Differences in hindlimb morphology of ducks and chickens: effects of domestication and selection

Pulsed alternating wavelength system lighting does not negatively impact production or welfare but reduces dopamine activity and may improve bone growth in grow-out Pekin ducks: Effects of PAWS lighting on meat ducks

The production and welfare of Pekin ducks can be affected by the lighting type they are housed under. There is no standard lighting system in industry and little data evaluating effects of different light systems on duck production and welfare. Pulsed Alternating Wavelength System (PAWS) is a novel LED technology that delivers multiple wavelengths of light in pulsating patterns. This study aimed to determine the effects of PAWS on brain serotonin turnover and skeletal quality in ducks. Ducks housed under PAWS were hypothesized to have lower brain serotonin turnover and equal bone quality compared to those housed under control lights (fluorescent with digital ballasts, 4500K, ∼40 lux). Ducks were placed in floor pens under PAWS or control lighting (1200 ducks/pen, n = 4 pens/treatment) at day of hatch until processing at 30 days of age (DOA). Body weights and feed intake were monitored weekly. Brains, femurs, tibiae, and humeri were collected on days 7, 14, 21 and 29 (n = 6 ducks/age/lighting type). Brain serotonin and metabolites were measured. Bone length, width, breaking strength, and ash were determined. Serotonin data were analyzed using 2-way ANOVA for age and lighting treatment with a post-hoc Fisher's LSD test. Bone data were analyzed with independent t-tests between treatments within each age. Ducks housed under PAWS were heavier by 29 DOA than controls (P < 0.001) with no differences in feed conversion. Brain analyses revealed no differences in serotonin turnover between lighting types. Early interstitial growth of PAWS femur and tibia was increased (P < 0.05), and PAWS femurs had increased bone mineral content at 29 DOA (P = 0.001). At 29 DOA, the PAWS humeri were wider than controls (P = 0.025) and had increased geometrical bone mechanical properties (P < 0.003), but no differences in breaking stress were evident. Results suggest that PAWS may have benefits for production traits and skeletal quality, however, a complete understanding of the welfare effects need further study.

Morphological, radiographic, three-dimensional computed tomographic, and histological features of the primary upstroke and downstroke muscles and bones in the domestic duck (Anas platyrhynchos domesticus) and the cattle egret (Bubulcus ibis, Linnaeus, 1758), reflecting the evolutionary transition towards the irreversible flightlessness

BACKGROUND

The purpose of this study was to explore whether domestication could lead to evolutionary changes towards flightlessness in the domestic duck (Anas platyrhynchos domesticus) compared to the cattle egret (Bubulcus ibis) as a nonflying and flying biological model, respectively. Bones of the pectoral girdle (scapula, clavicle, and coracoid) and the foramen triosseum were comparatively assessed using anatomical, radiographic, and 3D computed tomographic (CT) studies. Additionally, the muscles pectoralis and the supracoracoideus were histologically and immunohistochemically assessed.

RESULTS

Among the differences observed, radiographically, the distance between the paired clavicles was significantly wider (p < 0.05) in the domestic duck (mean ± SD 1.43 ± 0.23 cm) compared with the cattle egret (0.96 ± 0.13 cm). Unlike cattle egrets, there was no connection between the sternum and the hypocladium of furcula in domestic ducks. The scapula, clavicle, coracoid, sternum, and humerus were considerably longer in domestic ducks than in cattle egrets. The foramen triosseum appeared significantly (p < 0.01) wider in domestic ducks (0.7 ± 1.17 cm) compared to cattle egrets (0.49 ± 0.03 cm). Histologically, compared to cattle egrets, the muscle fibers in domestic ducks were loosely connected and contained fewer nuclei and perimysial/endomysial spaces. A higher myoglobin expression was evident in cattle egrets compared with domestic ducks.

CONCLUSIONS

Results of this study indicate that the bones and muscles of the pectoral girdle generally show specific morphological and structural changes reflective of the loss of prerequisites associated with flight behavior in domestic ducks due to domestication effects compared to cattle egrets.

Femora from an exceptionally large population of coeval ornithomimosaurs yield evidence of sexual dimorphism in extinct theropod dinosaurs

Sexual dimorphism is challenging to detect among fossils due to a lack of statistical representativeness. The Angeac-Charente Lagerstätte (France) represents a remarkable 'snapshot' from a Berriasian (Early Cretaceous) ecosystem and offers a unique opportunity to study intraspecific variation among a herd of at least 61 coeval ornithomimosaurs. Herein, we investigated the hindlimb variation across the best-preserved specimens from the herd through 3D Geometric Morphometrics and Gaussian Mixture Modeling. Our results based on complete and fragmented femora evidenced a dimorphism characterized by variations in the shaft curvature and the distal epiphysis width. Since the same features vary between sexes among modern avian dinosaurs, crocodilians, and more distant amniotes, we attributed this bimodal variation to sexual dimorphism based on the extant phylogenetic bracketing approach. Documenting sexual dimorphism in fossil dinosaurs allows a better characterization and accounting of intraspecific variations, which is particularly relevant to address ongoing taxonomical and ecological questions relative to dinosaur evolution.

Probiotics Treatment of Leg Diseases in Broiler Chickens: a Review

Normal development and growth of bones are critical for poultry. With the rapid growth experienced by broiler chickens, higher incidences of leg weakness and lameness are common problems in adolescent meat-type poultry that present huge economic and welfare issues. Leg disorders such as angular bone deformities and tibial dyschondroplasia have become common in broilers and are associated with poor growth, high mortality rates, increased carcass condemnation, and downgrading at slaughter. Probiotics have shown promise for a variety of health purposes, including preventing diarrhea, elevating carcass quality, and promoting growth of the poultry. In addition, recent studies have indicated that probiotics can maintain the homeostasis of the gut microbiota and improve the health of the gastrointestinal tract, which confers a potentially beneficial effect on bone health. This review mainly describes the occurrence of broiler leg disease and the role of probiotics in bone health through regulating the gut microbiota and improving intestinal function, thus providing a relevant theoretical basis for probiotics to hinder the development of skeletal disorders in broiler chickens.

Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing

BACKGROUND

Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation.

METHODS

In this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks.

RESULTS

Using fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions.

CONCLUSIONS

A wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China

Background

Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures.

Results

Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks.

Conclusion

Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07710-2.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

BACKGROUND

The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.

RESULTS

Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R).

CONCLUSIONS

Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

Removal of roosters alters the domestic phenotype and microbial and genetic profile of hens

Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.

A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks

Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of F_ST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

Transcriptome changes underlie alterations in behavioral traits in different types of chicken

In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Broilers spent less time gathered as a group in a novel arena (P < 0.01), suggesting reduced fearfulness in these birds. Broilers also showed a greater willingness to approach a model predator during a vigilance test but had a greater behavioral response when first exposed to the vocalization of the predator. Genes found to be upregulated and downregulated in previous work on chickens divergently selected for fear responses also showed consistent differences in expression between breeds in our study and indicated a reduction in fearfulness in broilers. Gene ACTB_G1 (actin) was differentially expressed between breeds and is a candidate gene involved with skeletal muscle growth and disease susceptibility in broilers. Furthermore, breed-specific alterations in the chicken domestic phenotype leading to differences in growth and egg production were associated with behavioral changes, which are probably underpinned by alterations in gene expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. The results highlight the change in behavior and gene expression of the broiler strain relative to the layer and a dual-purpose native breed.

Effect of dietary 25-hydroxycholecalciferol on the sternal mass of meat ducks under different vitamin regimens

Genetic selection and intensive nutrition for increased growth rate in meat-type ducks has resulted in an imbalance between pectorales increment and sternal mass, which is detrimental to productivity and welfare. Reducing body weight and increasing sternal mass probably reverses these adverse effects. Therefore, 2 experiments (Expt.) were conducted to investigate the effects of 25-hydroxycholecalciferol (25-OH-D3), a vitamin D3 metabolites, on sternal mass. In Expt. 1, 512 1-day-old male ducks were randomly assigned to 4 low-nutrient density diets and received following treatments in a 2 × 2 factorial arrangement: (i) NRC or China Agricultural industry standards (NY/T) vitamin premixes and (ii) 0.069 mg/kg 25-HyD in feed or not. At 49 D of age, regardless of 25-OH-D3, NY/T vitamin regimen inhibited bone turnover and consequently increased sternal trabecular bone volume and mineral deposition compared with NRC vitamin premix. Supplementing 25-OH-D3 to NRC but not NY/T vitamin regimen significantly improved sternal microarchitecture and mineral content, which companied by decreased serum bone resorption markers concentration, as well as downregulation of the gene expressions of osteoclast differentiation and activity. In Expt. 2, 256 1-day-old male ducks were fed a standard nutrient density diet contained NRC vitamin premix with 0 or 0.069 mg/kg of 25-OH-D3. Results also showed that 25-OH-D3 treatment significantly improved sternal mineral accumulation and microarchitecture, along with decreasing osteoblast and osteoclast numbers in bone surface, declining serum bone turnover markers levels, and increasing serum Ca concentration. Collectively, these findings indicated that the dietary administration of 25-OH-D3 increased sternal mass in NRC vitamin diet by suppressing bone resorption in 49-day-old meat duck.

Study on the morphology and mineralization of the tibia in meat ducks from 1 to 56 d

The objective of this current study was to characterize the basic physiological data on morphological and mineralized properties of the tibia from 1 to 56 days, as well as the interrelationships of body weight (BW) and bone traits for meat ducks. A total of 176 1-d-old ducks was allocated into eight pens and fed with the same diet until the age of 56 d. Eight birds (1 ducks/pen) were randomly selected weekly for measuring BW and tibia characteristics. The BW of duck was increased with age throughout the whole study. Tibial length and width rapidly grew from 1 to 35 d, when it leveled off. The fat-free weight, ash, calcium (Ca) and phosphorus (P) content of tibia increased rapidly from 1 to 42 d and reached its plateau from 42 d onward. Tibial density and tibia-breaking strength increased in a regular manner with age until 42 d. Serum alkaline phosphatase activity was higher between 1 to 7 d in the duck. Regression and ontogenetic scaling analysis showed the age of maximal growth rate in tibia dimension and mineralization was earlier than that in BW; when compared with BW, tibial fat-free weight and tibia-breaking strength increased isometrically, tibia length displayed a negative allometry, and tibial width showed a positive allometric growth. Results indicate that the tibia displayed rapid bone growth (1 to 35 d) and mineralization (1 to 42 d), and alkaline phosphatase (ALP) plays a critical role in the early stage of tibia mineralization of meat duck. Intensive selection for growth rate in ducks has resulted in tibial morphology changes, which represents an interesting compromise of adaptation for increasing BW.

Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection

Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication

Background

The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.

Results

Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our F_ST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus.

Conclusions

Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

Higher heritabilities for gait components than for overall gait scores may improve mobility in ducks

Background

Genetic progress in selection for greater body mass and meat yield in poultry has been associated with an increase in gait problems which are detrimental to productivity and welfare. The incidence of suboptimal gait in breeding flocks is controlled through the use of a visual gait score, which is a subjective assessment of walking ability of each bird. The subjective nature of the visual gait score has led to concerns over its effectiveness in reducing the incidence of suboptimal gait in poultry through breeding. The aims of this study were to assess the reliability of the current visual gait scoring system in ducks and to develop a more objective method to select for better gait.

Results

Experienced gait scorers assessed short video clips of walking ducks to estimate the reliability of the current visual gait scoring system. Kendall’s coefficients of concordance between and within observers were estimated at 0.49 and 0.75, respectively. In order to develop a more objective scoring system, gait components were visually scored on more than 4000 pedigreed Pekin ducks and genetic parameters were estimated for these components. Gait components, which are a more objective measure, had heritabilities that were as good as, or better than, those of the overall visual gait score.

Conclusions

Measurement of gait components is simpler and therefore more objective than the standard visual gait score. The recording of gait components can potentially be automated, which may increase accuracy further and may improve heritability estimates. Genetic correlations were generally low, which suggests that it is possible to use gait components to select for an overall improvement in both economic traits and gait as part of a balanced breeding programme.

Gait in ducks (Anas platyrhynchos) and chickens (Gallus gallus) - similarities in adaptation to high growth rate

Genetic selection for increased growth rate and muscle mass in broiler chickens has been accompanied by mobility issues and poor gait. There are concerns that the Pekin duck, which is on a similar selection trajectory (for production traits) to the broiler chicken, may encounter gait problems in the future. In order to understand how gait has been altered by selection, the walking ability of divergent lines of high- and low-growth chickens and ducks was objectively measured using a pressure platform, which recorded various components of their gait. In both species, lines which had been selected for large breast muscle mass moved at a slower velocity and with a greater step width than their lighter conspecifics. These high-growth lines also spent more time supported by two feet in order to improve balance when compared with their lighter, low-growth conspecifics. We demonstrate that chicken and duck lines which have been subjected to intense selection for high growth rates and meat yields have adapted their gait in similar ways. A greater understanding of which components of gait have been altered in selected lines with impaired walking ability may lead to more effective breeding strategies to improve gait in poultry.

Summary: Different bird species bred for meat production have adapted their gait in similar ways to handle the extra loads imposed on their legs by larger muscle masses.