Projects

2010
<ul> <li>Preparation of EST data: Sequences were extracted from dbEST and were subjected to quality control screening (vector, E. coli, polyA, T, or CT removal, minimum length = 100 bp, < 3% N).</li> <li>Preparation of transcript (ET) database: All sequences from the appropriate divisions of GenBank (including RefSeq) were extracted. Non-coding sequences were discarded and cDNAs and coding sequences from genomic entries were saved. Sequences and related information (e.g. PubMed links) are stored in the qcGene database (qcGene).</li> <li>Assembly: Cleaned EST sequences and non-redundant transcript (ET) sequences were combined. Using the Paracel Transcript Assembler Program, sequences were assembled into contigs. TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 94% sequence identity. These strict criteria help minimize the creation of chimeric contigs. These contigs are assigned a TC (Tentative Consensus) number. TCs may comprise ESTs derived from different tissues. The best hits for TC's were assigned by searching the TC set against a non-redundant amino acid database(nraa) using BLAT. The top five hits based on score were selected and displayed for each TC.</li> <li>Caveats: TCs are only as good as the ESTs underlying them; there may be unspliced or chimeric ESTs and thus TCs. There is still redundancy in the TC set because sequences must match end to end and at a certain percent identity to be combined. Directionality of the TCs should not be assumed. Not all TCs contain protein-coding regions.</li> </ul>
2010
The Medicago truncatula sequencing project was initiated with a generous grant from Samuel Roberts Noble Foundation to the University of Oklahoma. Beginning in 2003 (and renewed in 2006), the National Science Foundation and the European Union's Sixth Framework Programme provided funding to complete sequencing of the remaining euchromatic genespace. Among the eight chromosomes in Medicago, six are being sequenced by NSF project "Sequencing the Gene Space of the Model Legume, Medicago Truncatula," and two are being sequenced by partners in Europe. Nevin Young (University of Minnesota), Bruce Roe (ACGT, University of Oklahoma; chromosomes 1, 4, 6, 8), and Chris Town (TIGR; chromosomes 2, 7) are principal investigators of the U.S. project. In Europe, collaborators include Giles Oldroyd (John Innes Center) coordinating sequencing of chromosome 3 at the Sanger Center, and Frederic Deballe (INRA-CNRS) coordinating sequencing of chromosome 5 at Genoscope. The genome annotation was carried out by the International Medicago Genome Annotation Group (IMGAG), which involves participants from TIGR, INRA-CNRS, MIPS, UMN, Ghent University and NCGR.
2010
<p>Preparation of EST data: Sequences were extracted from dbEST and were subjected to quality control screening (vector, E. coli, polyA, T, or CT removal, minimum length = 100 bp, &lt; 3% N). Preparation of transcript (ET) database: All sequences from the appropriate divisions of GenBank (including RefSeq) were extracted. Non-coding sequences were discarded and cDNAs and coding sequences from genomic entries were saved. Sequences and related information (e.g. PubMed links) are stored in the qcGene database (qcGene). Assembly: Cleaned EST sequences and non-redundant transcript (ET) sequences were combined. Using the Paracel Transcript Assembler Program, sequences were assembled into contigs. TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 94% sequence identity. These strict criteria help minimize the creation of chimeric contigs. These contigs are assigned a TC (Tentative Consensus) number. TCs may comprise ESTs derived from different tissues. The best hits for TC's were assigned by searching the TC set against a non-redundant amino acid database(nraa) using BLAT. The top five hits based on score were selected and displayed for each TC. Caveats: TCs are only as good as the ESTs underlying them; there may be unspliced or chimeric ESTs and thus TCs. There is still redundancy in the TC set because sequences must match end to end and at a certain percent identity to be combined. Directionality of the TCs should not be assumed. Not all TCs contain protein-coding regions.</p>
2009
Development of cultivars with improved nutritional profile and agronomic characters are among the major objectives in field pea breeding at the Crop Development Centre (CDC).In this project, 169 pea accessions of the cultivated pea Pisum sativum, wild relative species P. fulvum and several wild sub-species accessions (subspp. abyssinicum, arvense, and elatius) collected from eastern Europe, Russia and Canada were screened for their nutritional profile including total starch, amylose, amylopectin, fiber and protein by wet chemistry and/or near infrared (NIR) methods, and for reaction to ascochyta blight under controlled and/or field conditions.
2009
Lentil is an economically important pulse crop for Canada produced mainly for the export market. In conventional breeding programs, several segregating generations must be grown in order to reach a certain level of homozygosity that allows the selection of traits of interest. In contrast, double-haploid (DH) technology produces instant homozygosity and thus can significantly reduce the time required for developing new varieties. The efficiency of the lentil breeding program will also be improved through the reduction in the population size required for screening.
2009
The project will evaluate the effect of growing mixtures of semileafless (cv. CDC Dakota) and leafy (cv. CDC Sonata) field peas on Mycosphaerella blight development, weed suppression, lodging, and yields. The objectives of the project are to identify an optimum ratio of semileafless to leafy peas for organic production, and to investigate the effect of different pea canopy environments on Mycosphaerella blight development.
2009
Colletotrichum truncatum is a pathogen of several leguminous plant species where it causes a disease called anthracnose. Host specialization, infertility and genetic differentiation among isolates from different hosts have been demonstrated. In the population of C. truncatum from lentil two races were described. Detailed histological studies of the infection process by isolates of both races have revealed quantitative rather than qualitative differences.
2009
Lentil anthracnose is currently the most important lentil disease in Saskatchewan. In a project about to be completed on molecular aspects of this pathogen, we generated an extensive library of genes activated by the anthracnose fungus and by lentil during the infection process. In order to fully benefit from the investment made in this NSERC-CRD, we received one-year funding to confirm the function of a number of genes in the anthracnose fungus, Colletotrichum truncatum, that we have identified and believe to be involved in virulence of the fungus.
2009
The project has three phases: In the first phase, chickpea genotypes were evaluated in the growth chambers for their flowering response under both long (16 h) and short days (10 h) and 22 0C and 16 0C day and night temperatures. Variability among the genotypes in their flowering response under either long or short days was identified. In the second phase of the study eight selected chickpea genotypes with extreme responses to photoperiod will be evaluated to determine the timing and duration of the photoperiod sensitive phase and the time of floral initiation and to establish whether photoperiod sensitivity ends at floral initiation or if it extends further into the phases of flower development. These same eight genotypes will be further characterized in a factorial combination of two photoperiods: 10 h and 16 h and three temperatures regimes: 16/8 0C, 20/12 0C and 24/16 0C (day/night). This study allows us to determine flowering response of chickpea genotypes grown in a range of thermal regimes combined with either long or short days. In the third phase of the study, chickpea RILs derived from a cross between ICCV 96029 and CDC Frontier and their parents will be used for mapping genes for early flowering, photoperiod insensitivity and reaction to ascochyta blight.
2009
Approximately 60-80% of total phosphorus is stored in crop seeds as phytate. Phytate is not readily available to humans and non-ruminant livestock because of their lack of phytase enzyme. The low-phytate lines had similar seedling emergence counts, vine length, lodging score, and mycosphaerella blight score when compared with CDC Bronco. The low-phytate lines had somewhat later days to flowering and days to maturity, and somewhat lower grain yield and seed weight than CDC Bronco. Harvested seeds of the low-phytate lines had substantially higher inorganic phosphorus (1.21-1.28 mg/g) concentration than CDC Bronco (0.24-0.25 mg/g) and the other normal-phytate cultivars.

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