Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens.

BACKGROUND: Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group. RESULTS: After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations. CONCLUSIONS: Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

A comparison of fast growing broiler chickens with a slower-growing breed type reared on Higher Welfare commercial farms.

Slowing the growth of modern broiler chickens can have a positive effect on a number of welfare outcomes. However, relatively few studies have compared fast and slower growing broiler chickens reared under the same commercial conditions. The main aim of this study was to evaluate a slower growing breed and standard fast growing broilers on commercial farms. Ross 308 broilers and slower growing Hubbard Redbro broilers were housed on six farms for 17 production cycles. Production data were available for all cycles. Behaviour and environmental measures were taken over one cycle on each of two farms. The farms were visited during weeks 3-6 for both breeds and week 7 for Redbros. We found that breed had a significant effect on a number of measures, including gait score, latency to lie, feather cover, avoidance distances, perch use and play behaviour (p < 0.05). Gait scores were consistently lower among the Redbro flocks during weeks 4, 5, 6 and 7. Redbro broilers generally had longer latency to lie times, better feather cover, and were more reactive to approaching observers. They also showed higher levels of perch use and play. Despite these indications of improved locomotion and physical ability, we found little difference in their general behaviour. However, Redbro broilers did perform longer activity bouts in week 7 than Ross 308s in their final week. There was no effect of breed on dust levels, ammonia concentration or litter condition. Redbro broilers were slaughtered 5.5 days later than Ross 308 birds at a lower average weight (2.32 vs 2.52kg) and had lower mortality, fewer culls and fewer carcasses downgraded at the abattoir. Our results suggest that the slower growing strain was healthier throughout the cycle and more capable of displaying some natural behaviours.

Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans.

microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.

Comparison of Marek's Disease Virus Challenge Strains and Bird Types for Vaccine Licensing.

Marek's disease virus (MDV) is an important poultry pathogen that is controlled through widespread vaccination with avirulent and attenuated strains. However, continued evolution of field viruses to higher virulence has required ongoing improvement of available vaccine strains, and these vaccine strains offer an attractive platform for designing recombinant vector vaccines with cross-protection against MDV and additional pathogens. Recent reports of failures in vaccine licensing trials of positive controls to reach appropriately high levels of Marek's disease incidence prompted us to evaluate possible combinations of outbred specific-pathogen-free layer lines and alternative virulent challenge strains that could provide more consistent models for serotype 3 vectored vaccine development. Choice of layer line and virulent MDV challenge strain each contributed to the ability of a challenge model to reach 80% virulence in unvaccinated positive control groups in the majority of trials, without overwhelming serotype 3 vectored vaccine protection in vaccinated groups. Conversely, reducing challenge virus dose by a factor of four, or vaccine dose by half, had no consistent effect across these models. Although MDV strain 617A had the most potential as an alternative to strains that are currently approved for licensing trials, no combination of layer line and challenge virus consistently met the goals for a successful challenge model in all study replicates, indicating that high variability is an inherent difficulty in MDV challenge studies, at least when outbred birds are used.

Artículo regular­Comparación de las cepas de desafío del virus de la enfermedad de Marek y los tipos de aves para la obtención de licencias de vacunas. El virus de la enfermedad de Marek (MDV) es un patógeno importante en la avicultura que se controla mediante la vacunación generalizada con cepas avirulentas y atenuadas. Sin embargo, la evolución continua de los virus de campo hacia una mayor virulencia ha requerido una mejora continua de las cepas vacunales disponibles y estas cepas vacunales ofrecen una plataforma atractiva para diseñar vacunas con vectores recombinantes que induzcan protección cruzada contra el virus de la enfermedad de Marek y patógenos adicionales. Los reportes recientes de fallas en los controles positivos para alcanzar niveles apropiadamente altos de incidencia de la enfermedad de Marek en los ensayos para obtener la licencia de vacunas llevaron a evaluar posibles combinaciones de líneas de postura híbridas libres de patógenos específicos y cepas de desafío virulentas alternativas que podrían proporcionar modelos más consistentes para el desarrollo de vacunas con vectores de serotipo 3. Tanto la elección de la línea de postura como de la cepa de desafío virulenta de Marek contribuyeron a obtener un modelo de desafío con capacidad para alcanzar el 80% de virulencia en grupos controles positivo no vacunados en la mayoría de los ensayos, sin una protección abrumadora de la vacuna con vector de serotipo 3 en los grupos vacunados. Por el contrario, la reducción de la dosis del virus de desafío en un factor de cuatro, o la dosis de vacuna a la mitad, no tuvieron un efecto constante en estos modelos. Aunque la cepa 617A de Marek mostró el mayor potencial como alternativa a las cepas que actualmente están aprobadas para ensayos de licenciar vacunas, ninguna combinación de línea de postura y virus de desafío cumplió consistentemente los objetivos de un modelo de desafío exitoso en todas las réplicas del estudio, lo que indica que la alta variabilidad es una dificultad inherente en los estudios de desafío para la enfermedad de Marek, al menos cuando se utilizan aves híbridas.

A Survey of Coccidia and Nematodes in Pastured Poultry in the State of Georgia.

The aim of this study was to evaluate and quantify the parasitological challenge in pastured poultry production in the state of Georgia. Over the course of 1 yr, fecal samples from six turkey flocks, 10 broiler flocks, and 13 layer flocks were collected on a pastured farm in 2-wk intervals to determine counts of Eimeria oocysts and nematode eggs. Average coccidia counts were 10,198 oocysts per gram of feces (OPG) in broiler flocks, 1470 OPG in layer flocks, and 695 OPG in turkey flocks. The means in broiler and turkey flocks were higher at their first week on pasture. Counts in broilers and layers were significantly higher in spring than in winter and summer. Coccidia counts in broilers were lower than published numbers in conventionally reared poultry, indicating the rotation system of the pastures might effectively reduce the infection pressure. Next-generation sequencing of PCR products showed the presence of most described Eimeria spp. in broilers, layers, and turkeys. In addition, operational taxonomic units (OTUs) x, y, and z were found. The frequency of species was similar for broilers and layers, with the exception that Eimeria praecox and OTU z were more common in layers. In layer flocks, the average count of roundworm eggs per gram of feces (EPG) was 509 EPG with 80% of the samples being positive. The mean counts had no clear pattern related to age. There was an increase of EPG with the increase of temperatures during spring and summer with the peak at midfall. Worm eggs from laying hens were identified as Ascaridia galli. The seasonal differences suggest that higher temperatures might result in an increase of egg survival and sporulation in the environment.

Artículo regular­Muestreo de coccidias y nematodos en aves en pastoreo en el estado de Georgia El objetivo de este estudio fue evaluar y cuantificar el desafío parasitológico en la producción avícola en pastoreo en el estado de Georgia. En el transcurso de un año, se recolectaron muestras fecales de seis parvadas de pavos, 10 parvadas de pollos de engorde y 13 parvadas de gallinas de postura en una granja de pastoreo en intervalos de dos semanas para determinar los conteos de ooquistes de Eimeria y huevos de nematodos. Los recuentos promedio de coccidias fueron 10,198 ooquistes por gramo de heces (OPG) en parvadas de pollos de engorde, 1470 ooquistes por gramo de heces en parvadas ponedoras y 695 ooquistes por gramo de heces en parvadas de pavos. Los promedios en las parvadas de pollos de engorde y pavos fueron más altos en su primera semana en pastoreo. Los conteos en pollos de engorde y ponedoras fueron significativamente más altos en primavera que en invierno y verano. Los recuentos de coccidios en pollos de engorde fueron más bajos que los números publicados en aves criadas de manera convencional, lo que indica que el sistema de rotación de pastizales podría reducir efectivamente la presión de infección. La secuenciación de próxima generación de los productos de PCR mostró la presencia de la mayoría de las especies de Eimeria spp descritas en pollos de engorde, gallinas de postura y pavos. Además, se encontraron unidades taxonómicas operativas (OTU) x, y, z. La frecuencia de especies fue similar para pollos de engorde y gallinas de postura, con la excepción de que Eimeria praecox y las unidades taxonómicas operativas z fueron más comunes en gallinas de postura. En las parvadas de gallinas de postura, el recuento promedio de huevos de helmintos intestinales por gramo de heces (EPG) fue de 509 EPG, con el 80% de las muestras positivas. Los recuentos medios no tenían un patrón claro relacionado con la edad. Hubo un aumento de huevos de helmintos intestinales por gramo de heces con el aumento de las temperaturas durante la primavera y el verano con el pico a la mitad del otoño. Los huevos de helmintos de las gallinas de postura se identificaron como Ascaridia galli. Las diferencias estacionales sugieren que las temperaturas más altas podrían resultar en un aumento de la supervivencia de los huevos y su esporulación en el medio ambiente.

Analysis of selection signatures on the Z chromosome of bidirectional selection broiler lines for the assessment of abdominal fat content.

BACKGROUND: The discovery of selection signatures has enabled the identification of genomics regions under selective pressure, enhancing knowledge of evolutionary genotype-phenotypes. Sex chromosomes play an important role in species formation and evolution. Therefore, the exploration of selection signatures on sex chromosomes has important biological significance. RESULTS: In this study, we used the Cross Population Extend Haplotype Homozygosity Test (XPEHH), F-statistics (FST) and EigenGWAS to assess selection signatures on the Z chromosome in 474 broiler chickens via Illumina chicken 60 K SNP chips. SNP genotype data were downloaded from publicly available resources. We identified 17 selection regions, amongst which 1, 11 and 12 were identified by XPEHH, FST, and EigenGWAS, respectively. Each end of the Z chromosome appeared to undergo the highest levels of selection pressure. A total of 215 candidate genes were located in 17 selection regions, some of which mediated lipogenesis, fatty acid production, fat metabolism, and fat decomposition, including FGF10, ELOVL7, and IL6ST. Using abdominal adipose tissue expression data of the chickens, 187 candidate genes were expressed with 15 differentially expressed genes (DEGs) in fat vs. lean lines identified. Amongst the DEGs, VCAN was related to fat metabolism. GO pathway enrichment analysis and QTL annotations were performed to fully characterize the selection mechanism(s) of chicken abdominal fat content. CONCLUSIONS: We have found some selection regions and candidate genes involving in fat metabolism on the Z chromosome. These findings enhance our understanding of sex chromosome selection signatures.

Genetic diversity in global chicken breeds in relation to their genetic distances to wild populations.

BACKGROUND: Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted by the theory of genetic isolation by distance. Consistent with that theory, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be explained well by their geographic expansion from their founders, which is correlated with genetic differentiation. METHODS: To investigate this in chicken, we estimated the relationship between the genetic diversity of 160 domesticated chicken populations and their genetic distances to wild chicken populations. RESULTS: Our results show a strong inverse relationship, i.e. 88.6% of the variation in the overall genetic diversity of domesticated chicken populations was explained by their genetic distance to the wild populations. We also investigated whether the patterns of genetic diversity of different types of single nucleotide polymorphisms (SNPs) and genes are similar to that of the overall genome. Among the SNP classes, the non-synonymous SNPs deviated most from the overall genome. However, genetic distance to the wild chicken still explained more variation in domesticated chicken diversity across all SNP classes, which ranged from 83.0 to 89.3%. CONCLUSIONS: Genetic distance between domesticated chicken populations and their wild relatives can predict the genetic diversity of the domesticated populations. On the one hand, genes with little genetic variation across populations, regardless of the genetic distance to the wild population, are associated with major functions such as brain development. Changes in such genes may be detrimental to the species. On the other hand, genetic diversity seems to change at a faster rate within genes that are associated with e.g. protein transport and protein and lipid metabolic processes. In general, such genes may be flexible to changes according to the populations' needs. These results contribute to the knowledge of the evolutionary patterns of different functional genomic regions in the chicken.

Geometrical characteristics of eggs from 3 poultry species.

We studied the correlations between egg geometrical parameters (i.e., egg shape index, sphericity, geometric mean diameter, surface area, and volume) and eggshell qualities, or the organic matrix in eggshell. Eggs were collected from 5 poultry breeds belonging to 3 species (commercial Hy-line Brown Chicken, Shaoxing Duck, Jinding Duck, Taihu Goose, and Zhedong White Goose). The geometrical parameters showed high variation among 3 species of poultry, and even between breeds in the same species. The five geometrical parameters were grouped into 2 sets, one contained shape index and sphericity, the other comprised geometric mean diameter, surface area, and volume. The parameters in the same set can be perfectly fitted to one another. Egg weight, shell membrane weight, and calcified shell weight were significantly correlated with geometric mean diameter, surface area, and volume. In accordance with false discovery rate-adjusted P value, both shell membrane relative weight and calcified shell thickness showed no significant correlations with any of the geometrical parameters. However, the correlations between geometrical parameters and other shell variables (calcified shell weight, shell relative weight, calcified shell thickness uniformity, and eggshell breaking strength) depend on breed. Both constitutive proportions and percentage contents of 3 eggshell matrix components (acid-insoluble, water-insoluble, and both acid and water facultative-soluble matrix) had no effects on egg shape and size. The correlations between the amounts of various shell matrix, egg shape and size depend on breed or species. This study provides a methodology and the correlation between geometrical parameters and eggshell qualities, and between geometrical parameters and organic matrix components in calcified shells.

Paracellular and Transcellular Leukocytes Diapedesis Are Divergent but Interconnected Evolutionary Events.

Infiltration of the endothelial layer of the blood-brain barrier by leukocytes plays a critical role in health and disease. When passing through the endothelial layer during the diapedesis process lymphocytes can either follow a paracellular route or a transcellular one. There is a debate whether these two processes constitute one mechanism, or they form two evolutionary distinct migration pathways. We used artificial intelligence, phylogenetic analysis, HH search, ancestor sequence reconstruction to investigate further this intriguing question. We found that the two systems share several ancient components, such as RhoA protein that plays a critical role in controlling actin movement in both mechanisms. However, some of the key components differ between these two transmigration processes. CAV1 genes emerged during Trichoplax adhaerens, and it was only reported in transcellular process. Paracellular process is dependent on PECAM1. PECAM1 emerged from FASL5 during Zebrafish divergence. Lastly, both systems employ late divergent genes such as ICAM1 and VECAM1. Taken together, our results suggest that these two systems constitute two different mechanical sensing mechanisms of immune cell infiltrations of the brain, yet these two systems are connected. We postulate that the mechanical properties of the cellular polarity is the main driving force determining the migration pathway. Our analysis indicates that both systems coevolved with immune cells, evolving to a higher level of complexity in association with the evolution of the immune system.

Meat quality and Raman spectroscopic characterization of Korat hybrid chicken obtained from various rearing periods.

Meat quality attributes vary with chicken age. Understanding the relationship between poultry age and the quality of the meat would be beneficial for efficient poultry farming to meet market needs. The Korat hybrid chicken (KC) is a new crossbred chicken whose meat quality is distinct from that of commercial broiler (CB) chickens and has not been well characterized. In this study, we characterized the physico-chemical properties of KC meat and correlate the findings with Raman spectral data. The protein content of KC breast and thigh meat increased with age. The pH of thigh meat decreased, while the water-holding capacity of breast meat increased as the age of the chickens increased. The amount of cholesterol in breast meat decreased as the rearing period was extended. Inosine 5'-monophosphate and guanosine 5'-monophosphate of breast meat decreased as KC grew older. The shear force values of meat from older birds increased concomitantly with an increase in total collagen. Principle component analysis revealed that the meat quality of CB was greatly different from that of KC meat. High shear force values of KC meat at 20 wk of age were well correlated with an increase in the ß-sheet structure (amide I) and amide III of collagen. Raman spectra at 3,207 cm-1 and relative α-helical content were negatively correlated with shear force values of KC breast meat. These could be used as markers to evaluate KC meat quality.

Fatty acid profile, oxidative status, and content of volatile organic compounds in raw and cooked meat of different chicken strains.

Chicken meat is rich in unsaturated fatty acids. Therefore, it is more susceptible to lipid oxidation and production of volatile organic compounds (VOC). In this study, we evaluated the fatty acids, antioxidants, and VOC profiles of raw and cooked meat samples derived from 4 strains of chicken differing in their growth rates, which were as follows: slow-growing (SG, Leghorn), medium-growing (MG, Hubbard and Naked Neck), and fast-growing (FG, Ross). The VOC profile of meat was measured using proton-transfer reaction-mass spectrometry (PTR-MS). The VOC were identified using PTR-time of flight-MS (PTR-ToF-MS). The data were analyzed using both univariate and multivariate models. Twenty main VOC were identified, which were classified into the following chemical categories: aldehydes, alkadienes, alkenes, furans, amides, alcohols, and other compounds. Our results revealed that the chicken genotype and the method of cooking strongly influenced the VOC profile of the meat. Identifying the relationships between these traits allowed us to highlight the trade-off of the main substrates such as n-3 and n-6 polyunsaturated fatty acids (PUFA), protective substances (antioxidants), and degradation products (VOC) of the poultry meat produced during cooking. The extent of VOC production and n-3 loss was found to be higher for the SG genotype. Reduction of n-6 was higher in MG, whereas small losses in antioxidants and PUFA were observed in the FG genotype, consequently, resulting in the lowest production of VOC. The SG and MG are genotypes more active from a kinetic point of view respect to the FG ones. For this reason, in the FG genotypes, the antioxidants are less involved in the oxidative stress induced by the movement; thus, they were available to protect the lipid of the meat during the cooking process. These results suggested that the use of SG and MG genotypes requires a specific dietary protocol (i.e., increasing the antioxidants content) to counteract the lipid oxidations in all the phases: in vivo, postmortem, and during/after cooking.

Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds.

The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds.

RFamide-related peptides' gene expression, polymorphism, and their association with reproductive traits in chickens.

RFamide-related peptides (RFRP) are synthesized by the hypothalamus and have a regulatory role in gonad development. The goal of this study was to investigate the association between SNP of the RFRP gene and the reproductive traits and hormone levels of Zhenning yellow chickens. The mRNA expression levels were detected based on different tissues, ages, and genotypes. Eleven mutation sites were detected in the RFRP gene, 4 of which were significantly related to reproductive traits and hormone levels. Association analysis revealed that A276G was associated with egg production at 300 d of age (EP300) and amount of prehierarchical follicles (P < 0.05). G1396A was associated with egg weight at 300 d of age and luteinizing hormone (LH) and prolactin levels (P < 0.05). G1694A showed significant associations with fertilization rate and LH levels (P < 0.05), and A2659G was associated with EP300 (P < 0.05). The results of expression analysis showed that the RFRP mRNA expression levels in the hypothalamus were higher than those in other tissues (P < 0.01). The expression in immature individuals was higher than that in mature ones (P < 0.01). There were also differences in mRNA expression levels between different genotypes (P < 0.05). In summary, the results of this study might provide potential markers and a theoretical basis for the improvement of chicken reproductive traits.

Research Note: The effects of genotype, sex, and feeding regime on performance, carcasses characteristic, and microbiota in chickens.

The aim of the present study was to evaluate the effects of quantitative feed restriction (FR) in fast-, medium-, and slow-growing meat-type male and female chickens on their growth, feed consumption, economic efficiency, carcass composition, and gastrointestinal microbiota. In the experiment, fast-growing Ross 308, medium-growing Hubbard JA 757 and slow-growing ISA Dual chickens of both sexes were exposed to quantitative FR between 14 and 21 d of age. During the FR, restricted chickens received 70% of the amount of feed consumed by the ad libitum (AL) group. Live weight at the end of the experiment was affected by genotype (P < 0.001), sex (P < 0.001), feeding regime (P < 0.001), and their interaction (P < 0.001). The highest final weight was in AL and FR ISA Dual males and the lowest was in AL and FR females of the same genotype. A similar tendency was observed in daily weight gain and feed intake. Carcass traits were predominantly affected by genotype. However, interactions of genotype, sex, and feeding regime were observed in thigh (P < 0.001) and abdominal fat (P < 0.001) proportions. Concerning gastrointestinal microbiota, only Escherichia coli was affected by genotype. Feed restriction in slow-growing dual-purpose chickens might improve economic potential; however, further research is needed to reveal the involvement of variable processes, which are unclear and affect production.

Effects of rhamnolipids on growth performance and intestinal health parameters in Linnan yellow broilers.

This study determined the effects of dietary supplementation of rhamnolipids (RLS) on the growth performance, gut morphology, immune function, intestinal volatile fatty acid, and microflora community in Linnan yellow broilers. A total of 480 1-day-old broiler chicks were randomly assigned to groups for supplementation with one of the following for 56 d: no supplement (control), 30 mg/kg bacitracin (ANT), 500 mg/kg RLS, or 1,000 mg/kg RLS (RLS2). The RLS2 diet was found to improve the final BW and ADG on day 56. The RLS diet reduced jejunal crypt depth, increased jejunal villus length, and increased serum IgA, IgM, IgY, IL-1ß, IL-6, and tumor necrosis factor-alpha (TNF-α) levels. The RLS broilers had higher cecum concentrations of acetic acid, propionic acid, butyrate, isobutyric acid, valerate, and isovalerate. High-throughput sequencing indicated that RLS affected microbial quantity and diversity in the cecum. Bacterial richness was higher in the RLS broilers than the ANT broilers. The RLS broilers had higher relative abundances of Megasphaera hypermegale and Lachnospiraceae bacterium 19gly4 on day 28 and Clostridium spiroforme and Alistipes obesi on day 56. These results suggest that RLS supplementation improves growth performance, benefits the intestinal villus morphology, regulates host immune function, and raises intestinal volatile fatty acid content and the relative abundance of the gut microbiota in broiler chickens.

In pursuit of a better broiler: growth, efficiency, and mortality of 16 strains of broiler chickens.

To meet the growing consumer demand for chicken meat, the poultry industry has selected broiler chickens for increasing efficiency and breast yield. While this high productivity means affordable and consistent product, it has come at a cost to broiler welfare. There has been increasing advocacy and consumer pressure on primary breeders, producers, processors, and retailers to improve the welfare of the billions of chickens processed annually. Several small-scale studies have reported better welfare outcomes for slower-growing strains compared to fast-growing, conventional strains. However, these studies often housed birds with range access or used strains with vastly different growth rates. Additionally, there may be traits other than growth, such as body conformation, that influence welfare. As the global poultry industries consider the implications of using slower growing strains, there was a need for a comprehensive, multidisciplinary examination of broiler chickens with a wide range of genotypes differing in growth rate and other phenotypic traits. To meet this need, our team designed a study to benchmark data on conventional and slower-growing strains of broiler chickens reared in standardized laboratory conditions. Over a 2-year period, we studied 7,528 broilers from 16 different genetic strains. In this paper, we compare the growth, efficiency, and mortality of broilers to one of two target weights (TW): 2.1 kg (TW1) and 3.2 kg (TW2). We categorized strains by their growth rate to TW2 as conventional (CONV), fastest-slow strains (FAST), moderate-slow strains (MOD), and slowest-slow strains (SLOW). When incubated, hatched, housed, managed, and fed the same, the categories of strains differed in body weights, growth rates, feed intake, and feed efficiency. At 48 d of age, strains in the CONV category were 835 to 1,264 g heavier than strains in the other categories. By TW2, differences in body weights and feed intake resulted in a 22 to 43-point difference in feed conversion ratios. Categories of strains did not differ in their overall mortality rates.

Effect of genotype and some shell quality traits on lysozyme content and activity in the albumen of eggs from hens under the biodiversity conservation program.

The aim of the study was to determine shell quality of eggs laid by some strains of native breed hens of different ages, with special consideration of their effect on lysozyme concentration and enzymatic activity. Evaluation was made of the eggshells from 6 breeds/strains of laying hens covered by the gene pool protection program in Poland: Greenleg Partridge (Z-11), Yellowleg Partridge (Z-33), Rhode Island Red (R-11), Rhode Island White (A-33), Sussex (S-66), and Leghorn (H-22). Significant (P ≤ 0.01) differences were established for all the shell quality characteristics between hen strains. As the birds aged, shell weight and porosity increased, and shell compression strength decreased in all the experimental groups. Lysozyme content was lowest in white-shelled eggs (H-22) and highest in cream-colored and light brown eggs (Z-11, Z-33, and R-11). Furthermore, age of hens had a greater effect on lysozyme concentration and activity in the eggs than on shell quality traits. Regardless of the layer genotype, eggs from older hens showed higher lysozyme concentration and enzymatic activity.

The use of behavioral tests of fearfulness in chicks to distinguish between the Japanese native chicken breeds, Tosa-Kukin and Yakido.

The aim of this study was to investigate the differences in fearfulness between two Japanese native chicken breeds, Tosa-Kukin (TOK) and Yakido (YKD). In a tonic immobility test, TOK breed chicks showed longer duration and lower induction number compared with YKD. The number of peeps in YKD in an isolation test was lower than that in TOK, whereas there were more bouts of peeping in YKD than in TOK. In a manual restraint test, YKD showed more active responses and initiated peeps and struggling earlier than TOK. The three behavioral tests all indicated that YKD are less fearful than TOK chickens. A latent structures discriminant (OPLS-DA) analysis was used to identify behavioral parameters that contributed to the differences between the breeds. The major parameters were duration and number of inductions in the tonic immobility test and number of struggle in the manual restraint test. These results suggest that three behavioral tests can be used together to evaluate fearfulness of Japanese native breeds of chickens.

Potential of 2D qNMR spectroscopy for distinguishing chicken breeds based on the metabolic differences.

Two-dimensional quantitative NMR spectroscopy (2D qNMR) was set up and multivariate analyses were performed on metabolites obtained from breast meat extracts of broilers and four native chicken (KNC) strains. It can accurately identify more metabolites than 1D 1H NMR via separation of peak overlap by dimensional expansion with good linearity, but has a problem of numerical quantification; Complementation of 1D and 2D qNMR is necessary. Among breeds, KNC-D had higher amounts of free amino acids, sugars, and bioactive compounds than others. Noticeable differences between KNCs and broilers were observed; KNCs contained higher amounts of inosine 5'-monophosphate, α-glucose, anserine, and lactic acid, and lower amounts of free amino acids and their derivatives. The 2D qNMR combined with multivariate analyses distinguished the breast meat of KNCs from broilers but showed similarities among KNCs. Also, 2D qNMR may provide fast metabolomics information compared to conventional analysis.

Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens.

Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10-6 mutations/site/year (95% HPD interval: 2.28 × 10-8 to 9.32 × 10-6) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.