Progress from chicken genetics to the chicken genome

Laying performance, genetic parameters, and the expression of FSHβ, LHβ, FSHR, and LHR genes in Japanese quails selected for early egg production

Investigating the impact of early egg production selection (the first 90 d of laying) on egg production features, cumulative selection response (CSR), and the mRNA expression of gonadotropins (FSHβ and LHβ), and their receptors (FSHR and LHR), in Japanese quails was the goal. The selection experiment involved 1293 females in all, 257 from the base group and 1036 from the 4 selected generations. Age and body weight at sexual maturity (ASM, BWSM), weight of the first egg (WFE), days to the first 10 eggs (DF10E), egg mass for the first 10 eggs (EMF10E), egg weight (EW), egg number at the first 90 d of laying (EN90D), and egg mass at the first 90 d of laying (EM90D) were all recorded. Most egg production traits had heritability estimates that were low to moderate and ranged from 0.17 to 0.33., where the highest estimates were reported for EN90D (0.33) and BWSM (0.32). With the exception of EN90D, low to moderate positive genetic correlations were observed between ASM and other egg production traits (0.17-0.44). The fourth generation showed significantly (P < 0.05) lower ASM and DF10E but higher BWSM, WFE, EN90D, EM10E, and EM90D when compared with the base generation. CSR were significant (P < 0.05) for ASM (-6.67 d), BWSM (27.13 g), WFE (0.93 g), DF10E (-1.25 d), EN90D (7.24 egg), EM10E (10.57 g), and EM90D (140.0 g). FSHβ, LHβ, FSHR, and LHR gene mRNA expression was considerably (P < 0.05) greater in the fourth generation compared to the base generation. In conclusion, selection programs depending on the efficiency of egg production (EN90D) could improve the genetic gain of egg production traits and upregulate the mRNA expression of FSHβ, LHβ, FSHR, and LHR genes in selected quails (fourth generation). These findings might help to enhance breeding plans and create commercial lines of high egg production Japanese quails.

The Histone Deacetylase Inhibitory Potential of Chicken Egg Yolk Fat and Their Fatty Acid Composition

Histone deacetylation is a key biochemical event associated with transcriptional regulation. Histone deacetylases (HDACs) mediate the deacetylation of histones. Fatty acids have been reported to function as histone deacetylase inhibitors (HDACi). The present instigation reports the HDAC inhibitory activity of egg yolks and egg yolk-derived fat of country and farm chicken for the first time. Egg yolks and fatty acids derived from both country (CCEF) and farm chicken (FCEF) demonstrated significant HDAC enzyme activity inhibition. Furthermore, egg yolks, CCEF, and FCEF exhibited DPPH free radical scavenging effects. The analysis of fatty acid profiles revealed varying degrees of saturated, mono-, and polyunsaturated fatty acids in the egg yolks. Palmitic acid (C16 : 0) was found to be the most abundant saturated fatty acid in both CCEF and FCEF. Among the monounsaturated fatty acids, oleic acid (C18 : 1) was the most abundant in both CCEF and FCEF. In terms of polyunsaturated fatty acids, a significant difference was observed in the content of linoleic acid (C18 : 2), an omega-6 fatty acid, and docosahexaenoic acid (C22 : 6), an omega-3 fatty acid, between CCEF and FCEF. These findings present exciting prospects for the development of histone deacetylase inhibitors based on egg yolk fat.

Carcass, visceral organ, and meat quality properties of two broiler hybrids differing in growth rates

This study aimed to determine the carcass, visceral organ, and meat properties according to the sex in slow growing broilers (SGB) and fast growing broilers (FGB). Six broilers from each genotype and sex group were slaughtered every week. It was determined that the difference between SGB and FGB in terms of carcass yield occurred at the highest level at 5 weeks and this difference continued until the age of 10 weeks. The weight percentages of all visceral organs examined in FGB were lower than in SGB. Higher values of pH, lightness, and cooking loss ​​were determined in breast and thigh meat of FGB compared with SGB (P < 0.05). The effects of genotype on protein levels of breast and leg meats were found to be insignificant. The fat level in breast meat was insignificant between genotypes after the fifth week of fattening period. There was no difference between the sexes regarding meat quality in both genotypes. When FGB and SGB were reared under the intensive conditions for 10 weeks, it was observed that visceral organs developed in harmony with body weight, especially in SGB during the 10 weeks of fattening period and SGB maintained their superiority in terms of meat quality.

Mapping QTLs for Breast Muscle Weight in an F2 Intercross between Native Japanese Nagoya and White Plymouth Rock Chicken Breeds

Nagoya (NAG), a native Japanese chicken breed, has high quality meat but low meat yield, whereas White Plymouth Rock (WPR), a parental breed of commercial broilers, has rapid growth but high body fat. We previously reported three quantitative trait loci (QTLs) for early postnatal growth in 239 F₂ chickens between NAG and WPR breeds. In this study, using the same F₂ chickens at 4 weeks of age, we performed genome-wide QTL analysis for breast muscle weight, fat weight and serum and liver levels of biochemical parameters. Two significant QTLs for pectoralis minor and/or major weights were revealed on chromosome 2 between 108 Mb and 127 Mb and chromosome 4 between 10 Mb and 68 Mb. However, no QTL for the other traits was detected. The two QTLs explained 7.0-11.1% of the phenotypic variances, and their alleles derived from WPR increased muscle weights. The chromosome 2 QTL may be a novel locus, whereas the chromosome 4 QTL coincided with a known QTL for meat quality. The findings provide information that is beneficial for genetic improvement of meat yield for the lean NAG breed and, furthermore, provide a better understanding of the genetic basis of chicken muscle development.

Sustainability in the Canadian Egg Industry—Learning from the Past, Navigating the Present, Planning for the Future

Like other livestock sectors, the Canadian egg industry has evolved substantially over time and will likely experience similarly significant change looking forward, with many of these changes determining the sustainability implications of and for the industry. Influencing factors include: technological and management changes at farm level and along the value chain resulting in greater production efficiencies and improved life cycle resource efficiency and environmental performance; a changing policy/regulatory environment; and shifts in societal expectations and associated market dynamics, including increased attention to animal welfare outcomes—especially in regard to changes in housing systems for laying hens. In the face of this change, effective decision-making is needed to ensure the sustainability of the Canadian egg industry. Attention both to lessons from the past and to the emerging challenges that will shape its future is required and multi- and interdisciplinary perspectives are needed to understand synergies and potential trade-offs between alternative courses of action across multiple aspects of sustainability. Here, we consider the past, present and potential futures for this industry through the lenses of environmental, institutional (i.e., regulatory), and socio-economic sustainability, with an emphasis on animal welfare as an important emergent social consideration. Our analysis identifies preferred pathways, potential pitfalls, and outstanding cross-disciplinary research questions.

Effects of a chromosome 9 quantitative trait locus for ascites on economically important traits in broilers

A quantitative trait locus on chromosome 9 was previously shown to be associated with ascites in multiple experimental and commercial populations. A study to evaluate the association of the QTL, based on variable number tandem repeat genotypes, with economically important traits was carried out on a commercial male elite line. Results indicated the highest fat and the lowest fillet mean were associated with the most resistant ascites genotype. All other traits measured for this genotype showed no trend towards positive or negatively impacting production values. The results suggest that a balanced approach could be undertaken in commercial broiler breeding operations to reduce ascites susceptibility in broiler populations without compromising overall genetic progress for traits of economic importance.

Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture

For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.

Rare phenotypes in domestic animals: unique resources for multiple applications

Preservation of specific and inheritable phenotypes of current or potential future importance is one of the main purposes of conservation of animal genetic resources. In this review, we investigate the issues behind the characterisation, utilisation and conservation of rare phenotypes, considering their multiple paths of relevance, variable levels of complexity and mode of inheritance. Accurately assessing the rarity of a given phenotype, especially a complex one, is not a simple task, because it requires the phenotypic and genetic characterisation of a large number of animals and populations and remains dependent of the scale of the study. Once characterised, specific phenotypes may contribute to various purposes (adaptedness, production, biological model, aesthetics, etc.) with adequate introgression programmes, which justifies the consideration of (real or potential) existence of such characteristics in in situ or ex situ conservation strategies. Recent biotechnological developments (genomic and genetic engineering) will undoubtedly bring important changes to the way phenotypes are characterised, introgressed and managed.

Genome-wide characterization of insertion and deletion variation in chicken using next generation sequencing

Insertion and deletion (INDEL) is one of the main events contributing to genetic and phenotypic diversity, which receives less attention than SNP and large structural variation. To gain a better knowledge of INDEL variation in chicken genome, we applied next generation sequencing on 12 diverse chicken breeds at an average effective depth of 8.6. Over 1.3 million non-redundant short INDELs (1-49 bp) were obtained, the vast majority (92.48%) of which were novel. Follow-up validation assays confirmed that most (88.00%) of the randomly selected INDELs represent true variations. The majority (95.76%) of INDELs were less than 10 bp. Both the detected number and affected bases were larger for deletions than insertions. In total, INDELs covered 3.8 Mbp, corresponding to 0.36% of the chicken genome. The average genomic INDEL density was estimated as 0.49 per kb. INDELs were ubiquitous and distributed in a non-uniform fashion across chromosomes, with lower INDEL density in micro-chromosomes than in others, and some functional regions like exons and UTRs were prone to less INDELs than introns and intergenic regions. Nearly 620,253 INDELs fell in genic regions, 1,765 (0.28%) of which located in exons, spanning 1,358 (7.56%) unique Ensembl genes. Many of them are associated with economically important traits and some are the homologues of human disease-related genes. We demonstrate that sequencing multiple individuals at a medium depth offers a promising way for reliable identification of INDELs. The coding INDELs are valuable candidates for further elucidation of the association between genotypes and phenotypes. The chicken INDELs revealed by our study can be useful for future studies, including development of INDEL markers, construction of high density linkage map, INDEL arrays design, and hopefully, molecular breeding programs in chicken.

Evolution of the Modern Broiler and Feed Efficiency

Although the chicken was domesticated during the Neolithic period, the development of the modern broiler is a recent event that has occurred within the past 100 years. The chicken’s adaptability has allowed it to be grown globally under a range of husbandry conditions. That is, the same genetic stock may be found in a range of environments, where it is noted for rapid growth to market weight and efficiency of feed use, which has increased dramatically, mainly through genetic selection. Under good husbandry and a high-energy diet, at 35 days of age a 1.40-kg broiler required 3.22 kg of feed in 1985. Twenty-five years later, we have a 2.44-kg broiler produced on 3.66 kg of feed. This review attempts to address the history of factors contributing to these changes, obstacles that have had to be overcome, and future limitations.

Genome-wide patterns of genetic variation in two domestic chickens

Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.

Poultry genome sequences: progress and outstanding challenges

The first build of the chicken genome sequence appeared in March, 2004 - the first genome sequence of any animal agriculture species. That sequence was done primarily by whole genome shotgun Sanger sequencing, along with the use of an extensive BAC contig-based physical map to assemble the sequence contigs and scaffolds and align them to the known chicken chromosomes and linkage groups. Subsequent sequencing and mapping efforts have improved upon that first build, and efforts continue in search of missing and/or unassembled sequence, primarily on the smaller microchromosomes and the sex chromosomes. In the past year, a draft turkey genome sequence of similar quality has been obtained at a much lower cost primarily due to the development of 'next-generation' sequencing techniques. However, assembly and alignment of the sequence contigs and scaffolds still depended on a detailed BAC contig map of the turkey genome that also utilized comparison to the existing chicken sequence. These 2 land fowl (Galliformes) genomes show a remarkable level of similarity, despite an estimated 30-40 million years of separate evolution since their last common ancestor. Among the advantages offered by these sequences are routine re-sequencing of commercial and research lines to identify the genetic correlates of phenotypic change (for example, selective sweeps), a much improved understanding of poultry diversity and linkage disequilibrium, and access to high-density SNP typing and association analysis, detailed transcriptomic and proteomic studies, and the use of genome-wide marker- assisted selection to enhance genetic gain in commercial stocks.

Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics

The chicken has been widely used in experimental research given its importance to agriculture and its utility as a model for vertebrate biology and biomedical pursuits for over 100 years. Herein we used advanced technologies to investigate the genomic characteristics of specialized chicken congenic genetic resources developed on a highly inbred background. An Illumina 3K chicken single nucleotide polymorphism (SNP) array was utilized to study variation within and among major histocompatibility complex (MHC)-congenic lines as well as investigate line-specific genomic diversity, inbreeding coefficients, and MHC B haplotype-specific GGA 16 SNP profiles. We also investigated developmental mutant-congenic lines to map a number of single-gene mutations using both the Illumina 3K array and a recently developed Illumina 60K chicken SNP array. In addition to identifying the chromosomes and specific subregions, the mapping results affirmed prior analyses indicating recessive or dominant and autosomal or sex chromosome modes of inheritance. Priority candidate genes are described for each mutation based on association with similar phenotypes in other vertebrates. These single-gene mutations provide a means of studying amniote development and in particular serve as invaluable biomedical models for similar malformations found in human.

Genetic mapping of the sex-linked barring gene in the chicken

The sex-linked barring gene of the chicken (Gallus gallus), first identified in 1908, produces an alternating pattern of white and black bars in the adult plumage. More recent studies have shown that melanocytes in the developing feather follicle of the Barred Plymouth Rock experience premature cell death, whereas initially it was thought that melanocytes remained viable in the region of the feather devoid of pigmentation but were simply inhibited from synthesizing melanin. In an attempt to reconcile these 2 different hypotheses at the molecular level, we have taken a gene mapping approach to isolate the sex-linked barring gene variant. We developed a mapping population consisting of 71 F2 chickens from crossing a single Barred Plymouth Rock female with a White Crested Black Polish male. Existing and novel microsatellite markers located on the chicken chromosome Z were used to genotype all individuals in our mapping population. Single marker association analysis revealed a 2.8-Mb region of the distal q arm of chicken chromosome Z to be significantly associated with the barring phenotype (P<0.001). Further analysis suggests that the causal mutation is located within a 355-kb region showing complete association with the barring phenotype and containing 5 known genes [micro-RNA 31 (miRNA-31), methylthioadenosine phosphorylase (MTAP), cyclin-dependent kinase inhibitor 2B (CDKN2B), tripartite motif 36 (TRIM36), and protein geranylgeranyltransferase type I, beta subunit (PGGT1B)], none of which have a defined role in normal melanocyte function. Although several of these genes or their homologs are known to be involved in processes that could potentially explain the barring phenotype, our results indicate that further work directed at fine-mapping this region is necessary to identify this novel mechanism of melanocyte regulation.

Focused microarrays as a method to evaluate subtle changes in gene expression

Recent studies using microarray technologies for the chicken have reported information regarding the effects of specific experimental treatments on gene expression levels often resulting in large gene lists and limitations on the statistical significance levels detected. In most cases, with these limitations, along with thresholds of +/-2-fold differences in expression levels, that are used to create these gene lists, much of the biological information may have been overlooked. In this study, a focused 70-mer oligonucleotide microarray was developed to address the apparent limits of detection and issues with multiple testing resulting from the use of microarrays that include only a single spot (probe) for each gene. Gene expression was assayed across the development of the chicken embryonic heart from d 7 to 20 of incubation. When using a mixed-model approach and ANOVA with Bonferroni correction for multiple testing, including replicates within the focused array significantly increased the sensitivity with which differences could be detected across sample groups, as compared with single-spot data. By incorporating replication into the focused array, 50 genes were detected as being differentially expressed in the embryonic heart across the time points sampled. This compares with only 7 genes detected as being differentially expressed when a more typical, less statistically stringent single-spot analysis is conducted. Based on our observations, the use of focused microarrays allows for the thorough investigation of gene expression patterns, with detection of significant changes in gene expression of +/-7%. This limit of detection is far superior to that of real-time PCR, which is able to detect significant changes in expression from +/-33 to 55%, depending on the specific application. The ability to detect small differences in expression will allow investigators to identify subtle effects that have perhaps been overlooked in many prior assays, including single-spot arrays. Subtle shifts in gene expression are exactly those that occur during embryonic development, nutritional manipulation, and the initial stages of disease before clinical signs appear.

Characterization of a newly developed chicken 44K Agilent microarray

Background

The development of microarray technology has greatly enhanced our ability to evaluate gene expression. In theory, the expression of all genes in a given organism can be monitored simultaneously. Sequencing of the chicken genome has provided the crucial information for the design of a comprehensive chicken transcriptome microarray. A long oligonucleotide microarray has been manually curated and designed by our group and manufactured using Agilent inkjet technology. This provides a flexible and powerful platform with high sensitivity and specificity for gene expression studies.

Results

A chicken 60-mer oligonucleotide microarray consisting of 42,034 features including the entire Marek's disease virus, two avian influenza virus (H5N2 and H5N3), and 150 chicken microRNAs has been designed and tested. In an important validation study, total RNA isolated from four major chicken tissues: cecal tonsil (C), ileum (I), liver (L), and spleen (S) were used for comparative hybridizations. More than 95% of spots had high signal noise ratio (SNR > 10). There were 2886, 2660, 358, 3208, 3355, and 3710 genes differentially expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum (P < 10^-7), respectively. There were a number of tissue-selective genes for cecal tonsil, ileum, liver, and spleen identified (95, 71, 535, and 108, respectively; P < 10^-7). Another highlight of these data revealed that the antimicrobial peptides GAL1, GAL2, GAL6 and GAL7 were highly expressed in the spleen compared to other tissues tested.

Conclusion

A chicken 60-mer oligonucleotide 44K microarray was designed and validated in a comprehensive survey of gene expression in diverse tissues. The results of these tissue expression analyses have demonstrated that this microarray has high specificity and sensitivity, and will be a useful tool for chicken functional genomics. Novel data on the expression of putative tissue specific genes and antimicrobial peptides is highlighted as part of this comprehensive microarray validation study. The information for accessing and ordering this 44K chicken array can be found at

Functional genomics of the chicken--a model organism

Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection ( approximately 600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of approximately 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.

The chicken genome: some good news and some bad news

The sequencing of the chicken genome has generated a wealth of good news for poultry science. It allows the chicken to be a major player in 21st century biology by providing an entrée into an arsenal of new technologies that can be used to explore virtually any chicken phenotype of interest. The initial technological onslaught has been described in this symposium. The wealth of data available now or soon to be available cannot be explained by simplistic models and will force us to treat the inherent complexity of the chicken in ways that are more realistic but at the same time more difficult to comprehend. Initial single nucleotide polymorphism analyses suggest that broilers retain a remarkable amount of the genetic diversity of predomesticated Jungle Fowl, whereas commercial layer genomes display less diversity and broader linkage disequilibrium. Thus, intensive commercial selection has not fixed a genome rich in wide selective sweeps, at least within the broiler population. Rather, a complex assortment of combinations of ancient allelic diversity survives. Low levels of linkage disequilibrium will make association analysis in broilers more difficult. The wider disequilibrium observed in layers should facilitate the mapping of quantitative trait loci, and at the same time make it more difficult to identify the causative nucleotide change(s). In addition, many quantitative traits may be specific to the genetic background in which they arose and not readily transferable to, or detectable in, other line backgrounds. Despite the obstacles it presents, the genetic complexity of the chicken may also be viewed as good news because it insures that long-term genetic progress will continue via breeding using quantitative genetics, and it surely will keep poultry scientists busy for decades to come. It is now time to move from an emphasis on obtaining "THE" chicken genome sequence to obtaining multiple sequences, especially of foundation stocks, and a broader understanding of the full genetic and phenotypic diversity of the domesticated chicken.

Perspectives in Chicken Genetics and Genomics

Poultry science has entered a new era with the completion of a century of investigative studies in chicken genetics, sequencing of the chicken genome, application of genomic tools into systems biology studies, and rapid advances in the development of the statistical theory for application of molecular genetic information in commercial breeding programs. This perspectives paper sets the context for the accompanying series of reviews on chicken genetics and genomics, introduces important issues in the field of poultry molecular genetics, and briefly describes the topics of each of the reviews.