Sexing chickens (Gallus gallus domesticus) with high-resolution melting analysis using feather crude DNA

Sex identification of ducklings based on acoustic signals

Sex identification of ducklings is a critical step in the poultry farming industry, and accurate sex identification is beneficial for precise breeding and cost savings. In this study, a method for identifying the sex of ducklings based on acoustic signals was proposed. In the first step, duckling vocalizations were collected and an improved spectral subtraction method and high-pass filtering were applied to reduce the influence of noise. Then, duckling vocalizations were automatically detected by using a double-threshold endpoint detection method with 3 parameters: short-time energy (STE), short-time zero-crossing rate (ZCR), and duration (D). Following the extraction of Mel-Spectrogram features from duckling vocalizations, an improved Res2Net deep learning algorithm was used for sex classification. This algorithm was introduced with the Squeeze-and-Excitation (SE) attention mechanism and Ghost module to improve the bottleneck of Res2Net, thereby improving the model accuracy and reducing the number of parameters. The ablative experimental results showed that the introduction of the SE attention mechanism improved the model accuracy by 2.01%, while the Ghost module reduced the number of model parameters by 7.26M and the FLOPs by 0.85G. Moreover, this algorithm was compared with 5 state-of-the-art (SOTA) algorithms, and the results showed that the proposed algorithm has the best cost-effectiveness, with accuracy, recall, specificity, number of parameters, and FLOPs of 94.80, 94.92, 94.69, 18.91M, and 3.46G, respectively. After that, the vocalization detection score and the average confidence strategy were used to predict the sex of individual ducklings, and the accuracy of the proposed model reached 96.67%. In conclusion, the method proposed in this study can effectively detect the sex of ducklings and serve as a reference for automated sex identification of ducklings.

Simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting analysis

Birds infected with duck circovirus (DuCV) can potentially cause immunosuppression by damaging lymphoid tissues, causing great losses in the duck breeding industry. Duck circovirus can be divided into two genotypes (DuCV-1 and DuCV-2), but simultaneous detection and differentiation of DuCV-1 and DuCV-2 by high-resolution melting (HRM) analysis is still lacking. Here, we designed specific primers according to the sequence characteristics of the newly identified ORF3 gene and then established a PCR-HRM method for the simultaneous detection and differentiation of DuCV-1 and DuCV-2 via high-resolution melting analysis. Our data showed that the established PCR-HRM assay had the advantages of specificity, with the lowest detection limits of 61.9 copies/μL (for DuCV-1) and 60.6 copies/μL (for DuCV-2). The melting curve of the PCR-HRM results indicated that the amplification product was specific, with no cross-reaction with common waterfowl origin pathogens and a low coefficient of variation less than 1.50% in both intra-batch and inter-batch repetitions, indicating the advantages of repeatability. We found that the percentage of DuCV-2-positive ducks was higher than that of DuCV-1-positive ducks, with 8.62% rate of DuCV-1 and DuCV-2 coinfection. In addition, we found DuCV-2-positive in geese firstly. In conclusion, this study provides a candidate PCR-HRM assay for the detection and accurate differentiation of DuCV-1 and DuCV-2 infection, which will help us for further epidemiological surveillance of DuCVs.

Xylanase and beta-glucanase improve performance parameters and footpad dermatitis and modulate intestinal microbiota in broilers under an Eimeria challenge

Coccidiosis is an enteric disease of poultry worldwide that compromises gut health and growth performance. The current research investigated the effects of 2 doses of a multienzyme preparation on broilers' performance, gut health, and footpad dermatitis (FPD) under an Eimeria challenge. A total of 512 mixed-sex day-old chicks (Cobb 500) were randomly allocated to 4 treatments of 8 replicates. Treatments were: 1) nonchallenged control (NC); 2) NC + Eimeria challenge (CC); 3) CC + recommended level of xylanase and glucanase (XG, 100 g/t feed [on top]); 4) CC + double XG (2XG, 200 g/t feed). Eimeria spp. vaccine strains were gavaged on d 9 to induce coccidiosis in chickens. Performance parameters were evaluated during starter, grower, and finisher phases, and 4 birds per pen were euthanized on d 16 for sampling, FPD was scored on d 35, and litter moisture was analyzed on d 17 and 35. The data were analyzed using 1-way ANOVA with Tukey's test to separate means, and Kruskal-Wallis test was used for non-normally distributed parameters. The results showed that the Eimeria challenge was successful based on reduced weight gain and feed intake during grower phase, and higher FITC-d concentration, lesion score (female), and oocyst counts (d 14) in CC group compared to N.C. group, while XG and 2XG increased (P < 0.001) weight gain and improved FCR compared to CC and NC groups during finisher phase. The addition of X.G. and 2XG decreased litter moisture (P = 0.003) and FPD (P < 0.001) in challenged broilers compared to the N.C. group (d 35). Supplementing XG and 2XG reestablished the population of Lactobacillus in the cecum of challenged birds to an intermediate level between the NC and CC groups (P > 0.05). The inclusion of XG tended to increase the expression of Junctional adhesion molecule 2 (JAM2), which was not different from CC and NC groups (P > 0.05). In conclusion, the combination of xylanase and glucanase (Natugrain TS) improved the performance and modulated jejunal microbiota of broilers under mild Eimeria challenge.

Buffered formic acid and a monoglyceride blend improve performance and modulate gut bacteria and immunity gene expression in broilers under necrotic enteritis challenge

Due to the removal of antibiotics from animal feed, alternatives have been sought to control necrotic enteritis (NE) in broilers. The current study investigated the effects of buffered formic acid (Amasil NA) and monoglycerides of short- and medium-chain fatty acids (Balangut LS P) on the performance and gut health of broilers challenged with NE. A total of 816 as-hatched 1-d-old chicks (Cobb 500) were randomly assigned to 6 treatments with 8 replicates. Treatments were: T1) nonchallenged control; T2) NE challenged control; T3) Amasil NA (challenge plus Amasil NA, 0.3% throughout all phases); T4) Balangut LS P (challenge plus Balangut LS P, 0.5%, 0.3%, and 0.2% in the starter, grower and finisher phases, respectively; T5) Combined (challenge plus combination of T3 and T4); T6) Antibiotic (challenge plus Zn bacitracin, 0.05 % throughout all phases). Birds were orally gavaged with live Eimeria vaccine species (d 9) and with Clostridium perfringens (d 14 and 15). On d 16, birds were sampled to evaluate gut permeability, microbiota, and mRNA abundance in the jejunum. The data were analyzed in JMP software using one-way ANOVA with Tukey's test to separate means, and Kruskal-Wallis test was used for non-normally-distributed parameters. Results showed that Balangut LS P decreased (P<0.05) feed conversion ratio compared to nonchallenged ones at the end of the study. Balangut LS P reduced (P < 0.05) the level of cecal Bacteriods compared to nonchallenged group, whereas Amasil NA shifted the levels of ileal Bifidobacteria, Enterobacteriaceae, and Lactobacillus towards nonchallenged control (P > 0.05). NE challenge upregulated (P < 0.001) the expression of IL-21R, zeta chain of T cell receptor (ZAP70), and dual specificity phosphatase 4 (DUSP4) compared to nonchallenged birds, whereas Balangut LS P showed an intermediate (P > 0.05) expression pattern of these genes towards nonchallenged and antibiotic groups. In conclusion, combination of Balangut LS P and Amasil NA has the potential to be used as an additive to improve the performance and gut health of broiler chickens, especially under challenging conditions such as NE infections.

Sex-specific markers undetected in green sunfish Lepomis cyanellus using restriction-site associated DNA sequencing

We used restriction-site associated DNA sequencing for SNP discovery and genotyping of known-sex green sunfish Lepomis cyanellus DNA samples to search for sex-diagnostic single nucleotide polymorphisms (SNPs) and restriction-site associated sequences present in one sex and absent in the other. The bioinformatic analyses discovered candidate SNPs and sex-specific restriction-site associated sequences that fit patterns of male or female heterogametic sex determination systems. However, when primers were developed and tested, no candidates reliably identified phenotypic sex. The top performing SNP candidate (ZW_218) correlated with phenotypic sex 63.0% of the time and the presence-absence loci universally amplified in both sexes. We recommend further investigations that interrogate a larger fraction of the L. cyanellus genome. Additionally, studies on the effect of temperature and rearing density on sex determination, as well as breeding of sex-reversed individuals, could provide more insights into the sex determination system of L. cyanellus.

Development and Application of a High-Resolution Melting Analysis with Unlabeled Probes for the Screening of Short-Tailed Sheep TBXT Heterozygotes

Simple Summary

TBXT (c.333G > C; c.334G > T) has been identified as a molecular genetic marker in short-tailed sheep. This paper describes a high-resolution melting (HRM) analysis using unlabeled probes and asymmetric PCR for the detection of genetic variants of TBXT in short-tailed sheep populations. The detection results of this method are consistent with those of Sanger sequencing and can help farmers with marker-assisted breeding.

Abstract

The short-tailed phenotype has long been considered one of the best traits for population genetic improvement in sheep breeding. In short-tailed sheep, not only is tail fat eliminated but also the pubic area is exposed due to the lack of a tail covering, giving them an advantage in reproduction. Recent studies have shown that two linked mutations in sheep TBXT at nucleotides 333 and 334 are associated with the short-tailed phenotype. In the population of short-tailed sheep, several heterozygous mutants of this gene are found. In our research, we used high-resolution melting (HRM) to identify homozygous and heterozygous genotypes in a flock of short-tailed sheep and compared the results with those of Sanger sequencing, which were identical. This demonstrates that our established HRM method, a rapid and inexpensive genotyping method, can be used to identify homozygous and heterozygous individuals in short-tailed sheep flocks.

Potential of a mixture of eugenol and garlic tincture to improve performance and intestinal health in broilers under necrotic enteritis challenge

Plant extracts (PE) are gaining increased attention as potential alternatives to in-feed antimicrobials (AM) due to their known antimicrobial activities. This study was conducted to examine the potential of PE, a microencapsulated product composed of eugenol and garlic tincture as an alternative to AM-agent on performance and intestinal health in broilers under necrotic enteritis (NE) challenge. A total of 960 day-old mixed-sex Cobb 500 chicks were randomly distributed to 48-floor pens with 6 treatments replicated 8 times with 20 birds each. The 6 treatments were as follows: UC, unchallenged control; CC, challenged control; PE, challenged group plus PE; AM, challenged group plus AM; FAP, challenged group plus a full dose of AM with PE; HAP, challenged group plus a half dose of AM with PE in starter, grower and finisher phases. Birds in the challenged groups were inoculated with Eimeria spp. on d 9 and Clostridium perfringens on d 14. The body weight gain (BWG), feed intake (FI), feed conversion ratio (FCR), and livability of birds were compromised, and intestinal lesions and mortality were increased (P < 0.05) by NE challenge, illustrating a successful clinical NE challenge. Birds fed AM had higher BWG and FI, and lower FCR, mortality, and intestinal lesions compared to the CC group (P < 0.05). Birds fed PE had improved FCR (P < 0.05) and livability (5.8%) in an overall period compared to the CC group. On d 16, PE supplementation reduced ileal lesion scores in only male birds (P < 0.05). Birds fed PE had decreased Eimeria maxima and Eimeria acervulina oocyst counts in caecal content (P < 0.05). Birds fed PE had decreased Escherichia brunetti and total oocyst counts in caecal content, and E. acervulina oocyst counts in ileal content in only female birds (P < 0.05). On d 35, PE supplementation reduced variation of BW in both male and female birds and increased yellowness (b∗ value, 14.4%) in the thigh. These findings suggest the potential of PE supplementation in diets to improve the performance and intestinal health of birds under clinical NE as indicated by improved FCR, livability, uniformity, reduced ileal lesions, oocyst counts and increased skin yellowness. However, the protective effect of PE may not be apparent in the presence of AM in the feed.

A Microencapsulated Mixture of Eugenol and Garlic Tincture Supplementation Mitigates the Effect of Necrotic Enteritis on Intestinal Integrity and Increases Goblet Cells in Broilers

This study was conducted to examine the effects of a plant extract mixture, a microencapsulated product composed of eugenol and garlic tincture (PE), on intestinal health in broilers under necrotic enteritis (NE) challenge. A total of 960 d-old mixed-sex Cobb 500 chicks were randomly distributed to 48-floor pens housing 20 birds per pen. Six treatments were applied: UC, unchallenged control; CC, challenged control; PE, challenged group plus PE; AM, challenged group plus antimicrobial (AM); FAP, challenged group plus a full dose of AM with PE; HAP, challenged group plus a half dose of AM with PE in starter, grower and finisher phases. Birds in the challenged groups were inoculated with Eimeria spp. on d 9 and Clostridiumperfringens on d 14. On d 16, the CC group had increased serum fluorescein isothiocyanate dextran (FITC-d), reduced villus surface area, goblet cell number, upregulated CLDN1, JAM2 genes and reduced microbial diversity compared to the UC group (p < 0.05). Birds fed PE had reduced FITC-d, increased goblet cell number and Bifidobacterium compared to the CC group (p < 0.05). Birds fed PE had reduced CLDN5 expression in male birds, and Bacteroides spp. in female birds than CC group (p < 0.05). These findings suggest that PE supplementation mitigates the effect of NE by improving the intestinal health of birds.

Multi-carbohydrase enzymes improve feed energy in broiler diets containing standard or low crude protein

This study evaluated the effect of multi-carbohydrase (MC) on energy and nitrogen (N) balance and gene expression in broilers fed diets with different crude protein (CP) contents. The study employed a 2 × 2 factorial arrangement of treatments. The factors were presence or absence of MC, and standard (SCP) or low (LCP) dietary CP concentration. A 3-phase feeding program was used, including starter (0 to 7 d), grower (8 to 17 d) and finisher (18 to 28 d) phases. The study was undertaken in closed calorimetry chambers. Each of the 4 dietary treatments was replicated 8 times in total across 2 runs, with 2 birds per replicate (n = 64). Data for energy partitioning and N balance were collected from d 25 to 28. On d 28, birds were euthanized to collect muscle and intestinal tissue samples for gene expression. The results showed that the MC increased apparent metabolizable energy (AME, P < 0.01) and net energy (NE, P < 0.05), and reduced the feed conversion ratio (FCR, P < 0.01) in all diets. The proportion of energy retained as fat per total energy retention (REf/RE) was positively correlated with feed AME and NE (r = 0.541, P < 0.01 and r = 0.665, P < 0.001, respectively), suggesting that feed energy augmented with increased fat gain. Muscle ATP synthase subunit alpha (ATP5A1W) gene expression had a positive correlation with REf/RE and feed NE (r = 0.587, P < 0.001 and r = 0.430, P < 0.05, respectively). Similarly, muscle peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1A) expression was negatively correlated with weight gain and positively correlated with FCR (r = −0.451, P < 0.05 and r = 0.359, P < 0.05, respectively). These correlations show that over-expressions of muscle genes related to energy production reduce bird performance. This study demonstrated that MC increase dietary energy utilization, regardless of dietary CP concentration. However, the energy released by the enzymes increases feed energy-to-CP ratio, meaning there is excess energy that is then deposited as body fat. This suggests that supplemental MC in broiler feeds is beneficial if diets are formulated to contain marginal energy levels.

Efficacy of supplemental multi-carbohydrases in broiler diets depends on soluble arabinoxylan-to-total arabinoxylan content

1. The objective of this study was to investigate the effect of multi-carbohydrase enzymes (MC) on net energy (NE), performance and gene expression in Cobb 500 broilers fed diets containing different levels of soluble and total arabinoxylan (sAX/tAX) ratios.2. The study employed a 2 × 3 factorial arrangement of treatments, with factors including with or without MC and three ratios of sAX/tAX: high (HS, 27.3%), intermediate (IS, 21.3%) and low (LS, 15.7%).3. Six dietary treatments were formulated, with each diet replicated five times in the calorimetric study (Experiment 1) and eight times for a floor pen feeding trial (Experiment 2).4. Experiment 1 showed significant (P < 0.01) MC × sAX/tAX interactions for apparent metabolisable energy (AME) and NE. These interactions indicated that the supplemental MC increased AME only in the HS diet, and NE in the HS and LS diets.5. Experiment 2 results showed MC × sAX/tAX interactions for feed conversion ratio (FCR, P < 0.01) and ileal digesta viscosity (P < 0.05), demonstrating that MC lowered FCR only in the LS-fed birds, and reduced digesta viscosity only in the HS-fed birds. Apparent ileal digestible crude protein (AID CP) was negatively correlated with ileal digesta viscosity (r = -0.735, P < 0.001), which suggested that increasing ileal digesta viscosity reduced AID CP.6. A significant (P < 0.05) MC × sAX/tAX interaction was observed for duodenal COX III mRNA gene expression, which indicated that this gene was upregulated in the IS-fed birds relative to the HS-fed birds, but only when MC was added. This gene was downregulated (P < 0.05) in the muscle in the presence of MC application in all diets.7. The results from this study showed that supplemental MC can improve NE and FCR in birds fed diets containing the low sAX/tAX ratios.