A Whole Genome Integrated Map for the Alpaca

Compared to other domestic species, alpaca genomics is still in its infancy. Recently developed alpaca genome sequence assemblies, vicPac1 (Sanger) and vicPac2 (454 GS-FLX), have not been integrated with each other or exhaustively annotated for genes and functional elements. The radiation hybrid (RH) map is still under development and only 44 genes have been physically assigned to alpaca chromosomes by fluorescence in situ hybridization (FISH). Currently, no common platform aligns various maps and assigns them to individual chromosomes in camelids. Therefore, the goal of this study was to integrate alpaca genome sequence scaffolds with various maps and physical chromosomes. This was achieved by mapping CHORI-246 genomic BAC library clones to alpaca chromosomes using FISH. The BACs were selected based on Zoo-FISH, RH map and genome sequence data to target evolutionarily conserved genes throughout the alpaca genome. The integrated map is comprised of 250 markers distributed in all 36 alpaca autosomes, as well as the sex chromosomes. Comparative mapping of 50 selected markers in the dromedary camel showed exceptional synteny and linkage conservation between the New and Old World camelids. The integrated map facilitates improvement of the assembly and annotation of the alpaca genome sequence and the discovery of genes of interest; it also provides tools for clinical cytogenetics and for the study of camelid karyotype evolution. Moreover, the collection of annotated and physically mapped BAC clones constitutes a unique resource for targeted re-sequencing and mutation discovery in camelids.