Detection of QTL controlling digestive efficiency and anatomy of the digestive tract in chicken fed a wheat-based diet

OMICs approaches and technologies for understanding low-high feed efficiency traits in chicken: implication to breeding

In poultry production, there has been a trend of continuous increase in cost of feed ingredients which represents the major proportion of the production costs. Feed costs can be reduced by improving feed efficiency traits which increase the possibility of using various indigestible feed sources and decrease the environmental impact of the enhanced poultry production. Therefore, feed efficiency has been used as one of the most important economic traits of selection in the breeding program of chickens. Recently, many OMICs experimental studies have been designed to characterize biological differences between the high and low feed efficiency chicken phenotypes. Biological complexity cannot be fully captured by main individual OMICs such as genomics, transcriptomics, proteomics and metabolomics. Therefore, researchers have combined multiple assays from the same set of samples to create multi-OMICs datasets. OMICs findings are crucial in improving existing approaches to poultry breeding. The current review aimed to highlight the components of feed efficiency and general OMICs approaches and technologies. Besides, individual and multi-OMICs based understanding of chicken feed efficiency traits and the application of the acquired knowledge in the chicken breeding program were addressed.

Phenotypic timeline of gastrointestinal tract development in broilers divergently selected for digestive efficiency

Sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, to favor the use of a wider variety of feedstuffs. The objective of the study was to better characterize the kinetics of development of the digestive tract in broilers, in relationship with digestive efficiency by measuring various digestive parameters as well as serum color. Absolute and relative growth of gastrointestinal tract organs were compared between 2 divergent chicken lines selected on digestive efficiency (AMEn) during 7 wk of development. We show that as early as 7 d of age, these 2 lines differs for several organs developments and that these differences remain visible later on. In addition, the allometry of the gizzard and intestine segments is different between the 2 lines, with efficient birds putting more effort in the upper part of the digestive tract during postnatal development and less-efficient birds putting more effort in the lower part of the gastrointestinal tract. Interestingly, we also showed that differences in serum pigmentation, which is a good biomarker for digestive capacity, could be a convenient diagnostic tool to discriminate between chickens with high or low digestive efficiency at early stages of development. In conclusion, this study showed that selection of chickens for AMEn had large impacts in gastrointestinal development including at early stages and is a valuable resource for further studies on the genetic and physiological control of the response of the animal to feed variations.

New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens

Background

Improving the feed efficiency would increase profitability for producers while also reducing the environmental footprint of livestock production. This study was conducted to investigate the relationships among feed efficiency traits and metabolizable efficiency traits in 180 male broilers. Significant loci and genes affecting the metabolizable efficiency traits were explored with an imputation-based genome-wide association study. The traits measured or calculated comprised three growth traits, five feed efficiency related traits, and nine metabolizable efficiency traits.

Results

The residual feed intake (RFI) showed moderate to high and positive phenotypic correlations with eight other traits measured, including average daily feed intake (ADFI), dry excreta weight (DEW), gross energy excretion (GEE), crude protein excretion (CPE), metabolizable dry matter (MDM), nitrogen corrected apparent metabolizable energy (AMEn), abdominal fat weight (AbF), and percentage of abdominal fat (AbP). Greater correlations were observed between growth traits and the feed conversion ratio (FCR) than RFI. In addition, the RFI, FCR, ADFI, DEW, GEE, CPE, MDM, AMEn, AbF, and AbP were lower in low-RFI birds than high-RFI birds (P < 0.01 or P < 0.05), whereas the coefficients of MDM and MCP of low-RFI birds were greater than those of high-RFI birds (P < 0.01). Five narrow QTLs for metabolizable efficiency traits were detected, including one 82.46-kb region for DEW and GEE on Gallus gallus chromosome (GGA) 26, one 120.13-kb region for MDM and AMEn on GGA1, one 691.25-kb region for the coefficients of MDM and AMEn on GGA5, one region for the coefficients of MDM and MCP on GGA2 (103.45–103.53 Mb), and one 690.50-kb region for the coefficient of MCP on GGA14. Linkage disequilibrium (LD) analysis indicated that the five regions contained high LD blocks, as well as the genes chromosome 26 C6orf106 homolog (C26H6orf106), LOC396098, SH3 and multiple ankyrin repeat domains 2 (SHANK2), ETS homologous factor (EHF), and histamine receptor H3-like (HRH3L), which are known to be involved in the regulation of neurodevelopment, cell proliferation and differentiation, and food intake.

Conclusions

Selection for low RFI significantly decreased chicken feed intake, excreta output, and abdominal fat deposition, and increased nutrient digestibility without changing the weight gain. Five novel QTL regions involved in the control of metabolizable efficiency in chickens were identified. These results, combined through nutritional and genetic approaches, should facilitate novel insights into improving feed efficiency in poultry and other species.

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems

Improving the digestive efficiency of broiler chickens (Gallus gallus) could reduce organic waste, increase the use of alternative feed not used for human consumption and reduce the impact of feed in production costs. By selecting chicken lines divergently for their digestive efficiency, we showed previously that digestive efficiency is under genetic control and that the two resulting divergent lines, D+ (high digestive efficiency or “digestibility +”) and D- (low digestive efficiency or “digestibility -”), also differ for the abundance of specific bacteria in their caeca. Here we perform a more extensive census of the bacteria present in the digestive microbiota of 60 chickens selected for their low apparent metabolizable energy corrected for nitrogen balance (AMEn-) or high (AMEn+) digestive efficiency in a [D+ x D-] F8 progeny of 200 individuals. We sequenced the 16S rRNA genes of the ileal, jejunal and caecal microbiotas, and compared the compositions and predicted functions of microbiotas from the different intestinal segments for 20 AMEn+ and 19 AMEn- birds. The intestinal segment of origin was the main factor structuring the samples. The caecal microbiota was the most impacted by the differences in digestive efficiency, with 41 bacterial species with abundances differing between highly and poorly efficient birds. Furthermore, we predicted that the caecal microbiota of efficient birds might be enriched in genes contributing to the degradation of short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of the genetic selection led on digestibility on the caecal microbiota taxonomic composition. They open the way toward the identification of specific, causal genes of the host controlling variations in the abundances of bacterial taxons.

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

BACKGROUND

Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs.

RESULTS

Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes.

CONCLUSIONS

The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.

Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation

Genome wide association study was conducted using a mixed linear model (MLM) approach that accounted for family structure to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with body weight (BW) and feed efficiency (FE) traits in a broiler chicken population. The results of the MLM approach were compared with the results of a general linear model approach that does not take family structure in to account. In total, 11 quantitative trait loci (QTL) and 21 SNPs, were identified to be significantly associated with BW traits and 5 QTL and 5 SNPs were found associated with FE traits using MLM approach. Besides some overlaps between the results of the two GWAS approaches, there are considerable differences in the detected QTL. Even though the genomic inflation factor (λ) values indicate that there is no strong family structure in this population, using models that account for the existing family structure may reduce bias and increase accuracy of the estimated SNP effects in the association analysis. The SNPs and candidate genes identified in this study provide information on the genetic background of BW and FE traits in broiler chickens and might be used as prior information for genomic selection.

Functional genomics of the digestive tract in broilers

Background

The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum.

Results

Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions.

Conclusion

This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5344-z) contains supplementary material, which is available to authorized users.

Genetic aspects of feed efficiency and reduction of environmental footprint in broilers: a review

Currently, optimization of feed efficiency is one of the main challenges in improvement programs of livestock and poultry genetics. The objective of this review is to present the genetic aspects of feed efficiency related traits in meat-type chicken and possible ways to reduce the environmental impact of poultry meat production with effective breeding. Basic measures of feed efficiency are defined and the genetic background of these traits, including a review of heritabilities is described. Moreover, a number of genomic regions and candidate genes determining feed efficiency traits of broilers that were detected over the past decades are described. Classical and genomic selection strategies for feed efficiency in the context of its relationships with other performance traits are discussed as well. Finally, future strategies to improve feed digestibility are described as it is expected that they will decrease wastes and greenhouse gas emission. Further genetic improvement of feed efficiency, should be examined jointly with appropriate feeding strategies in broilers.

Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study

Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

Detection of QTL controlling feed efficiency and excretion in chickens fed a wheat-based diet

Background

Improving feed efficiency is a major goal in poultry production in order to reduce production costs, increase the possibility of using alternative feedstuffs and decrease the volume of manure. However, in spite of their economic and environmental impact, very few quantitative trait loci (QTL) have been reported on these traits. Thus, we undertook the detection of QTL on 820 meat-type chickens from a F2 cross between D− and D+ lines that were divergently selected on low or high digestive efficiency at 3 weeks of age. Birds were measured for growth between 0 and 23 days, feed intake and feed conversion ratio between 9 and 23 days, breast and abdominal fat yields at 23 days, and the anatomy of their digestive tract (density, relative weight and length of the duodenum, jejunum, ileum, and ratio of proventriculus to gizzard weight) was examined. To evaluate excretion traits, fresh and dry weight, water content, pH, nitrogen to phosphorus ratio from 0 to 23 days, and pH of gizzard and jejunum contents at 23 days were measured. A set of 3379 single nucleotide polymorphisms distributed on 28 Gallus gallus (GGA) autosomes, the Z chromosome and one unassigned linkage group was used for QTL detection.

Results

Using the QTLMap software developed for linkage analyses by interval mapping, we detected 16 QTL for feed intake, 13 for feed efficiency, 49 for anatomy-related traits, seven for growth, six for body composition and ten for excretion. Nine of these QTL were genome-wide significant (four for feed intake on GGA1, one for feed efficiency on GGA2, and four for anatomy on GGA1, 2, 3 and 4). GGA16, 19, and 26 carried many QTL for different types of traits that co-localize at the same position.

Conclusions

This study identified several QTL regions that are involved in the control of digestive efficiency in chicken. Further studies are needed to identify the genes that underlie these effects, and to validate these in other commercial populations and for different breeding environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0156-y) contains supplementary material, which is available to authorized users.

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken

Objectives

Feed efficiency and its digestive component, digestive efficiency, are key factors in the environmental impact and economic output of poultry production. The interaction between the host and intestinal microbiota has a crucial role in the determination of the ability of the bird to digest its food and to the birds’ feed efficiency. We therefore investigated the phenotypic and genetic relationships between birds’ efficiency and the composition of the cecal microbiota in a F2 cross between broiler lines divergently selected for their high or low digestive efficiency.

Methods

Analyses were performed on 144 birds with extreme feed efficiency values at 3 weeks, with feed conversion values of 1.41±0.05 and 2.02±0.04 in the efficient and non-efficient groups, respectively. The total numbers of Lactobacillus, L. salivarius, L. crispatus, C. coccoides, C. leptum and E. coli per gram of cecal content were measured.

Results

The two groups mainly differed in larger counts of Lactobacillus, L. salivarius and E. coli in less efficient birds. The equilibrium between bacterial groups was also affected, efficient birds showing higher C. leptum, C. coccoides and L. salivarius to E. coli ratios. The heritability of the composition of microbiota was also estimated and L. crispatus, C. leptum, and C. coccoides to E. coli ratios were moderately but significantly heritable (0.16 to 0.24). The coefficient of fecal digestive use of dry matter was genetically and positively correlated with L. crispatus, C. leptum, C. coccoides (0.50 to 0.76) and negatively with E. coli (-0.66). Lipid digestibility was negatively correlated with E. coli (-0.64), and AMEn positively correlated with C. coccoides and with the C. coccoides to Lactobacillus ratio (0.48 to 0.64). We also detected 14 Quantitative Trait Loci (QTL) for microbiota on the host genome, mostly on C. leptum and Lactobacillus. The QTL for C. leptum on GGA6 was close to genome-wide significance. This region mainly includes genes involved in anti-inflammatory responses and in the motility of the gastrointestinal tract.