BackgroundThe cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.ResultsWe sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene.ConclusionsWe present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0780-4) contains supplementary material, which is available to authorized users.

ObjectiveThis study estimated the genetic parameters for body weight gain and growth curve parameter traits in Korean native chicken (KNC).MethodsA total of 585 F1 chickens were used along with 88 of their F0 birds. Body weights were measured every 2 weeks from hatching to 20 weeks of age to measure weight gain at 2-week intervals. For each individual, a logistic growth curve model was fitted to the longitudinal growth dataset to obtain three growth curve parameters (α, asymptotic final body weight; β, inflection point; and γ, constant scale that was proportional to the overall growth rate). Genetic parameters were estimated based on the linear-mixed model using a restricted maximum likelihood method.ResultsHeritability estimates of body weight gain traits were low to high (0.057 to 0.458). Heritability estimates for α, β, and γ were 0.211±0.08, 0.249±0.09, and 0.095±0.06, respectively. Both genetic and phenotypic correlations between weight gain traits ranged from −0.527 to 0.993. Genetic and phenotypic correlation between the growth curve parameters and weight gain traits ranged from −0.968 to 0.987.ConclusionBased on the results of this study population, we suggest that the KNC could be used for selective breeding between 6 and 8 weeks of age to enhance the overall genetic improvement of growth traits. After validation of these results in independent studies, these findings will be useful for further optimization of breeding programs for KNC.

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The melanocortin 1 receptor (MC1R) gene is related to the plumage color variations in chicken. Initially, the MC1R gene from 30 individuals was sequenced and nine polymorphisms were obtained. Of these, three and six single nucleotide polymorphisms (SNPs) were confirmed as synonymous and nonsynonymous mutations, respectively. Among these, three selected SNPs were genotyped using the restriction fragment length polymorphism (RFLP) method in 150 individuals from five chicken breeds, which identified the plumage color responding alleles. The neighbor-joining phylogenetic tree using MC1R gene sequences indicated three well-differentiated different plumage pigmentations (eumelanin, pheomelanin and albino). Also, the genotype analyses indicated that the TT, AA and GG genotypes corresponded to the eumelanin, pheomelanin and albino plumage pigmentations at nucleotide positions 69, 376 and 427, respectively. In contrast, high allele frequencies with T, A and G alleles corresponded to black, red/yellow and white plumage color in 69, 376 and 427 nucleotide positions, respectively. Also, amino acids changes at position Asn23Asn, Val126Ile and Thr143Ala were observed in melanin synthesis with identified possible alleles, respectively. In addition, high haplotype frequencies in TGA, CGG and CAA haplotypes were well discriminated based on the plumage pigmentation in chicken breeds. The results obtained in this study can be used for designing proper breeding and conservation strategies for the Korean native chicken breeds, as well as for the developing breed identification markers in chicken.

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10−49) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10−16). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and a* (PMGA = 1.69×10−28; PQTDT = 2.40×10−25). The strongest associations were between BCDO2 g.9367 A>C and b* (PMGA = 3.56×10−66; PQTDT = 1.68×10−65). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

Most reproductive traits have low heritability and are greatly affected by environmental factors. Teat number and litter size are traits related to the reproduction ability of pigs. To identify quantitative trait loci (QTLs) for teat number traits, a genome-wide association study (GWAS) was conducted using an F2 intercross between Landrace and Korean native pigs. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. When a genome-wide threshold was determined using the Bonferroni method (P = 1.61 × 10(-6)), 38 single nucleotide polymorphism (SNP) markers in pig chromosome 7 (SSC7) were significantly associated with three teat number traits (total teat number, left teat number, and right teat number). Among these, SNPs in 5 genes (HDDC3, LOC100156276, LOC100155863, ANPEP, SCAMP2) were selected for further study based primarily on their statistical significance. A significant association was detected in SCAMP2 g.25280 G>A for total teat number (P = 2.0 × 10(-12)), HDDC3 g.1319 G>A SNP for left teat number (P = 2.3 × 10(-7)), and SCAMP2 g.14198 G>A for right teat number (P = 4.7 × 10(-12)). These results provide valuable information about the selective breeding for desirable teat numbers in pigs.

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Body and carcass weights are always being main focus in poultry industry. The aim of current study was to estimate the heritability, genetic and phenotypic correlations of growth-related traits in Korean native chicken. A total of 596 chickens representing five lines of Korean native chicken (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared under the standard breeding procedures in the National Institute of Animal Science (NIAS), Korea. Their body weights were observed every two weeks from hatched to 20 weeks of age. In addition, shank length and carcass weight were also measured before and after slaughter, respectively. The ASReml-R program was used to compute genetic parameters. The body weight traits were moderate to high heritability values (ranged 0.29∼0.63). The heritablilites of carcass weight (h 2 =0.20) and shank length (h 2 =0.20) were categorized as moderate. Moreover, both genetic and phenotypic correlations were ranged form 0.62 to 0.99 and ranged from 0.42 to 0.98, respectively. These findings can be useful information for quantitative genetic studies and breeding plan of Korean native chicken.