) as well as its severity (the length of the staminate tip). This QTL seems to be linked to, but at a distinct position from, a previously mapped QTL controlling the proportion of staminate florets in ears in progeny from crosses between maize and teosinte. Two additional QTL affecting staminate ear tip severity overlapped with QTL controlling photoperiod response previously mapped in this population. Alleles conferring photoperiod sensitivity for delayed flowering at these QTL seem to enhance the production of staminate ear tips under long daylengths

    Sequencing and distribution analysis of Dissociation transposon events throughout the Zea mays genome

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    The transposon Dissociation is a nonautonomous element derived from Activator. The Ac/Ds project, a collaborative effort to cast stable Ds insertions throughout the maize genome, is a valuable tool for generating a reverse genetics resource. By using Ac::immobilized, an Ac element that cannot mobilize but can produce transposase, a Ds element in the anthocyanin regulating allele r1-sc:m3 can be mobilized. As of October 5th, 2007, 816 unlinked and 126 linked families have been produced and sequenced, with a 77% success rate. Repeat masking shows a low content of repetitive sequence, implying that these events in genic regions. By examining transposition events into the donor chromosome, transposition patterns can be observed. 95% of hits land within 40 cM of the donor site. Because the Ac/Ds project uses the W22 inbred line, sequence from large fDs fragments was compared against GSS assemblies from B73. The identity between B73 and W22 is 96.5%

    Characterization of Lipoxygenase (LOX) Gene Family and SNP Validation in Relation to Aflatoxin Resistance in Maize (Zea Mays L.)

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    An efficient approach to combat the accumulation of aflatoxin is the development of germplasm resistant to infection and spread of A. flavus in maize, one of the most important cereal grains in the world. Lipoxygenases (LOXs) are a group enzymes that catalyze oxygenation of polyunsaturated fatty acids (PUFAs). LOX derived oxilipins play critical roles in plant defense against pathogens such as A. flavus. The objectives of this study were to report sequence diversity and expression patterns for all LOX genes, and map their effect on aflatoxin accumulation via linkage and association mapping. Genes GRMZM2G102760 (ZmLOX 5) and GRMZM2G104843 (ZmLOX 8) fell under previously published QTL in one of four mapping populations and appear to have a measurable effect on the reduction of aflatoxin in maize grains. The association mapping result shows 19 of the total 215 SNPs found within the sequence of the ZmLOXs were associated with reduced aflatoxin levels

    Multicellular Phenotypic Studies of Single Gene Variants in Myxococcus xanthus

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    There are several systematic methods designed to link genes to cellular processes. These methods are derived from different hypotheses and are largely complementary to each other. This dissertation presents a systematic study of functional genetics and related phenotypes using quantitative methods. The first part of this dissertation will report the successful identification and characterization of 28 genes in the multicellular bacterium Myxococcus xanthus using three different methods: sequence homology, transcription activation and protemoics. The results from this research extended the list of M. xanthus genes involved in multicellularity, and expanded our knowledge regarding the possible molecular pathways underlying physiological and morphological changes. Although the cellular function of some of the genes in the genome of an organism can be deduced from effects of mutation on phenotype, the disruption or deletion of most genes produces little or no discernible phenotypic impact. The reason for this may be redundancy or complementation, or it may be due to the limitations inherent in available assays. The second part of this dissertation will focus on a population genetics approach to the characterization of phenotype for a collection of mutant strains containing insertion mutations in each of the ~200 ABC transporter component genes in M. xanthus. More than 50% of those mutant strains exhibit at least one phenotypic characteristic that is different from the wild type, and an average of 6% of mutant strains have a gain-of-function phenotype. We also demonstrated that the morphological features used to measure phenotype are not entirely independent variables. These results indicate that a rigorous and quantitative phenotypic characterization will provide significantly more data to understand the phenotypic space of M. xanthus, and that a more rigorous definition of phenotype may help us establish a more accurate connection between genotype and phenotype

    Genome diversity in Triticum aestivum

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    Quantitative trait loci analysis to identify modifiers genes of the gene opaque2 in maize endosperm

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    The protein quality of maize can be improved by replacing normal Opaque2 alleles with non-functional recessive alleles opaque2 (o2). The allele o2 produces a severe phenotype with soft endosperm enhancing its protein quality but decreasing its agronomical value. Plant breeders have restored a desirable ratio of hard to soft endosperm in o2 germplasm known as Quality Protein Maize (QPM). Neither the mechanism nor the genetic components by which the modification of the endosperm in QPM lines occurs are well understood. To increase the understanding of the genetics of endosperm modification, a population of 146 recombinant inbred lines derived from a cross between the o2 inbred line B73o2 and the QPM inbred line CML161 was evaluated in two Texas locations from 2004 to 2006. Four traits related to endosperm texture were measured and showed significant effect of the inbred lines, high heritability estimates and high genetic correlations. Relative content of the essential amino acids lysine, tryptophan and methionine were measured and showed significant effects of the lines and considerable high genetic correlations and heritabilities. Negative correlation was observed between endosperm texture traits and amino acid content. Quantitative trait loci (QTL) were mapped for traits related to the modification of endosperm texture and the content of lysine, tryptophan and methionine. QTLs clusters for endosperm texture traits were detected on chromosomes 3, 5, 6 and 8 explaining 62-68% of the variation. QTLs clusters for amino acid contents were located on chromosomes 7 and 8 that explained up to 39% of the observed variation. The product of the O2 gene is a transcription factor that affects the expression of a number of endosperm genes. A group of 29 endosperm genes associated with the O2 activity were evaluated in developing endosperm of the recombinant inbred lines. Genomic regions controlling gene transcript abundance in developing endosperm were identified by expression QTL mapping. Evidence is presented of QTL hot spots that segregate in association with endosperm texture modification or amino acid contents and are associated with the regulation of the expression of a group of endosperm genes

    Important information, data centers, tools and news items are accessible from the MaizeGDB home page

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    <p><b>Copyright information:</b></p><p>Taken from "MaizeGDB's new data types, resources and activities"</p><p>Nucleic Acids Research 2007;35(Database issue):D895-D900.</p><p>Published online Jan 2007</p><p>PMCID:PMC1899092.</p><p>© 2006 The Author(s)</p> Data and bulletin boards as well as links to noteworthy or high profile projects are accessible directly on the front page. All MaizeGDB pages have the same header, which is loaded with functionality enabling, e.g. searches of all data from any page () and access to tools including the Community Curation Tools. The ‘Maps’ Data Center () can limit results by contained loci, chromosome, source or mapping panel and also allows direct access to unique map types including the Recombination Nodule maps through its ‘Map Reports and Tools’ section. Likewise, the ‘Stocks’ Data Center () enables queries by focus linkage group, genotypic variation, karyotypic variation and other limitors. Bulletin boards that keep researchers connected with the community include the Editorial Board (), the Maize Genetics Executive Committee pages (), and the Annual Maize Genetics Conference, (which is referred to simply as ‘The Maize Meeting’) site (). Dates of database updates are available directly on the front page (), as are important major efforts of interest to all maize researchers like the Maize Genome Sequencing project
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