Dataset Information

MC1R genotype and plumage colouration in the zebra finch (Taeniopygia guttata): population structure generates artefactual associations.

ABSTRACT: Polymorphisms at the melanocortin-1 receptor (MC1R) gene have been linked to coloration in many vertebrate species. However, the potentially confounding influence of population structure has rarely been controlled for. We explored the role of the MC1R in a model avian system by sequencing the coding region in 162 zebra finches comprising 79 wild type and 83 white individuals from five stocks. Allelic counts differed significantly between the two plumage morphs at multiple segregating sites, but these were mostly synonymous. To provide a control, the birds were genotyped at eight microsatellites and subjected to Bayesian cluster analysis, revealing two distinct groups. We therefore crossed wild type with white individuals and backcrossed the F1s with white birds. No significant associations were detected in the resulting offspring, suggesting that our original findings were a byproduct of genome-wide divergence. Our results are consistent with a previous study that found no association between MC1R polymorphism and plumage coloration in leaf warblers. They also contribute towards a growing body of evidence suggesting that care should be taken to quantify, and where necessary control for, population structure in association studies.

SUBMITTER: Hoffman JI

PROVIDER: S-EPMC3906038 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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MC1R genotype and plumage colouration in the zebra finch (Taeniopygia guttata): population structure generates artefactual associations.

Hoffman Joseph I JI Krause E Tobias ET Lehmann Katrin K Krüger Oliver O

PloS one 20140129 1

Polymorphisms at the melanocortin-1 receptor (MC1R) gene have been linked to coloration in many vertebrate species. However, the potentially confounding influence of population structure has rarely been controlled for. We explored the role of the MC1R in a model avian system by sequencing the coding region in 162 zebra finches comprising 79 wild type and 83 white individuals from five stocks. Allelic counts differed significantly between the two plumage morphs at multiple segregating sites, but ...[more]

PMID: 24489736

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Project description:BACKGROUND:The proteins of avian eggshell organic matrices are thought to control the mineralization of the eggshell in the shell gland (uterus). Proteomic analysis of such matrices identified many candidates for such a role. However, all matrices analyzed to date come from species of one avian family, the Phasianidae. To analyze the conservation of such proteins throughout the entire class Aves and to possibly identify a common protein toolkit enabling eggshell mineralization, it is important to analyze eggshell matrices from other avian families. Because mass spectrometry-based in-depth proteomic analysis still depends on sequence databases as comprehensive and accurate as possible, the obvious choice for a first such comparative study was the eggshell matrix of zebra finch, the genome sequence of which is the only songbird genome published to date. RESULTS:The zebra finch eggshell matrix comprised 475 accepted protein identifications. Most of these proteins (84 %) were previously identified in species of the Phasianidae family (chicken, turkey, quail). This also included most of the so-called eggshell-specific proteins, the ovocleidins and ovocalyxins. Ovocleidin-116 was the second most abundant protein in the zebra finch eggshell matrix. Major proteins also included ovocalyxin-32 and -36. The sequence of ovocleidin-17 was not contained in the sequence database, but a presumptive homolog was tentatively identified by N-terminal sequence analysis of a prominent 17 kDa band. The major proteins also included three proteins similar to ovalbumin, the most abundant of which was identified as ovalbumin with the aid of two characteristic phosphorylation sites. Several other proteins identified in Phasianidae eggshell matrices were not identified. When the zebra finch sequence database contained a sequence similar to a missing phasianid protein it may be assumed that the protein is missing from the matrix. This applied to ovocalyxin-21/gastrokine-1, a major protein of the chicken eggshell matrix, to EDIL3 and to lactadherin. In other cases failure to identify a particular protein may be due to the absence of this protein from the sequence database, highlighting the importance of better, more comprehensive sequence databases. CONCLUSIONS:The results indicate that ovocleidin-116, ovocleidin-17, ovocalyxin-36 and ovocalyxin-32 may be universal avian eggshell-mineralizing proteins. All the more important it is to elucidate the role of these proteins at the molecular level. This cannot be achieved by proteomic studies but will need application of other methods, such as atomic force microscopy or gene knockouts. However, it will also be important to analyze more eggshell matrices of different avian families to unequivocally identify other mineralization toolkit proteins apart from ovocleidins and ovocalyxins. Progress in this respect will depend critically on the availability of more, and more comprehensive, sequence databases. The development of faster and cheaper nucleotide sequencing methods has considerably accelerated genome and transcriptome sequencing, but this seems to concur with frequent publication of incomplete and fragmented sequence databases.

Project description:Avian animals are visually inclined, which has caused them to attract increasing attention for visual neurophysiology or electrophysiology studies, including the study of the visual evoked potential (VEP). VEP has developed into an investigative tool for understanding the physiology and the pathology of the visual pathway. Chemical restraint is a common method to minimize motion artifacts in animals when acquiring VEP data, but little is known about its influence on the signal in an avian animal. In addition, it is difficult to make comparisons between conscious state data when the animals are ultimately under anesthesia. Therefore, finding drugs and developing protocols that have an acceptable effect is valuable. We compared the local field potentials of physically and chemically restrained zebra finches (Taeniopygia guttata), a small avian species, to simulate a relatively challenging recording condition. Finches were sedated with midazolam-butorphanol, and anesthesia was maintained by isoflurane. Electrodes were implanted into the left nucleus rotundus, which is a visual nucleus in birds. The VEPs of the control group (N = 3) were recorded after they fully recovered and were restrained by towels. The other birds (N = 3) were recorded under anesthesia. The results show that without the visual stimuli, anesthesia generally suppressed the overall power of field potentials. However, by focusing on the spectra during VEPs, visual stimuli still triggered significant VEPs in frequencies below 30.8 Hz, which were even stronger than towel-restrained birds. The drugs also prolonged the latency of the VEP, increased the duration of the VEP when compared to towel-restrained birds. As regard to towel-restrained zebra finches, the field potentials were less synchronized and may need data preprocessing to have clear VEPs. In conclusion, the current study presents evidence of basic VEP for zebra finch under midazolam-butorphanol-isoflurane anesthesia with a protocol that is a safe and feasible anesthetic combination for chemical restraint, which is particularly useful for small animals when obtaining evoked potentials.

Dataset Information

MC1R genotype and plumage colouration in the zebra finch (Taeniopygia guttata): population structure generates artefactual associations.

Publications

MC1R genotype and plumage colouration in the zebra finch (Taeniopygia guttata): population structure generates artefactual associations.

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