Comparative Mapping of the Alpaca Genome

Abstract

The development of gene maps constitutes a key feature for understanding genome architecture and comparative evolution. The genomes of some livestock species such as cattle, horses and pigs, have received considerable attention over the years due to their economic importance. In contrast, though camelids are gaining worldwide popularity as production and companion animals, cytogenetics and genome mapping in these species lag far behind those of other mammals.

One of the reasons for the scarce body of knowledge regarding the camelid genome is their particularly difficult karyotype for analysis. All six extant camelid species have a diploid number of 74 chromosomes; the gross morphological similarities shared by many of the autosomes, combined with the relatively small size of some chromosome pairs, present serious challenges for identifying individual chromosomes using conventional cytogenetic techniques. The Alpaca Genome Project includes whole genome sequencing, radiation hybrid (RH) mapping and human-camel comparative chromosome painting (Zoo-FISH). However, there is no common platform that aligns various maps and precisely assigns them to individual chromosomes.

Therefore, the goal of this research project was to construct a cytogenetic map for the alpaca genome by fluorescence in situ hybridization (FISH) of large insert clones from the alpaca CHORI-246 genomic BAC library. The BACs were selected based on the available Zoo-FISH, RH and sequence map data to target evolutionarily conserved genes and to get uniform distribution of markers throughout the alpaca genome. Candidate genes for traits of interest such as various congenital and reproduction-related disorders, as well as for phenotypic traits such as fiber color and texture, were also selected for mapping. A total of 230 markers were mapped to the 36 alpaca autosomes and the sex chromosomes; moreover, comparative mapping showed exceptional conservation of both gene synteny and order between alpaca and dromedary camel chromosomes.

The cytogenetic map of the alpaca genome is a platform that effectively integrates the whole genome sequence and the radiation hybrid map with cytogenetic data, thus facilitating the discovery of genes of interest and providing tools for studying chromosome evolution and for clinical cytogenetics by means of a collection of chromosome-specific markers for camelids.