ANCHORING THE GENOME SEQUENCE TO THE GENETIC LINKAGE MAP OF BLUEBERRY
Genetic Improvement of Fruits and Vegetables
2013 Annual Report
1a.Objectives (from AD-416):
To anchor the blueberry whole genome sequence to the genetic linkage map of blueberry by mapping SSR markers from scaffolds of the genome assembly.
1b.Approach (from AD-416):
ARS will add SSR markers, developed from the largest scaffolds of the current whole genome assembly provided by the collaborator, to the genetic linkage map of blueberry. ARS will attempt to map two SSRs per scaffold whenever possible, one from each end to orient the scaffold on the map.
In order to anchor the blueberry genome sequence to the genetic linkage map of blueberry, a variety of markers are being designed from sequence data and will be added to the current map of the diploid blueberry population. The diploid highbush genotype being sequenced is one of the parents of the mapping population. This year NCSU identified a graduate student who will work on this project, and ARS provided DNA from all the individual plants of the mapping population to NCSU. In addition, 1000 SSR primer pairs were designed from the 500 largest scaffolds of the genome assembly (two SSR primer pairs per scaffold), and 100 primer pairs were screened on parents of the population. Efforts to add these markers to the map are underway. In addition, leaf tissue is currently being collected from the individual plants of the mapping population and will be provided to NCSU for efforts to generate a transcript map of the population as well as use a genotyping x sequencing approach to saturate the map. This work will help scientists identify genes underlying traits important to the blueberry industry.