Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens

Gut-brain bidirectional determination in regulating the residual feed intake of small-sized meat ducks

The gut-brain axis is essential in maintaining the homeostasis of neuronal system, endocrine system, and intestinal microbiota in both the afferent and efferent directions. This axis is considered to be a key mechanism that regulates feed efficiency (FE). This study aimed to investigate the regulatory mechanisms of gut-brain axis-related genes on the residual feed intake (RFI) in H-strain small-sized meat ducks. A total of 500 ducks with similar initial BW (635.2 ± 15.1 g) were selected and reared in the same experimental facility until slaughter at 42 d of age. RFI was calculated from the average daily gain (ADG), average daily feed intake (ADFI), and metabolic body weight (MBW0.75). Thirty high-RFI (H-RFI) and 30 low-RFI (L-RFI) birds were selected for further evaluation of growth performance, carcass characteristics, and blood biochemical parameter measurements. Six L-RFI and 6 H-RFI birds were then subjected to hypothalamic transcriptomic and cecal microbial sequencing analyses. Results indicated that L-RFI birds exhibited lower production performance (ADFI, FCR, and RFI) and blood biochemical indices (total cholesterol and ghrelin content) compared with H-RFI birds (P < 0.05). Gene expression differed significantly between the L-RFI and H-RFI birds, with 70 upregulated and 50 downregulated genes. The bacterial communities of L-RFI birds showed higher abundances of Bacteroides, Bifidobacterium, and Lactococcus, and lower abundances of Erysipelatoclostridium, Parasutterella, Fournierella, and Blautia compared with H-RFI birds (P < 0.05). Interactive analysis revealed bacterial communities associated with FE were significantly correlated with hypothalamic genes (P < 0.05), for example, Bacteroides was positively correlated with DGKH and LIPT2, while negatively correlated with CAPN9, GABRD, and PDE1A. Bifidobacterium showed significant correlations with ATP2A3, CALHM6, and TMEM121B. Overall, RFI was a crucial indicator of FE, regulated by interactions between brain gene expression and gut microbiota through cAMP signaling, neuroactive ligand-receptor interaction, and calcium signaling pathways. Notably, increased expression of hypothalamic genes and abundance of carbohydrate-utilization microbiota in L-RFI meat ducks improved FE by enhancing energy metabolism and volatile fatty acids absorption.

Hypothalamic transcriptome profile from laying period to incubation period of Changshun green-shell laying hens

Incubation behavior in chickens is closely associated with hypothalamus. Here, RNA sequencing of hypothalamus from Changshun green-shell laying hens, an indigenous chicken breed from China, in egg-laying period (LP) and incubation period (BP) was conducted to identify critical pathways and candidate genes involved in controlling the incubation behavior in hypothalamus. A total of 637 up-regulated and 305 down-regulated differently expressed genes (DEGs) were identified in chicken hypothalamus between LP and BP groups. Gene ontology term (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further revealed that neuroactive ligand-receptor interaction, hippo signaling pathway, and focal adhesion were significantly enriched. Five candidate genes (POMC, IGF1R, CHAD, VCL, and MYL9) were suggested to play crucial roles in the regulation of chicken incubation behavior. Our results further indicated the complexity of reproductive behavior of different chicken breeds.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

Comparative study and relationship analysis between purine content, uric acid, superoxide dismutase, and growth traits in purebred and crossbred Thai native chickens

The objective was to compare and analyze the relationship between growth, purine content, uric acid, and superoxide dismutase (SOD) in purebred and crossbred Thai native chickens. A total of 300 Thai native chickens were divided into 3 groups. Group 1 was purebred Thai native chickens (100%TN), Group 2 was 50% Thai native chickens (50%TN), and Group 3 was 25% Thai native chickens (25%TN). Data included the body weight (BW), average daily gain (ADG), and breast circumference (BrC). At 6, 8, and 10 weeks of age, 10 chickens from each group were randomly euthanized to collect breast meat, liver, and blood samples to analyze the purine content consisting of total purine, adenine, guanine, xanthine, and hypoxanthine, and uric acid, in breast meat and liver and SOD in blood. A general linear model, Pearson correlation and principal component analysis were used to analyze the significant differences and relationship between variables. The results showed the 25%TN group had the highest growth traits at every age, while the 100%TN group had the lowest (p < 0.05). Consistent with the analysis results of purine values, purine content and uric acid in breast meat and liver and SOD in blood decreased with age (p < 0.05). The correlations between purine content (total purine, adenine, guanine, xanthine, and hypoxanthine) and growth traits (BW, ADG, and BrC) ranged from moderate negative to moderate positive (-0.542 to 0.253)(p < 0.05). The correlations between uric acid and growth traits (0.348-0.760) and SOD and growth traits (0.132-0.516) were low to moderate positive with significant differences (p < 0.05). The principal component plot, which highlighted three principal components (PC 1, PC 2, and PC 3), explained 86.44 and 86.53% of the total information in breast meat and liver for selecting animals for optimal balance of the variation in the growth traits, purine content, uric acid, and SOD. Although purebred Thai native chickens showed the lowest growth traits, purine content, uric acid, and SOD were also lowest compared to crossbred Thai native chickens. Therefore, the development of genetics in Thai native chickens to produce healthy food could be possible.

Thigh muscle metabolic response is linked to feed efficiency and meat characteristics in slow-growing chicken

The Korat chicken (KR) is a slow-growing Thai chicken breed with relatively poor feed efficiency (FE) but very tasty meat with high protein and low fat contents, and a unique texture. To enhance the competitiveness of KR, its FE should be improved. However, selecting for FE has an unknown effect on meat characteristics. Thus, understanding the genetic basis underlying FE traits and meat characteristics is needed. In this study, 75 male KR birds were raised up to 10 wk of age. For each bird, the feed conversion ratio (FCR), residual feed intake (RFI), and physicochemical properties, flavor precursors, and biological compounds in the thigh meat were evaluated. At 10 wk of age, thigh muscle samples from 6 birds (3 with high FCR and 3 with low FCR values) were selected, and their proteomes were investigated using a label-free proteomic method. Weighted gene coexpression network analysis (WGCNA) was used to screen the key protein modules and pathways. The WGCNA results revealed that FE and meat characteristics significantly correlated with the same protein module. However, the correlation was unfavorable; improving FE may result in a decrease in meat quality through the alteration in biological processes including glycolysis/gluconeogenesis, metabolic pathway, carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, and protein processing in the endoplasmic reticulum. The hub proteins of the significant module (TNNT1, TNNT3, TNNI2, TNNC2, MYLPF, MYH10, GADPH, PGK1, LDHA, and GPI) were also identified to be associated with energy metabolism, and muscle growth and development. Given that the same proteins and pathways are present in FE and meat characteristics but in opposite directions, selection practices for KR should simultaneously consider both trait groups to maintain the high meat quality of KR while improving FE.

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks

Introduction

The objective of this study was to determine the regulatory effects of gut microbiota on the feed efficiency (FE) of small-sized meat ducks by evaluating correlations between gut microbiota and residual feed intake (RFI).

Methods

A total of 500 21-day-old healthy male ducks with similar initial body weights (645 ± 15.0 g) were raised contemporaneously in the same experimental facility until slaughter at 56 days of age. In total, nine low-RFI (LR) and nine high-RFI (HR) birds were selected for further gut microbiota composition and functional analyses based on the production performance, and the RFI was calculated from 22 to 56 days of age.

Results

Growth performance results indicated a significantly lower RFI, feed conversion ratio, feed intake, and average daily feed intake in the LR ducks (P < 0.05). Taxonomy results of gut microbiota showed the identification of 19 kinds of phyla and more than 250 kinds of genera in all samples. No significant discrepancies in cecal bacterial α-diversity were discovered between the LR and HR groups, which indicated that the microbial modulatory effects on RFI may be attributed to the bacterial composition, rather than the species diversity. Differential analysis of bacterial communities between the LR and HR groups showed a significant increment of Firmicutes and a significant decline of Bacteroidetes in the LR group (P < 0.05). Specifically, genera of Erysipelatoclostridium, Parasutterella, Fournierella, and Lactococcus significantly proliferated, while Bacteroides significantly decreased in the LR group (P < 0.05). Furthermore, correlation analysis showed that the RFI was significantly correlated with carbohydrate metabolism-related bacteria including Bacteroides, Alistipes, Bifidobacterium, Ruminiclostridium_9, Sellimonas, Oscillibacter, Escherichia-Shigella, Lactococcus, and Streptococcus.

Conclusion

In conclusion, the communities related to carbohydrate metabolism had positive regulatory effects on the FE of small-sized meat ducks, promoting it by improving the relative abundance and utilization of these communities. The present study provides valuable insight into the dynamics of gut microbiota underlying the variations in the FE of small-sized meat ducks.

Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits

Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.

Phenotypic correlations between feed efficiency, growth, and meat quality of slow-growing chickens

1. Korat (KR) chicken is a new meat-type chicken breed established with the purpose of developing Small and Micro Community Enterprise Production. This slow-growing chicken has been recognised for its good texture and flavour, but its low feed efficiency is associated with high cost of production which can hamper the development of local production. This has highlighted the importance of studying the trade-off between feed efficiency and meat quality in KR chicken.2. This study investigated the phenotypic correlations between feed efficiency, growth performance, and meat quality in KR chicken. Individual body weight and feed intake were recorded weekly for 75 male KR chickens for the calculation of feed conversion ratio (FCR) and residual feed intake (RFI). The growth curve was modelled by Gompertz function and meat quality evaluated at 10 weeks of age, through the measurement of pH (pH_u), water-holding capacity (WHC) and drip loss (DL) in breast and thigh muscle.3. Faster growth rate at young age appeared favourable, regarding feed efficiency, since a moderate negative correlation was found between FCR and initial growth rate. Chickens with a higher initial growth and maturation rates were characterised by lower water-holding capacity in meat. This was not associated with acidic meat, since a higher speed of growth (especially in the first weeks) was positively associated with final pH in breast meat. Relationships between RFI and meat quality traits appeared to be weak. While better FCR could be achieved by increased initial growth rate, this seemed to negatively impact water-holding capacity of the meat.4. RFI appeared as an interesting alternative as a compromise between FCR and meat quality.

Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks

Simple Summary

Good feed efficiency (FE) is an important trait to ensure the economic output of the livestock and poultry industries. Herein, a genome-wide association study was conducted to identify potential variants and genes associated with seven FE measures in ducks. Genomic DNA samples of 308 ducks were collected and sequenced. All animals were evaluated concerning body weight gain (BWG), feed intake (FI), residual feed intake (RFI), feed conversion ratio (FCR), and weight at 21 (BW21) and 42 days of age (BW42). Overall, 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) single nucleotide polymorphisms (SNPs) were significantly associated with these FE traits, respectively. Moreover, candidate genes close to the identified variants were found to be mainly involved in key pathways and terms related to metabolism. In summary, these findings improve our understanding of poultry genetics and provide new foundations for breeding programs aimed at maximizing the economic potential of duck breeding and farming.

Abstract

Feed efficiency (FE) is the most important economic trait in the poultry and livestock industry. Thus, genetic improvement of FE may result in a considerable reduction of the cost and energy burdens. As genome-wide association studies (GWASs) can help identify candidate variants influencing FE, the present study aimed to analyze the phenotypic correlation and identify candidate variants of the seven FE traits in ducks. All traits were found to have significant positive correlations with varying degrees. In particular, residual feed intake presented correlation coefficients of 0.61, 0.54, and 0.13 with feed conversion ratio, and feed intake, respectively. Furthermore, data from seven FE-related GWAS revealed 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) SNPs were significantly associated with body weight gain, feed intake, residual feed intake, feed conversion ratio, and weight at 21 and 42 days, respectively. Candidate SNPs of seven FE trait-related genes were involved in galactose metabolism, starch, propanoate metabolism, sucrose metabolism and etc. Taken together, these findings provide insight into the genetic mechanisms and genes involved in FE-related traits in ducks. However, further investigations are warranted to further validate these findings.