Projects

2009 to 2011
Eight germplasm were chosen for this project:CDC WM-2, BAT 93, Expresso, Higuera-E, Jalo EEP-558, PI 430219, SMARC1N-PN1, and W6-15578. Tissue was collected from multiple plants at various developmental stages for RNA extraction which led to the generation of 3'-anchored cDNA libraries using the method described in Parkin et al., 2010. Each line was sequenced using the Roche 454 Titanium sequencing protocol. Sequencing reads were aligned directly to the Phaseolus vulgaris genomic build v0.9 using GMap. Then loci which were polymorphic between at least two of the lines were identified resulting in 133,108 SNPs. All SNPs were re-mapped to the published genome assembly 1.0 (Phytozome.org; Schmutz et al. 2014).
2011
An Illumina Golden Gate array was developed using SNPs identified as part of the Pea 454 Sequencing & Genotyping Project. Loci where chosen such that the SNPs should be distributed evenly across the genome based on comparison to Medicago truncatula.
2004 to 2010
Pea yields on the prairies are not consistent in amount from year to year due to stress in the growing season. Pea yields are substantially reduced in warm summers. A preliminary analysis of the check varieties, as well as newly released varieties (cultivars) from the Saskatchewan and Western Canada Cooperative pea yield trials (2000 to 2009) shows that days to maturity and length of reproductive growth are both reduced in warm or dry summers, resulting in low yield. With a warming climate, the pea crop is going to be stressed more often, resulting in shorter times of growth and substantial reductions in yield amount and quality. An analysis of the COOP yield trials should be completed by late 2010.
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.

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