Progress 07/01/04 to 12/31/05
Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and National Scientific Research Center, Paris. Additional details of research can be found in the report for the parent CRIS 6204-21000-009-00D, Pests, Parasites, Diseases, and Stress of Honey Bees Used in Honey Production and Pollination. The honey bee genetic map was substantially improved in the duration of the project. The map is now composed of 2,000 markers as compared to 1,316 markers at the beginning of the project. The number of markers added is, in fact, higher than the difference between these two numbers, because about 100 markers were eradicated that represented polymorphic bands, markers of low quality and primers that did not amplify the expected regions. The rate of 30 loci added per week has been sustained during several months. In addition, the genotyping errors were eradicated, using double recombination method.
The quality of the map was greatly improved after correction of errors, and there is now almost perfect co-linearity between the sequence and the map. According to the latest calculation, the 205 Mb (90%) of the genome is now organized into the assembly. The mapping of the centromeric regions has also been improved. All chromosomes in the last assembly are oriented in the correct direction, from the centromeric to the telomeric regions. The properties of the chromosomes (A+T content, rate of recombination, gene density) are highly dependant on this orientation. Honey bee genetic map developed in this project served as a basis for improvement of the genome assembly Amel 3.0 and development of a new Amel 3.1 assembly due to addition of the large sequences previously labeled as unknowns and due to correction of the discrepancies attributable to the mis-assembled contigs. The scaffold of the complete genome sequence has been organized in groups and subgroups following information
available in the genetic map. The honey bee genetic map developed during this project was very useful for sequence of the genome, and in the future will be of great help for a number of molecular applications.
Impacts
(N/A)
Publications
|
Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and National Scientific Research Center, Paris. Additional details of research can be found in the report for the parent CRIS 6204-21000-009-00D "Pests, Parasites Diseases and Stress of Honey Bees Used in Honey Production and Pollination." The most recent mapping activity was done in the framework of the Honey Bee genome assembly Amel 3.0 (July 2004) and assembly Amel 4.0 (January 2005) to choose the scaffolds and design primers for the new markers. Each of these assemblies was itself based on a map calculated after a previous round of markers. Amel 3.0 and Amel 4.0 roughly contained 1,300 markers and 1,700, respectively. Half of the 400 markers that were added at the time corresponded to unknown scaffolds larger than 100 kb. Consequently, the size of the sequence in the assembly increased from 131 Mb to 159 Mb. Another 300 new markers were added
later, and the corresponding map with 2,000 markers will be calculated before the end of July 2005. These new markers were designed in the scaffolds larger than 73 Kb of the Amel 4.0. For the next six months another strategy will be used. We will choose those potentially helpful scaffolds (from the pool of < 73 Kb) to connect already assembled scaffolds into super-scaffolds. The very last phase of the project will be eradication of the rare genotyping errors to improve the order of closely located markers and generation of the genetic map with highly reliable genetic distances.
Impacts
(N/A)
Publications
|
|