Avian genomics in the 21st century

Potential Application of Muscle Precursor Cells from Male Specific-Pathogen-Free (SPF) Chicken Embryos in In Vitro Agriculture

This study examined the potential benefits of male specific-pathogen-free (SPF) White Leghorn embryos in cellular agriculture for sustainable and ethical poultry meat production-addressing traditional farming challenges, including disease outbreaks of Salmonella and Avian influenza. We isolated myogenic precursor cells (MPCs) from the thigh muscles (Musculus femoris) of 12.5-day-old embryos from 10 SPF White Leghorns that tested negative for Salmonella. We randomly selected MPCs from three males and three females, isolated them using a modified pre-plating (pp) method, and compared their in vitro development. After 1 h (pp1) and 2 h (pp2) of incubation, they were transferred to a new dish to remove fast-adhering cells and cultured (pp3). Isolated MPCs had a 69% positive reaction to Pax7. During proliferation, no differences were observed in PAX7, MYF5, or MYOD expression between the male and female MPCs. However, after five days of differentiation, the expression of late myogenic factors-MYOG and MYF6-significantly increased in all MPCs. Notably, MYOG expression was 1.9 times higher in female than in male MPCs. This impacted MYMK's expression pattern. Despite this, the myotube fusion index did not differ between the sexes. Muscle cells from male SPF-laying chicken embryos are promising for developing clean animal-cell-derived protein sources via resource recycling.

Different breeds, different blood: Cytometric analysis of whole blood cellular composition in chicken breeds

While haematological variation is well known in birds, variation in avian breeds (distinct morphotypes of the same species) remains unexplored. Poultry breeds, in particular, may show interesting evolutionary patterns and economically-relevant physiological differences. We performed a comparative examination of blood cellular composition in five chicken (Gallus gallus domesticus) breeds: Araucana, Booted bantam, Czech, Minorca and Rosecomb bantam. In standard-environment-reared hens whole-blood flow cytometry revealed remarkable differences in most erythrocyte- and leukocyte-related parameters. We identified two extremes: Czech, a European breed, with a low heterophil/lymphocyte (H/L) ratio and high CD4⁺ levels, and Araucana, a South-American breed, with a high H/L ratio and high relative monocyte count. Such variation may reflect a combination of artificial and natural selection acting on health- and stress-related traits in domestic populations. Different breeds have evolved different immunological adaptations reflecting their original need to fight pathogens and physiological constraint resulting from dissimilar physiological trade-offs.

Transcriptome-wide investigation of genomic imprinting in chicken

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.

Development of a high density 600K SNP genotyping array for chicken

Background

High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.

Results

We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.

Conclusions

This Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.

Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail

Background

As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.

Results

The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.

Conclusions

These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix.

The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis

Feathers have complex forms and are an excellent model to study the development and evolution of morphologies. Existing chicken feather mutants are especially useful for identifying genetic determinants of feather formation. This study focused on the gene F, underlying the frizzle feather trait that has a characteristic curled feather rachis and barbs in domestic chickens. Our developmental biology studies identified defects in feather medulla formation, and physical studies revealed that the frizzle feather curls in a stepwise manner. The frizzle gene is transmitted in an autosomal incomplete dominant mode. A whole-genome linkage scan of five pedigrees with 2678 SNPs revealed association of the frizzle locus with a keratin gene-enriched region within the linkage group E22C19W28_E50C23. Sequence analyses of the keratin gene cluster identified a 69 bp in-frame deletion in a conserved region of KRT75, an α-keratin gene. Retroviral-mediated expression of the mutated F cDNA in the wild-type rectrix qualitatively changed the bending of the rachis with some features of frizzle feathers including irregular kinks, severe bending near their distal ends, and substantially higher variations among samples in comparison to normal feathers. These results confirmed KRT75 as the F gene. This study demonstrates the potential of our approach for identifying genetic determinants of feather forms.

With the availability of a sequenced chicken genome, the reservoir of variant plumage genes found in domestic chickens can provide insight into the molecular mechanisms underlying the diversity of feather forms. In this paper, we identify the molecular basis of the distinctive frizzle (F) feather phenotype that is caused by a single autosomal incomplete dominant gene in which heterozygous individuals show less severe phenotypes than homozygous individuals. Feathers in frizzle chickens curve backward. We used computer-assisted analysis to establish that the rachis of the frizzle feather was irregularly kinked and more severely bent than normal. Moreover, microscopic evaluation of regenerating feathers found reduced proliferating cells that give rise to the frizzle rachis. Analysis of a pedigree of frizzle chickens showed that the phenotype is linked to two single-nucleotide polymorphisms in a cluster of keratin genes within the linkage group E22C19W28_E50C23. Sequencing of the gene cluster identified a 69-base pair in-frame deletion of the protein coding sequence of the α-keratin-75 gene. Forced expression of the mutated gene in normal chickens produced a twisted rachis. Although chicken feathers are primarily composed of beta-keratins, our findings indicate that alpha-keratins have an important role in establishing the structure of feathers.

The red jungle fowl leukocyte receptor complex contains a large, highly diverse number of chicken immunoglobulin-like receptor (CHIR) genes

The chicken Ig-like receptor (CHIR) gene family is located on microchromosome 31, the orthologous region to the mammalian leukocyte receptor complex. CHIR are equally related to the mammalian killer Ig-like receptors and leukocyte Ig-like transcripts, but they occur in a much higher number and diversity. The chicken microchromosome 31 has been neglected in the genome sequence analysis. Here, we provide a first analysis of this region. For this purpose bacterial artificial chromosome (BAC) sequences originating from a single inbred red jungle fowl that served as basis for the chicken genome project were screened for the presence of CHIR sequences and eight BACs were identified as major CHIR containing regions. Since the sequences of these BACs that were available in the database were not complete, sequence gaps were further closed by novel data from the chicken genome project. The entire sequence was aligned into 26 contigs covering 875kbp that contained 84 functional CHIR and 46 CHIR pseudogenes that were hampered by different reasons such as premature stop codons. The 84 functional CHIR were further categorized into 35 activating (CHIRA), 26 inhibitory (CHIRB) and 23 bifunctional (CHIRAB) genes. A detailed comparison of the annotated sequence taking also into account the previously published CHIR BAC sequence originating from an Lohman selected leghorn chicken revealed that the CHIR locus seems to be a very active region with a high degree of gene reorganization that resembles a constant birth and death evolution. The present report provides a framework for the future completion of the CHIR locus. It further suggests that the entire microchromosome 31 may resemble a locus of extraordinary genomic diversity that is beneficial for the development of a large CHIR repertoire, but that has therefore lost all other genes, where such a diversification would be fatal.

The chicken embryo as a model for developmental endocrinology: development of the thyrotropic, corticotropic, and somatotropic axes

The ease of in vivo experimental manipulation is one of the main factors that have made the chicken embryo an important animal model in developmental research, including developmental endocrinology. This review focuses on the development of the thyrotropic, corticotropic and somatotropic axes in the chicken, emphasizing the central role of the pituitary gland in these endocrine systems. Functional maturation of the endocrine axes entails the cellular differentiation and acquisition of cell function and responsiveness of the different glands involved, as well as the establishment of top-down and bottom-up anatomical and functional communication between the control levels. Extensive cross-talk between the above-mentioned axes accounts for the marked endocrine changes observed during the last third of embryonic development. In a final paragraph we shortly discuss how genomic resources and new transgenesis techniques can increase the power of the chicken embryo model in developmental endocrinology research.

Testis-specific novel transcripts in chicken: in situ localization and expression pattern profiling during sexual development

Tissue-specific novel transcripts expressed during sexual development were examined by RT-PCR, quantitative RT-PCR (qRT-PCR), and in situ hybridization to provide data for chicken genomics. Public databases for transcript data have been constructed with known and unknown sequences of various tissues from different animals. However, the expression patterns and functions of the transcripts are less known. From the The Institute for Genomics Research Gallus gallus library, we examined 291 tentative consensus (TC) sequences that assembled 100% with transcripts by RT-PCR during male and female sexual development from Embryonic Day 6 to 25 wk of age. We found 85 TC sequences that were specific to testicular development; of these, 43 TC sequences were exclusively upregulated in 25-wk-old testis. Another 52 TC sequences were not specific to one tissue, but occurred in the testis and ovary at different developmental ages. Twelve testis-specific TC sequences upregulated in 25-wk-old testis were randomly selected and further examined with qRT-PCR. For precise localization, these 12 testis-specific TC sequences were examined by in situ hybridization with 25-wk-old adult testis. Six TC sequences were strongly expressed in secondary spermatocytes and haploid spermatids until spermatozoa release. Another six TC sequences were differentially expressed in the adluminal compartment of seminiferous tubules. Among the testis-specific TC sequences, TC120901 is a known gene, phospholipase C, zeta (PLCZ1). Our data provide potential insight into gene expression and genomic information on novel transcripts that are important to avian reproduction.