The optimum valine: lysine ratios on performance and carcass traits of male broilers based on different regression approaches

Large-scale genomic and transcriptomic analyses elucidate the genetic basis of high meat yield in chickens

INTRODUCTION

Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems.

OBJECT

Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood.

METHOD

We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis-eQTL mapping and the Mendelian randomization was applied.

RESULT

We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes.

CONCLUSION

Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory target (SOX6-MYH1s axis) for breast muscle yield and myopathy, which could aid in the development of genome-scale selective breeding aimed at high meat yield in broiler chickens.

Optimal dietary standardized ileal digestible lysine level for pigs during the grower, early and late finisher periods

BACKGROUND

Lysine (Lys) is the first limiting amino acid for pigs fed corn-soybean meal diets. Three experiments were conducted to estimate the optimal standardized ileal digestible (SID) Lys requirement for growing (Exp. 1), early finishing (Exp. 2), and late finishing (Exp. 3) pigs under commercial conditions.

RESULTS AND CONCLUSIONS

In Exp. 1, a total of 650 growing pigs (32.21 ± 0.33 kg bodyweight), were allocated to 5 dietary treatments supplemented with 0.75, 0.85, 0.94, 1.03, and 1.13% SID Lys. Each treatment had 5 replicate pens with 26 pigs per pen. The lowest feed to gain ratio (F:G) was obtained by pigs fed the 1.03% Lys diet and F:G showed both a linear and a quadratic response with increasing Lys (P < 0.05). Based on broken-line and quadratic analysis models, dietary SID Lys levels for the minimum F:G were 0.94%. In Exp. 2, 650 finishing pigs (57.24 ± 2.00 kg bodyweight) were allotted to 5 dietary treatments providing SID Lys of 0.63, 0.71, 0.79, 0.87, and 0.95%. Each treatment had 5 replicates, 26 pigs per replication. The highest final bodyweight was achieved by 0.79% Lys while the highest average daily gain (ADG) and average daily feed intake (ADFI) was achieved by pigs consuming the 0.87% Lys diet (P < 0.05). Additionally, the lowest F:G was obtained by pigs fed the 0.79 and 0.87% Lys diet (P < 0.05). Based on broken-line and quadratic analysis models, the optimum Lys was 0.81 and 0.82% for ADG and F:G, respectively. In Exp. 3, 600 late finishing pigs (92.22 ± 2.41 kg bodyweight), were divided into 5 treatments providing Lys levels of 0.53, 0.60, 0.66, 0.73, and 0.79%. Each treatment had 5 replicates, 24 pigs per replication. Results showed that final bodyweight, ADG, ADFI, and F:G was not affected by increasing dietary Lys level, suggesting that the lowest SID Lys (0.53%) was sufficient for this group of pigs. Taken together, the SID Lys requirement for pigs from 30 to 60 kg, 60 to 90 kg, 90 to 120 kg was 0.94%, 0.81 to 0.82, and 0.53%, respectively, depending on the response criteria with performance maximized.

Biomarkers and De Novo Protein Design Can Improve Precise Amino Acid Nutrition in Broilers

Simple Summary

Almost half of the protein ingested by broilers is not retained and is excreted, impairing the nitrogen utilization, health and productivity of the animals, and intensifying the environmental impact of poultry meat production. This work proposes two potential tools, combining traditional nutrition with biotechnological, metabolomics, computational and protein engineering knowledge, which can contribute to improving precise amino acid nutrition in broilers in the future: (i) the use of serum uric nitrogen content as a rapid biomarker of amino acid imbalances, and (ii) the design and modeling of de novo proteins that are fully digestible and fit exactly to the animal’s requirements. Both tools can open up new opportunities to form an integrated framework for precise amino acid nutrition in broilers, helping us to achieve more efficient, resilient, and sustainable production. This information can help to determine the exact ratio of amino acids that will improve the efficiency of the use of nitrogen by poultry.

Abstract

Precision nutrition in broilers requires tools capable of identifying amino acid imbalances individually or in groups, as well as knowledge on how more digestible proteins can be designed for innovative feeding programs adjusted to animals’ dynamic requirements. This work proposes two potential tools, combining traditional nutrition with biotechnological, metabolomic, computational and protein engineering knowledge, which can contribute to improving the precise amino acid nutrition of broilers in the future: (i) the use of serum uric nitrogen content as a rapid biomarker of amino acid imbalances, and (ii) the design and modeling of de novo proteins that are fully digestible and fit exactly to the animal’s requirements. Each application is illustrated with a case study. Case study 1 demonstrates that serum uric nitrogen can be a useful rapid indicator of individual or group amino acid deficiencies or imbalances when reducing dietary protein and adjusting the valine and arginine to lysine ratios in broilers. Case study 2 describes a stepwise approach to design an ideal protein, resulting in a potential amino acid sequence and structure prototype that is ideally adjusted to the requirements of the targeted animal, and is theoretically completely digestible. Both tools can open up new opportunities to form an integrated framework for precise amino acid nutrition in broilers, helping us to achieve more efficient, resilient, and sustainable production. This information can help to determine the exact ratio of amino acids that will improve the efficiency of the use of nitrogen by poultry.

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW.

Transcriptome Analysis and Expression of Selected Cationic Amino Acid Transporters in the Liver of Broiler Chicken Fed Diets with Varying Concentrations of Lysine

Amino acids are known to play a key role in gene expression regulation. Amino acid signaling is mediated via two pathways: the mammalian target of rapamycin complex 1 (mTORC1) and the amino acid responsive (AAR) pathways. Cationic amino acid transporters (CATs) are crucial in these pathways due to their sensing, signaling and transport functions. The availability of certain amino acids plays a key role in the intake of other amino acids, hence affecting growth in young birds. However, the specific mechanism for regulating lysine transport for growth is not clear. In this study, we analyze the transcriptome profiles and mRNA expression of selected cationic amino acid transporters in the livers of broilers fed low and high lysine diets. Birds consumed high-lysine (1.42% lysine) or low-lysine (0.85% lysine) diets while the control group consumed 1.14% lysine diet. These concentrations of lysine represent 125% (high lysine), 75% (low lysine) and 100% (control), respectively, of the National Research Council's (NRC) recommendation for broiler chickens. After comparing the two groups, 210 differentially expressed genes (DEGs) were identified (fold change >1 and false discovery rate (FDR) <0.05). When comparing the high lysine and the low lysine treatments, there were 67 upregulated genes and 143 downregulated genes among these DEGs. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) enrichment analysis show that cellular growth, lipid metabolism and lysine metabolism pathways were among the significantly enriched pathways. This study contributes to a better understanding of the potential molecular mechanisms underlying the correlation between lysine intake, body weight gain (BWG) and feed intake (FI) in broiler chickens. Moreover, the DEGs obtained in this study may be used as potential candidate genes for further investigation of broiler growth customized responses to individualized nutrients such as amino acids.

Response of broilers to supplementation of branched-chain amino acids blends with different valine contents in the starter period under summer conditions

Objective

The objectives of this study were to compare the effects of normal and low protein content (PC) of starter diet supplemented or not with blends of branched-chain amino acids (BCAAs) on growth performance of broilers under summer conditions and to investigate whether these effects altered some quality traits and the characteristics of gastrointestinal tract.

Methods

A total of 768 mixed-sex broiler chicks (Ross 308, one-d-old) with an average initial body weight (BW) of 47.6±1.03 g were allocated into six treatments with four replications in 2×3 factorial arrangement. Factors were: PC, normal (N, 22% to d 15); and low (L, 20% to d 15); and added BCAA blends, L-leucine, L-isoleucine, and L-valine at zero (0L:0I:0V); 1.0, 0.25, and 0.25 (4L:1I:1V); or 1.0, 0.25, 0.75 (4L:1I:3V) g/kg of diet. Hence, six dietary treatments were named as N0L:0I:0V, N4L:1I:1V, N4L:1I:3V, L0L:0I:0V, L4L:1I:1V, and L4L:1I:3V. Average indoor temperature and humidity were 32.8°C±1.7°C and 61.1% ±4.12%, respectively.

Results

BW, feed conversion ratio (FCR) and carcass weight were not affected by PC, BCCA and their interaction (p>0.05). The L diets decreased the water holding capacity of the breast (p = 0.002) and thigh (p = 0.050) meats and dressing percentage (p = 0.005) compared to the N diets. The 4L:1I:1V diet decreased breast yield compared to the 0L:0I:0V diets (p = 0.041). The effect of PC on feed intake, mortality and gastrointestinal trait weight were depended on the L:I:V ratios under summer conditions due to interactions between factors (p<0.05). The FI and mortality of L4L:1I:1V broilers were lower than those of N4L:1I:1V birds (p<0.05).

Conclusion

It was concluded that the blends of BCAAs used failed to improve performance and to promote breast yields, because diets with normal or with reduced protein supplemented or not with BCAAs up to d 15 produced a similar BW and FCR in broilers raised in hot-climate conditions.

Plant extract supplementation as a strategy for substituting dietary antibiotics in broiler chickens exposed to low ambient temperature

The present study was conducted to investigate the effects of two plant extracts as alternatives to dietary antibiotics in broiler chickens exposed to low ambient temperature. A total of 300 one-day-old male broiler chickens were randomly assigned to four dietary treatments (5 replicate pens; 15 broiler chickens each) which consisted of starter (d 0 to 10), and grower (d 10 to 28) diets. Dietary treatments included a basal diet (negative control, NC) and three similar diets that were either supplemented with 200 mg/kg of Prosopis farcta extract (PFE), Rhus coriaria L. extract (RCE) or an antibiotic premix containing oxytetracycline (positive control, PC). In order to simulate low ambient temperature, room temperature was maintained at 32°C during the first 3 d of the trial and afterwards, the temperature was gradually reduced by approximately 1.5°C each day to 14°C on d 21. PFE and PC treatments exerted a significant effect on body weight gain at d 28. Diet PFE was effective in reducing mortality when compared with diet NC (p < 0.05). Furthermore, diet PFE caused increases in ileal  digestibility of gross energy, dry matter and organic matter when compared with diet NC (p < 0.05). Diets PFE and PC decreased coliforms, total aerobic bacteria and total anaerobic bacteria loads in the caeca when compared with diet NC (p < 0.05). Moreover, the addition of PFE to the diet improved villous height in all small intestinal segments as well as villous height:crypt depth ratio in the duodenum when compared with diet NC (p < 0.05). The results indicated that PFE is not only a valid alternative to oxytetracycline under cold stress conditions, with no antibiotic resistance, but also has the potential to increase the resistance of broiler chickens against ascites syndrome. Moreover, the addition of RCE at the concentration of 200 mg/kg to the diet was not sufficient to improve the performance of broiler chickens (similar to diet PC) but maybe more effective at higher concentrations.