Phenotypic selection for residual feed intake and its effect on humoral immune responses in growing layer hens

Transcriptomic analysis of intestinal organoids, derived from pigs divergent in feed efficiency, and their response to Escherichia coli

BACKGROUND

There is increasing interest in using intestinal organoids to study complex traits like feed efficiency (FE) and host-microbe interactions. The aim of this study was to investigate differences in the molecular phenotype of organoids derived from pigs divergent for FE as well as their responses to challenge with adherent and invasive Escherichia coli (E. coli).

RESULTS

Colon and ileum tissue from low and high FE pigs was used to generate 3D organoids and two dimensional (2D) monolayers of organoid cells for E. coli challenge. Genome-wide gene expression was used to investigate molecular differences between pigs that were phenotypically divergent for FE and to study the difference in gene expression after challenge with E. coli. We showed, (1) minor differences in gene expression of colon organoids from pigs with low and high FE phenotypes, (2) that an E. coli challenge results in a strong innate immune gene response in both colon and ileum organoids, (3) that the immune response seems to be less pronounced in the colon organoids of high FE pigs and (4) a slightly stronger immune response was observed in ileum than in colon organoids.

CONCLUSIONS

These findings demonstrate the potential for using organoids to gain insights into complex biological mechanisms such as FE.

Growth performance, carcass traits, meat quality, and blood variables of small-sized meat ducks with different feed efficiency phenotypes

The study investigated the effects of feed efficiency (residual feed intake, RFI and residual intake and gain, RIG) on the production performance of small-sized meat ducks. Ninety ducks with intermediate and extreme (high and low) RFI values were selected from 1,083 male ducks of similar body weight, and the 3 groups were then redivided according to RIG. For both efficiency measures, the feed conversion ratio (FCR) and average daily feed intake (ADFI) of efficient ducks were significantly lower than those of inefficient ducks (P < 0.05), while the residual body weight gain (RG) was significantly higher in efficient ducks (P < 0.05). Inefficient-RFI animals showed greater skin fat yield (P < 0.05), but no other differences in carcass traits were observed (P > 0.05). RIG had positive effects on the pH1 value of the breast muscle (P < 0.05), but feed efficiency did not affect the other meat quality traits (P > 0.05). With regard to blood biochemical parameters, efficient ducks had significantly lower triglycerides (TG) (P < 0.05). Correlation analysis demonstrated that RFI was positively correlated with average daily feed intake and feed conversion ratio (P < 0.05), while RIG exhibited a strong negative correlation with both (P < 0.05). The average daily body weight gain was positively correlated with RIG (P < 0.05). RIG had a positive effect on the pH1 value of the breast muscle (P < 0.05). Furthermore, triglyceride and high-density lipoprotein cholesterol levels correlated with both efficiency classifications (P < 0.05). Overall, the efficiency measures did not affect the carcass and meat quality of small-sized meat ducks but could identify ducks with lower feed consumption and fast growth.

Trade-off between feed efficiency and immunity in specialized high-performing chickens

Based on resource allocation theory, ignoring importance of immunity, and focus on growth and feed efficiency (FE) traits in breeding plans may lead to serious weakness in immune system performance. However, in poultry the adverse effects of selection for FE on the immune system are unclear. Therefore, an experiment was conducted to study the trade-off between FE and immunity using a total of 180 high-performing specialized male chickens from a commercial broiler line which were selected over 30 generations for growth (body weight gain, BWG) and FE (residual feed intake, RFI). Birds were reared for 42 d and 5 FE-related traits of the birds in the last week were considered including daily feed intake (DFI), feed conversion ratio (FCR), residual feed intake (RFI), residual BW gain (RG), and residual intake and gain (RIG). For all 180 chickens, immune system performance including humoral immune response, cell-mediated immunity (CMI), and the activity of lysozyme enzyme (L. activity) as innate immunity was measured. After ascending sort of each FE records, 10% of higher records (H-FE: N = 18) and 10% of lower records (L-FE: N = 18) were determined, and immunity between L-FE and H-FE groups were compared. Moreover, L-BWG and H-BWG were analyzed because BWG is one of components in the FE formula. Performance of the immune system was not statistically different for CMI in none of the studied FE groups. Moreover, high and low groups for DFI and BWG were not different regarding the immunity of the birds. Antibody titers against Newcastle disease virus (NDV) were different between low and high groups of FCR, RG, and RIG. Likewise, SRBC-derived antibodies were significantly different between RFI groups. Rather than humoral immunity, RIG had adversely effect on the innate immunity. Results of the present study showed that although RIG is a more appropriate indicator for FE, choosing for high RIG can weaken the performance of the both humoral and innate immune systems, while RFI had fewer adverse effects.

Direct and maternal genetic effects for preinflection point growth traits and humoral immunity in quail

Early growth traits in quails are considered as the growth performances before the inflection point which are genetically different from body weights (BW) at later stages. Moreover, in addition to growth performance, humoral immunity is moderately heritable and is considered in some breeding programs. However, estimating the direct genetic, particularly the maternal genetic correlations between growth and immunity in quail, are not studied sufficiently, which were the aims of the present study. The quails' BW were recorded at hatch (BW0) to 25 d of age with a 5-d interval and body weight gains (BWG) were measured as average growth performance of the birds in a 5-d period. Antibody titer against Newcastle disease virus (IgN) was measured through the hemagglutination inhibition (HI) test. For titration of anti-SRBC antibodies (IgY and IgM), a hemagglutination microtiter assay was used. In general, growth records in 4,181 birds and humoral immune responses in 1,023 birds were assigned to the study. The genetic parameters were estimated by single-trait analysis via Gibb's sampling. After finding the best model for each trait, multi-trait analysis was done to estimate the direct and maternal genetic correlations. Direct heritabilities (h²) were estimated to be moderate for BW (0.481-0.551) and BWG (0.524-0.557), while h² for immune responses were low (0.035-0.079). Maternal environmental effect (c²) was only significant for BW0, BW5, and BWG0-5. Maternal heritabilities (m²) for BW and BWG were all lower than corresponding h², ranging from 0.072 (BW25) to 0.098 (BW0). The m² for IgN (0.098) was more than 2.5 times greater than h² (0.040) for this trait. Direct (r_a) and maternal (r_m) genetic correlations between IgN-BW, IgY-BW, and IgY-BWG were negative, while ra and rm for IgM-BW, IgN-BWG, and IgM-BWG were positive. The r_a between humoral immune responses were low to moderate and rm was significant only for IgY-IgM (0.339). Given positive genetic correlations in BWG-IgN and BWG-IgM as well as positive genetic correlations between both IgN and IgM with IgY, it is suggested that including the BWG in the breeding programs would directly result in the improvement of the birds' growth performance. It would also contribute indirectly to the improvement of the birds' humoral immune responses.

Long-term divergent selection for residual feed intake in Chinese broiler chickens

This study aimed to assess the effect of inbreeding on production traits using a long-term closed-line population recorded for residual feed intake (RFI). The study first used data from a previously reported population to determine the appropriate period of divergent selection for RFI. The results showed that RFI had similar moderate heritability estimates (0.28-0.34) during the fast-growing period (7-12 wk), and RFI at 7 to 10 wk had the highest heritability (0.34). Therefore, divergent selection was performed in a Chinese broiler population for RFI at 7 to 10 wk; the total sample size from generations zero (G0) to 13 was 9050. The divergence between the 2 lines increased steadily throughout generations, resulting in G13 with average RFI values of 304.55 in high RFI (HRFI) males, -160.31 in low RFI (LRFI) males, 296.30 in HRFI females and -157.55 in LRFI females. The feed intake (FI) and feed conversion ratio were almost higher in HRFI broilers than in LRFI broilers, and the magnitude of the difference in FI increased from approximately 4% for both sexes in G1 to approximately 33% in G13. Body weight gain was irregular from G1 to G13 and higher in LRFI broilers than in HRFI broilers after G10. Indeed, the HRFI broilers consumed more food, but they were lighter than LRFI broilers. In G13, LRFI males had heavier slaughter weight, longer cecum length, more white blood cells (WBC), red blood cells (RBC) and hemoglobin (HGB), but triglycerides, lower dressed percentage, percentage of half eviscerated yield, and eviscerated yield than HRFI males. LRFI females had a higher percentage of breast muscle and gizzard yield, longer cecum length, and more WBCs, RBCs and HGB but less abdominal fat and serum total cholesterol than HRFI females. This study was the first to verify that long-term divergent selection for RFI in Chinese broiler chickens is positive and beneficial.

Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens

Background

In all organisms, life-history traits are constrained by trade-offs, which may represent physiological limitations or be related to energy resource management. To detect trade-offs within a population, one promising approach is the use of artificial selection, because intensive selection on one trait can induce unplanned changes in others. In chickens, the breeding industry has achieved remarkable genetic progress in production and feed efficiency over the last 60 years. However, this may have been accomplished at the expense of other important biological functions, such as immunity. In the present study, we used three experimental lines of layer chicken—two that have been divergently selected for feed efficiency and one that has been selected for increased antibody response to inactivated Newcastle disease virus (ND3)—to explore the impact of improved feed efficiency on animals’ immunocompetence and, vice versa, the impact of improved antibody response on animals’ growth and feed efficiency.

Results

There were detectable differences between the low (R+) and high (R−) feed-efficiency lines with respect to vaccine-specific antibody responses and counts of monocytes, heterophils, and/or T cell population. The ND3 line presented reduced body weight and feed intake compared to the control line. ND3 chickens also demonstrated an improved antibody response against a set of commercial viral vaccines, but lower blood leucocyte counts.

Conclusions

This study demonstrates the value of using experimental chicken lines that are divergently selected for RFI or for a high antibody production, to investigate the modulation of immune parameters in relation to growth and feed efficiency. Our results provide further evidence that long-term selection for the improvement of one trait may have consequences on other important biological functions. Hence, strategies to ensure optimal trade-offs among competing functions will ultimately be required in multi-trait selection programs in livestock.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00636-z.

The significant influence of residual feed intake on flavor precursors and biomolecules in slow-growing Korat chicken meat

Objective

This study investigated the association between feed efficiency, physicochemical properties, flavor precursors and biomolecules in the thigh meat of Korat (KR) chickens.

Methods

The feed intake and body weight of individual male KR chickens were recorded from 1 to 10 weeks old to calculate the individual residual feed intake (RFI) of 75 birds. At 10 weeks of age, chickens with the 10 highest (HRFI) and lowest RFI (LRFI) were slaughtered to provide thigh meat samples. The physicochemical properties (ultimate pH, water holding capacity [WHC], drip loss) and flavor precursors (guanosine monophosphate, inosine monophosphate (IMP), adenosine monophosphate and inosine) were analyzed conventionally, and Fourier transform infrared spectroscopy was used to identify the composition of biomolecules (lipids, ester lipids, amide I, amide II, amide III, and carbohydrates) and the secondary structure of the proteins. A group t-test was used to determine significant differences between mean values and principal component analysis to classify thigh meat samples into LRFI and HRFI KR chickens.

Results

The physicochemical properties of thigh meat samples from LRFI and HRFI KR chickens were not significantly different but the IMP content, ratios of lipid, lipid ester, protein (amide I, amide II) were significantly different (p<0.05). The correlation loading results showed that the LRFI group was correlated with high ratios of lipids, lipid esters, collagen content (amide III) and beta sheet protein (rg loading >0.5) while the HRFI group was positively correlated with protein (amide I, amide II), alpha helix protein, IMP content, carbohydrate, ultimate pH and WHC (rg loading >0.5).

Conclusion

The thigh meat from chickens with different RFI differed in physiochemical properties affecting meat texture, and in the contents of flavor precursors and biomolecules affecting the nutritional value of meat. This information can help animal breeders to make genetic improvements by taking more account of traits related to RFI.

Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies

The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as “starch and sucrose metabolism,” “phenylalanine, tyrosine and tryptophan biosynthesis,” and “carbohydrate metabolism” were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.

Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Background

Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associated with high and low feed efficiency and their regulator genes in Danish Holstein and Jersey cows.

RNA-sequencing data from Holstein and Jersey cows with high and low residual feed intake (RFI) and treated with two diets (low and high concentrate) were used. Approximately 26 million and 25 million pair reads were mapped to bovine reference genome for Jersey and Holstein breed, respectively. Subsequently, the gene count expressions data were analysed using a Weighted Gene Co-expression Network Analysis (WGCNA) approach. Functional enrichment analysis from Ingenuity® Pathway Analysis (IPA®), ClueGO application and STRING of these modules was performed to identify relevant biological pathways and regulatory genes.

Results

WGCNA identified two groups of co-expressed genes (modules) significantly associated with RFI and one module significantly associated with diet. In Holstein cows, the salmon module with module trait relationship (MTR) = 0.7 and the top upstream regulators ATP7B were involved in cholesterol biosynthesis, steroid biosynthesis, lipid biosynthesis and fatty acid metabolism. The magenta module has been significantly associated (MTR = 0.51) with the treatment diet involved in the triglyceride homeostasis. In Jersey cows, the lightsteelblue1 (MTR = − 0.57) module controlled by IFNG and IL10RA was involved in the positive regulation of interferon-gamma production, lymphocyte differentiation, natural killer cell-mediated cytotoxicity and primary immunodeficiency.

Conclusion

The present study provides new information on the biological functions in liver that are potentially involved in controlling feed efficiency. The hub genes and upstream regulators (ATP7b, IFNG and IL10RA) involved in these functions are potential candidate genes for the development of new biomarkers. However, the hub genes, upstream regulators and pathways involved in the co-expressed networks were different in both breeds. Hence, additional studies are required to investigate and confirm these findings prior to their use as candidate genes.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2553-z) contains supplementary material, which is available to authorized users.

Feed conversion ratio, residual feed intake and cholecystokinin type A receptor gene polymorphisms are associated with feed intake and average daily gain in a Chinese local chicken population

Background

The feed conversion ratio (FCR) and residual feed intake (RFI) are common indexes in measuring feed efficiency for livestock. RFI is a feed intake adjusted for requirements for maintenance and production so these two traits are related. Similarly, FCR is related to feed intake and weight gain because it is their ratio. Cholecystokinin type A receptor (CCKAR) plays an important role in animal digestive process. We examined the interplay of these three parameters in a local Chinese chicken population.

Results

The feed intake (FI) and body weights (BW) of 1,841 individuals were monitored on a daily basis from 56 to 105 d of age. There was a strong correlation between RFI and average daily feed intake (ADFI) and a negative correlation between the FCR and daily gain (r_g = − 0.710). Furthermore, we identified 51 single nucleotide polymorphisms (SNPs) in the CCKAR and 4 of these resulted in amino acid mutations. The C334A mutation was specifically associated with FI and the expected feed intake (EFI) (P <  0.01) and significantly associated with the average daily gain (ADG) (P <  0.05). G1290A was significantly associated with FI and EFI (P < 0.05).

Conclusion

FCR is apply to weight selecting, and RFI is more appropriate if the breeding focus is feed intake. And C334A and G1290A of the CCKAR gene can be deemed as candidate markers for feed intake and weight gain.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0261-1) contains supplementary material, which is available to authorized users.

Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low-abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.

Comparative transcriptome analysis of the Pacific White Shrimp (Litopenaeus vannamei) muscle reveals the molecular basis of residual feed intake

Feed efficiency is an economically important trait in genetic improvement programs of L. vannamei. Residual feed intake (RFI), an ideal measure of feed efficiency, is the difference between observed feed intake and expected feed requirement predicted from maintenance and production. Exploring the molecular basis of RFI is essential to facilitate the genetic breeding of feed efficiency in L. vannamei. However, few studies have been reported in this aspect. In this study, we sequenced muscle transcriptomes of a high-efficiency group, a low-efficiency group and a control group originating from two families, and compared the gene expression patterns between each extreme group and the control group. A total of 383 differentially expressed genes were identified, most of which were involved in cell proliferation, growth and signaling, glucose homeostasis, energy and nutrients metabolism. Functional enrichment analysis of these genes revealed 13 significantly enriched biological pathways, including signaling pathways such as PI3K-Akt signaling pathway, AMPK signaling pathway and mTOR signaling pathway, as well as some important pathways such as ubiquitin mediated proteolysis, cell cycle, pentose phosphate pathway and glycolysis/gluconeogenesis. These genes and pathways provide initial insight into the molecular mechanisms driving the feed efficiency in L. vannamei.

Assessing serum metabolite profiles as predictors for feed efficiency in broiler chickens reared at geographically distant locations

1. The objective of this study was to investigate differences in growth performance, serum intermediary metabolites, acute-phase proteins and white blood cells in low, medium and high-residual feed intake (RFI) chickens. It was also assessed if the environment affects the feed efficiency (FE) and FE-related performance and serum profiles of chickens. 2. Individual body weight (BW) and feed intake (FI) were recorded from d 7 of life. At 5 weeks of age, female and male broiler chickens (Cobb 500) were selected according to their RFI (L1: Austria; L2: UK; n = 9/RFI group, sex and locatity -45on) and blood samples were collected. 3. Chickens at L1 had similar FI but a 15% higher BW gain compared to chickens at L2. The RFI values of female chickens were -231, 8 and 215 g and those of male chickens -197, 0 and 267 g for low, medium and high RFI, respectively. 4. Location affected serum glucose, urea, cholesterol, non-esterified fatty acids (NEFA) and ovotransferrin in females, and serum glucose and triglycerides in male chickens. Serum uric acid and NEFA linearly increased from low to high RFI in females, whereas in males, cholesterol showed the same linear response from low to high RFI. Serum alpha-1-acid glycoprotein and blood heterophil-to-lymphocyte ratio linearly increased by 35% and 68%, respectively, from low to high RFI but only in male chickens at L1. 5. Regression analysis showed significant positive relationships between RFI and serum uric acid (R² = 0.49) and cholesterol (R² = 0.13). 6. It was concluded that RFI-related variation in serum metabolites of chickens was largely similar for the two environments and that serum metabolite patterns could be used to predict RFI in chickens.

Haematological and febrile response to Escherichia coli lipopolysaccharide in 12-week-old cockerels of genetically diverse layer lines fed diets with increasing L-arginine levels

Due to its decisive function in the avian metabolic, endocrine and immune system L-arginine (Arg) is dietary indispensable for chickens. In 12-week-old cockerels of two high- and two low-performing purebred layer lines, the effects of increasing dietary Arg on the haematological and febrile response were studied over 48 h after single lipopolysaccharide (LPS) injection. The offered diets contained Arg equivalent to 70%, 100% and 200% of recommended supply. Pathophysiological alterations in weight gain, feed intake, body temperature and differential blood count were examined in comparison with their physiological initial values. Within the first 24 h after LPS injection, cockerels reduced feed intake and lost body weight subsequently. Thereby, low-performing genotypes lost body weight to a lesser extent than high-performing ones. The loss of body weight was further intensified by deficient dietary Arg. Within the following 24 h, cockerels recovered by improving feed intake and weight gain. Furthermore, LPS induced genotype-specific fever response: both brown genotypes showed initial hypothermia followed by longer lasting moderate hyperthermia, whereas the white genotypes exhibited biphasic hyperthermia. Fever response was accompanied by significant changes in differential blood counts. Characterized by lymphopenia and heterophilia, a severe leucopenia was observed from 4 to 8 h after LPS injection and replaced by a marked leucocytosis with longer lasting monocytosis up to 48 h after LPS injection. Under given pathophysiological conditions, deficiently Arg-supplied cockerels showed higher total leucocyte counts than adequately and excessively Arg-supplied cockerels. However, deficient and surplus dietary Arg tended to cause higher ratios between heterophils and lymphocytes. To conclude, present results confirmed that LPS induced numerous immunological changes in 12-week-old cockerels and emphasized that chicken's genotype is a source of variation to be considered for immunological studies. Deficient dietary Arg intensified acute changes in differential blood counts and weight gain during LPS-induced inflammation.

Effects of ambient temperature, feather cover, and housing system on energy partitioning and performance in laying hens

Environmental factors, such as ambient temperature (T), feather cover (FC), and housing system (HS), probably affect energy requirements of laying hens. Using a 3 × 2 × 2 factorial arrangement, interaction effects of T (11, 16, and 21°C), FC (100 and 50%), and HS (cage and floor housing) on energy partitioning and performance of laying hens were investigated. Six batches of 70 H&N Brown Nick laying hens, divided over 2 respiration chambers, were exposed to the T levels in three 2-wk periods. Heat production (HP) was determined by indirect calorimetry. The ME intake was calculated by subtracting energy in manure/litter from that in feed and wood shavings. The NE was calculated by subtracting HP from ME. The ME intake increased by 1% for each degree reduction in T. In hens with intact plumage, HP was not affected by T, whereas at decreasing T, HP increased in hens with 50% FC (P < 0.01). At 21°C, HP was not affected by HS, whereas in the floor system, HP at 16 and 11°C was 5.8 and 3.0% higher, respectively, than in cages (P < 0.05). The NE for production was 25.7% higher in cages compared to the floor system (P < 0.05). In cages, 24.7% of NE for production was spent on body fat deposition, whereas in the floor system, 9.0% of NE for production was released from body fat reserves. The ME intake was predicted by the equation (R(2) = 0.74) ME intake (kJ/d) = 612 BW(0.75) - (8.54 × T) + (28.36 × ADG) + (10.43 × egg mass) - (0.972 × FC). Hen performances were not affected by treatments, indicating the adaptive capacity of young laying hens to a broad range of environmental conditions.

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq

Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.

Association of single nucleotide polymorphisms in the microRNA miR-1596 locus with residual feed intake in chickens

MicroRNAs are an abundant class of small non-coding RNAs that regulate gene expression. Genetic variations in microRNA sequences may be associated with phenotype differences by influencing the expression of microRNAs and/or their targets. This study identified two single nucleotide polymorphisms (SNPs) in the genomic region of the microRNA miR-1596 locus of chicken. Of the two SNPs, one was 95 bp upstream of miR-1596 (g.5678784A>T) and the other was in the middle of the sequence producing the mature microRNA gga-miR-1596-3p (g.5678944A>G). Genotypic distribution of the two SNPs had large differences among 12 chicken breeds (lines), especially between the fast-growing commercial lines and the slow-growing Chinese indigenous breeds for the g.5678784A>T SNP. Only the g.5678784A>T SNP was significantly associated with residual feed intake (RFI) in the F2 population derived from a fast-growing and a slow-growing broiler as well as in the pure Huiyang bearded chicken. The birds with the AA genotype of the g.5678784A>T SNP had lower RFI and higher expression of the mature gga-miR-1596-3p microRNA of miR-1596 than did those with the other genotypes of the same SNP. We also found that the expression of the mature gga-miR-1596-3p microRNA of miR-1596 was significantly associated with RFI. These findings suggest that miR-1596 can become a candidate gene related to RFI, and its genetic variation may contribute to changes in RFI by altering expression levels of the mature gga-miR-1596-3p microRNA in chicken.

Development of ileal cytokine and immunoglobulin expression levels in response to early feeding in broilers and layers

Provision of feed in the immediate posthatch period may influence interaction between intestinal microbiota and immune system, and consequently immunological development of the chick. This study addressed ileal immune development in response to early feeding in 2 chicken breeds selected for different production traits: broilers and layers. Chicks of both breeds either received feed and water immediately posthatch or were subjected to a 72-h feed and water delay. Ileal cytokine and immunoglobulin mRNA expression levels were determined at different time points. Effects of early feeding were limited, but breeds differed strikingly regarding cytokine and immunoglobulin expression levels. Cytokine expression levels in broilers were low compared with layers and showed a transient drop in the second to third week of life. In contrast, broilers showed considerably higher expression levels of IgA, IgM, and IgY. These findings indicate that the 2 breeds use different immune strategies, at least on the ileal level.

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of copy number variations (CNVs) using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intake (RFI). We detected 443 candidate CNV regions (CNVRs) that represent 18.4 Mb (0.6 %) of the genome. To investigate the functional impacts of CNVs, we created two groups of 30 individual animals with extremely low or high estimated breeding values (EBVs) for RFI, and referred to these groups as low intake (LI; more efficient) or high intake (HI; less efficient), respectively. We identified 240 (~9.0 Mb) and 274 (~10.2 Mb) CNVRs from LI and HI groups, respectively. Approximately 30-40 % of the CNVRs were specific to the LI group or HI group of animals. The 240 LI CNVRs overlapped with 137 Ensembl genes. Network analyses indicated that the LI-specific genes were predominantly enriched for those functioning in the inflammatory response and immunity. By contrast, the 274 HI CNVRs contained 177 Ensembl genes. Network analyses indicated that the HI-specific genes were particularly involved in the cell cycle, and organ and bone development. These results relate CNVs to two key variables, namely immune response and organ and bone development. The data indicate that greater feed efficiency relates more closely to immune response, whereas cattle with reduced feed efficiency may have a greater capacity for organ and bone development.

Correlated effects of selection for immunity in White Leghorn chicken lines on natural antibodies and specific antibody responses to KLH and M. butyricum

Background

The effect of selection for three general immune response traits on primary antibody responses (Ab) to Mycobacterium butyricum or keyhole limpet hemocyanin (KLH) was studied in four experimental lines of White Leghorn chicken. Birds underwent 12 generations of selection for one of three different general immune criteria; high antibody response to Newcastle disease virus 3 weeks after vaccination (ND3), high cell-mediated immune response, using the wing web response to phytohemglutinin (PHA) and high phagocytic activity, measured as carbone clearance (CC). Line ND3-L was selected on ND3, line PHA-L was selected on PHA, and line CC-L on CC, but all lines were measured for all three traits. The fourth line was a contemporary random bred control maintained throughout the selection experiment. Principal component analysis was used to distinguish clusters based on the overall set of immune measures.

Results

In the KLH immunised group, no differences were present between lines for natural antibodies binding to KLH and LPS, and, lines ND3-L and PHA-L had higher titers to LTA and anti-Gal titers measured before the immunisation protocol. The measure of ND3 was correlated positively with LPS titers measured post KLH immunisation and with the difference between LPS titers measured at day 0 and 7 post immunisation. In the M. butyricum immunised group, Line ND3-L showed significantly higher specific antibody response to M. butyricum, and this result agrees well with the hypothesis that the Th-1 pathway was expected to be selected for in this line.

Conclusion

This study has shown that the two different antigens KLH and M. butyricum gave rise to different responses in the set of selected lines, and that the response was only enhanced for the antigen associated with the same response mechanism as that for the trait (ND3, PHA or CC) for which the line was selected. Interactions between innate and acquired immunity have been observed mainly for the high antibody selected trait, indicating there was a specific interaction due to the selection criterion. Furthermore, the results confirmed the independence between the three selected traits. Finally, principal component analysis contributed to visually discriminate high and low responders to the two new antigens in the four lines.

Semiquantitative assessment of the distribution of Salmonella in the environment of caged layer flocks

AIMS

To evaluate a semiquantitative technique for the enumeration of Salmonella in the environment of layer flocks and to compare findings with those of a standard qualitative technique.

METHODS AND RESULTS

Samples were taken from faeces, floor dust, dust on cages, feeders and egg belts. After mixing with buffered peptone water, serial dilutions were prepared and culture was performed using pre-enrichment, then plating on semisolid selective and solid isolation media. Comparison with a qualitative pre-enrichment technique indicated a similar sensitivity for both methods despite smaller sample sizes. The numbers of Salmonella detected for a site or sample type did not correlate closely with the prevalence of positive samples.

CONCLUSIONS

The sensitive detection and quantification of Salmonella in the flock environment is practicable with the technique described. Quantitative data in many cases do not correlate with qualitative findings.

SIGNIFICANCE AND IMPACT OF THE STUDY

The significance of certain environmental factors and interventions in the maintenance and dissemination of Salmonella in poultry houses may be over- or under-represented by prevalence data alone. The technique described allows the issue of poultry house contamination to be examined from a new perspective.

Effect of selection for resistance and susceptibility to viral diseases on concentrations of dopamine and immunological parameters in six-week-old chickens

White Leghorn chickens were inbred respectively from their parent lines, which were diversely selected for resistance (line 6(3)) or susceptibility (lines 7(2) and 15I(5)) to Marek's disease and lymphoid leukosis. The differences in disease resistance may have been due to differential regulation of immune and neuroendocrine homeostasis. At 5 wk of age, chickens from the same line were randomly assigned to cages at 4 birds per cage. Blood samples were collected from the chickens at 6 wk of age (n = 10/line). Subsets of T lymphocytes (CD4+ and CD8+) and B cells were measured using flow cytometry. Concentrations of plasma IgG and dopamine were quantified with ELISA and HPLC assay, respectively. Line 6(3) chickens had a higher percentage of CD8+ cells but not CD4+ cells than the chickens of the lines 7(2) and 15I(5) (P < 0.01). In contrast, both lines 7(2) and 15I(5) had a greater percentage of B cells (P < 0.01). The concentrations of plasma IgG and dopamine were also regulated differently among the lines; both were in an order of 7(2) > 15I(5) > 6(3) (P < 0.05 and P < 0.01, respectively). These results suggested that genetic selection for disease resistance also directly or indirectly modified the corresponding genetic components that govern the immune and neuroendocrine systems. The genetic lines of chickens may be used as animal models for investigation of the cellular mechanisms of genetic-environmental interactions on disease resistance.

Energy Partitioning and Thyroid Hormone Levels During Salmonella enteritidis Infections in Pullets with High or Low Residual Feed Intake

This experiment was conducted to investigate whether feed efficiency, as measured by residual feed intake as a phenotypic trait, affects energy partitioning in pullets that have received Salmonella inoculation as an immune challenge. In each of 8 trials, energy partitioning was measured during 5 wk in 15-wk-old efficient (R-) and nonefficient (R+) pullets, which were housed per efficiency group in 2 identical climate respiration chambers. After 1 wk of adaptation, the pullets in 4 trials were orally inoculated with 10(8) cfu of Salmonella enteritidis; pullets in the remaining trials were not inoculated and served as controls. Heat production was calculated from continuous recordings of O(2) consumption and CO(2) production. Energy and N partitioning were recorded on a weekly basis. Blood samples for analyses on thyroid hormones were taken at 16, 17, and 19 wk of age. There were no interactions between efficiency type and Salmonella treatment or Salmonella treatment effects in energy partitioning, except for a short-term increase in heat production in inoculated pullets. Nonefficient pullets had higher gross energy and ME intake, higher estimated ME for maintenance, lower ME:gross energy ratio, and higher total heat production and nonactivity-related heat production compared with R- pullets. Triiodothyronine levels in R+ pullets were higher at 16 and 17 wk but were lower at 19 wk of age compared with R- pullets. Thyroxine levels were higher in R- at 16 wk and showed interactions between efficiency type and Salmonella treatment at 17 and 19 wk of age. Body weights and spleen weights did not differ between efficiency groups. Nonefficient pullets had higher heart, liver, and ovary weights and more large yellow follicles than R- pullets. There were no Salmonella effects on body and organ weights. We conclude that R+ pullets have a faster running energy metabolism and that they put more resources into organ development than R- pullets. Inoculation with Salmonella has a short-term effect on nonactivity-related heat production but does not affect energy partitioning, regardless of efficiency type.

Natural anti-Gal and Salmonella-specific antibodies in bile and plasma of hens differing in diet efficiency

Specific anti-Salmonella enteritidis (SE) and natural anti-alpha-gal epitope (Galalpha1-3Galbeta-1-4GlcNAc-R; anti-Gal) antibodies were measured in plasma sample pools and individual bile specimens obtained from hens differing in diet efficiency. More SE somatic (O) and flagellar (H) antibodies were found in plasma pools from efficient hens (R-) compared with nonefficient hens (R+) after oral challenge with live SE. Mean titers of somatic agglutinins in bile were 2.3 in R- hens and 1.9 in R+ hens (P = 0.06) following live challenge. Salmonella enteritidis antibodies were also found in bile of nonchallenged hens of both types but their levels were not significantly different. Flagellar (H) agglutinin scores were higher in SE-challenged hens compared with nonchallenged hens (3.1 vs. 2.1; P < or = 0.004) but efficiency types did not differ. Bile also contained high titers of the anti-Gal antibody indicated by the agglutination of glutaraldehyde-stabilized rabbit erythrocytes. The average titer of all SE-nonexposed hens was 9.0 corresponding to 1:5,120 when corrected for the initial dilution and expressed in conventional terms. Salmonella enteritidis exposure was associated with higher anti-Gal titers. The average anti-Gal titer for all SE-exposed hens was 10.0, corresponding to 1:10,240 in conventional terms; this difference was significant (P < or = 0.016). Diet efficiency type-associated differences in anti-Gal titers were not significant. Collectively, our data indicate that diet efficiency status is not associated with compromised Salmonella-specific immune responses. Rather it appears that the immune responses of diet efficient hens (R-) are also more efficient. This is because R- hens produced higher levels of O- and H-type antibody only as the result of direct exposure to living SE. On the contrary, R+ hens produced H-type antibody because of challenge with heat-killed SE, a circumstance that will not result in disease. Moreover, the hen type difference does not seem to occur at the expense of innate immunity as measured by anti-Gal antibody levels.

Salmonella Challenge Affects the Antibody Isotype Profile of Bile in Hens Differing in Metabolic Efficiency

Gel precipitation reactions determined antibody isotypes in bile from hens differing in dietary efficiency. Ouchterlony double diffusion employing alpha-chain specific goat-anti-chicken IgA, rabbit anti-chicken IgG, goat anti-chicken IgM, black turtle bean (BTB), and Jacalin lectins as precipitating reagents detected bile IgA, IgG, and IgM from Salmonella exposed and nonexposed hens. The IgA was present in 1 of 3 forms designated by reagent and frequency: IgAB (precipitated by BTB lectin) 100%; IgAA (precipitated by anti-alpha chain antibody) 98%, and IgAJ (precipitated by Jacalin) 97%. That both BTB and Jacalin precipitates contain IgA was confirmed by immuno-dot blots using affinity purified alpha-chain specific antibody, establishing each as IgA glycoforms. Three measurements of Ouchterlony precipitates were made; d1 and d2 indicate diffusion from sample or reagent wells, lambda indicates arc length. Mean values for lambda, estimating quantity, were IgAA (11.3 mm) and IgAB (11.6 mm) and IgAJ (8.3 mm). The crescent shape IgAJ arc and its slower diffusion (d1) suggested its molecular weight is greater than either IgAA or IgAB. Arc lengths of individual samples were not significantly correlated suggesting that these are independent components of bile. Oral Salmonella enteritidis challenge resulted in a highly significant difference in bile IgA profiles. The IgAJ arc lengths (lambda) in R- hens increased by 20% over those in nonchallenged R- hens. Conversely S. enteritidis challenge was associated with a decrease of 10% in IgAJ arc lengths in nonefficient (R+) hens. Salmonella enteritidis challenge was not associated with arc length differences in either IgAA or IgAB. The IgG was present in all specimens, and in 9 of 59 (15%) 2 forms were detected. The IgG quantity was unaffected by either efficiency type or S. enteritidis challenge. The IgM was detected in only 2 of 59 (3.4%) specimens. Our observations suggest IgA of bile is composed of multiple forms influenced both by diet efficiency status and S. enteritidis exposure. It appears that the latter resulted in an increased quantity of IgAJ in R- hens, and suggests the existence of functional differences among the various IgA types.

Residual feed intake and its effect on Salmonella enteritidis infection in growing layer hens

Previous phenotypic selection on residual feed intake (RFI) identified 20 efficient R- chickens and 20 nonefficient R+ chickens. Residual feed intake was defined as the difference between observed feed intake (FI) and expected FI based on metabolic BW and BW gain, and was used as a measure for feed efficiency. Body weight and BW gain were similar for both groups. Feed intake and RFI were significantly higher in R+ birds. It is hypothesized that nonefficient R+ birds are more flexible to divert resources from production processes toward maintenance processes, thus being better capable of handling a bacterial challenge. Chickens of both groups were randomly allocated to immunization with heat-inactivated Salmonella enteritidis bacteria, or inoculation with live Salmonella bacteria. Transportation to the isolation units caused a decrease in FI in R+ birds. This may reflect a particular way of coping with stress in R+ birds. More R+ birds stopped bacterial shedding considering a nonshedding interval of 10 or 11 d (P = 0.041). Nonantigen-specific antibody responses against keyhole limpet hemocyanin (KLH) were higher in R- birds. We conclude that R+ birds are able to keep their metabolism at a higher level, as indicated by higher heart and liver weights, and that Salmonella infection leads to reduced heart, liver, and gizzard weights. Oviduct weight and number of small yellow follicles were reduced in infected birds. Antigen-specific antibody responses were not different between the groups, indicating high priority for this parameter as a life trait. Possible differences in stress susceptibility between efficient and nonefficient chickens need further examination.