Genome Studies for Conservation of the California Condor
Construction of a physical and genetic map of the California condor
Through collaboration with the Children’s Hospital of Oakland Research Institute (CHORI), a bacterial artificial chromosome (BAC) library CHORI-262 containing large pieces of California condor DNA was constructed. Using OVERGO hybridization approach (Romanov et al., 2003), DNA probes derived from the chicken genome and New World vulture sequences were utilized to identify homologous pieces of DNA in the BAC library (Figure 1).
As a result, the arrayed library was probed with 172 OVERGO probes, including 164 from chicken, two condor probes, and six probes derived from DNA sequences from New World vultures. One vulture and 77 chicken probes did not produce any hits. The library screening resulted in 236 BAC-gene assignments and 2.5 positive BAC clones per probe. The 54% of chicken probes that produced successful hits, as well as the condor and New World vulture probes, provided the basis for the first BAC clone-based genome map of the California condor, constructed in comparison to the chicken genome map (Wallis et al., 2004). The first-generation chicken-condor comparative physical map contains 93 loci on 23 chicken chromosomes (12 macro- and 11 microchromosomes), with an average interval of about 10 Mb (Figure 2, Romanov et al., 2005).
These results show the usefulness of chicken genome sequences for identifying homologous sequences in the California condor through cross-species hybridization, in spite of their approximately 100 million years of evolutionary divergence.
Utilizing the small insert short tandem repeat (microsatellite) library previously prepared by Genetic Identification Services (GIS), we conducted genotyping for 17 polymorphic microsatellite loci on 60 California condors. These included the founders of the captive population and the other condors included in our 1993 study (Geyer et al., 1993). Allelic diversity was low in California condors based on microsatellite analysis. The number of alleles ranged from 2-5 and only 7 out of 17 loci had more than 2 alleles. Several condors have nearly identical genotypes at the 17 examined loci. One locus behaved anomalously and was discarded. For the other 16 loci, average heterozygosity was 0.25, quite low for a vertebrate species. These results imply that ancient population bottlenecks affected the condor gene pool (Ryder et al., 2005).
Kinship among the California condor founders is being analyzed with the microsatellite data to compare with an earlier DNA fingerprinting study (Geyer et al., 1993), as these kinship estimates are useful for recommending matings in the California condor breeding program.
Additional microsatellite loci are being identified from the California condor library constructed by GIS. We contracted with a commercial firm, High-Throughput Sequencing Solutions, to sequence in both directions a total of 1,920 microsatellite clones from the microsatellite enriched library that resulted in 928 sequence contigs. The sequences of the regions flanking the tandem repeats, characteristic of microsatellite loci, will be evaluated in several ways. OVERGOs produced from the newly identified microsatellite loci can be utilized to identify the location of these loci in the California condor BAC library arrays, thereby adding additional genetic markers to the comparative California condor map. Approximately 85% of the clones in the library contain microsatellites, affording an opportunity to add a significant number of loci to the condor map. These loci can also be utilized for genetic linkage studies resulting in a recombination-based linkage map of the California condor genome. This will greatly assist in homing in on the region of the California condor genome that is associated with heritable chondrodystrophy. Comparison of sequences flanking the microsatellite repeats to the chicken genome DNA sequence database will provide a basis for aligning additional large fragments of condor DNA (as are contained in the array BAC library) with the chicken genome, thereby helping construct the physical map of the condor genome.
As a separate effort, the NIH Intramural Sequencing Center generates several more condor BAC sequences within the Comparative Vertebrate Sequencing Initiative that is related to the Human Genome Project. The genomic target for this project is a human chromosome 7 region (HSA7q31), and a condor-human comparative physical map of this region is under construction.
California condor genome resources:
Rationale for Sequencing Selected BAC Clones of the Genome of the California Condor (Gymnogyps californianus)
Poster for the 2nd International Symposium of Conservation Genetics, Sept. 25-28, 2005, Pacific Grove, CA
Abstract for the Plant & Animal Genomes XIV Conference, Jan. 14-18, 2006, San Diego, CA
California Condor Genome Project: Introduction
Evaluating candidate loci for heritable chondrodystrophy in California condors
California Condor Genetic Studies: Sex Determination, Identification of Clan Structure and Coping with a Genetic Disease
Wild Animal Park: Condor Ridge
California Condor Recovery Program
Milestones in California Condor Conservation
California Condor Mortality Challenges
Social Development and Reintroduction of California Condors
Studies of Courtship and Parental Care in Reintroduced California Condors in the U.S. and Mexico