Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

Comparative BAC-based mapping in the whitethroated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization Romanov et al. Romanov et al. BMC Research Notes 2011, 4:211 http://www.biomedcentral.com/1756-0500/4/211 (21 June 2011) Romanov et al. BMC Research Notes 2011, 4:211 http://www.biomedcentral.com/1756-0500/4/211 SHORT REPORT Open Access Comparative BAC-based mapping in the whitethroated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization Michael N Romanov1, Jerry B Dodgson2, Rusty A Gonser1 and Elaina M Tuttle1* Abstract Background: The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new “nonmodel” organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings: We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions: These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms. Background Much of our current knowledge of genetics and genomics comes from traditional model organisms that are often raised for many generations in the laboratory. Although model organisms offer several advantages, as with inbred strains where it is often easier to isolate the factors associated with particular traits (e.g. [1]), they can also show altered behaviors, physiologies, and genetic responses due to extended exposures to laboratory environments (e.g. [2-5]). Traits of interest may not be expressed or might be entirely absent from the phenotypic repertoire of a model organism [6]. Finally, in laboratory systems it is difficult to determine the relative influence of genes and environments, which can be absolutely essential considering that many complex * Correspondence: 1 Dept. of Biology, Indiana State University, Terre Haute, Indiana 47809, USA Full list of author information is available at the end of the article traits have low heritabilities, exhibit strong gene-byenvironment effects, or are influenced by epigenetics. Studies of “non-model” organisms can therefore advance our understanding of genetic and genomic patterns and processes as these species are still subject to evolutionary forces such as selection, gene flow, and drift [6,7]. For non-model organisms to be useful for genomic inquiry, their genomes need to be structurally and functionally characterized. Genomic tools and resources, initially developed from species determined to be either medically or economically significant, have paved the way for comparative studies of the genomes of nonmodel organisms. For example, the first avian genome to be sequenced was the chicken (Gallus gallus) [8,9]. Since then, several other avian genomes have been sequenced and/or characterized to some extent, including other economically important species such as the turkey (Meleagris gallopavo) [10], main neurobiological © 2011 Tuttle et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Romanov et al. BMC Research Notes 2011, 4:211 http://www.biomedcentral.com/1756-0500/4/211 models such as the zebra finch (Taeniopygia guttata) [11], ecologically essential species such as flycatchers (Ficedula spp.) [12-15], and species critical to conservation such as the California condor (Gymnogyps californianus) [16-18]. Comparative genomics methodologies have illuminated many similarities [14,15,19-21] and differences [11,12,22-24] across these taxonomic groups. Birds occupy a unique evolutionary position and many have been so well studied that continued comparative work within this group promises to remain fruitful and open new avenues for fundamental and applied biological research. The white-throated sparrow (Zonotrichia albicollis), with its morphological, behavioral and chromosomal polymorphisms, represents a new system to study genomic mechanisms underlying variation [17]. Males and females in this species occur as either white or tan morphs [25] (Figure 1) that exhibit alternate behaviors. White morphs are promiscuous and show lower parental effort, whereas tan morphs are monogamous and exhibit higher levels of parental care [26]. Behavioral and morphological differences in the two morphs appear to have a genetic basis [27,28]: white birds are heterozygous for a complex rearrangement on chromosome 2 (i. e. ZAL2 m /ZAL2), whereas tan birds do not carry the rearrangement (i.e. ZAL2/ZAL2) [17,29,30]. Homozygous white birds (ZAL2m/ZAL2m ) are rarely found (< 0.06%; Tuttle, unpublished data). Karyotypic evidence also suggests inter-chromosomal linkage with chromosome 3 [17]. White and tan morphs mate disassortatively [25,27,28], maintaining polymorphism in this species and resulting in pair types that differ in the amount of biparental care they provide [31]. The disassortative pair types also differ in other key behavioral and ecological attributes [26,32-34]. Together, these traits make the species not only an ideal model in which to study the genomics of social behavior, but study of the genomics in this species will also advance our understanding of chromosome structure, immunity and disease, language and learning, as well as fertility and reproduction. The availability of a genomic BAC library for the white-throated sparrow [30] allows physical mapping, followed by refined cytogenetic and linkage mapping. The integration of these maps, coupled with in-depth sequencing of the targeted regions on white-throated sparrow chromos (...truncated)