Multi-generational genome wide association studies identify chromosomal regions associated with ascites phenotype

Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium

Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits

Background

The goal of this study was to evaluate marker-assisted selection (MAS) in broiler chickens using previously mapped gene regions associated with ascites syndrome incidence. The second-generation MAS products were assessed for impact on ascites phenotype and whether there were associated changes in important production traits. Previously, we used whole genome resequencing (WGR) to fine-map 28 chromosomal regions as associated with ascites phenotype in our experimental ascites broiler line (Relaxed, REL) based on a hypobaric chamber challenge. Genotypes for single nucleotide polymorphisms (SNPs) in mapped regions on chromosomes 2 and 22, were used for MAS in our REL line. After two generations, birds homozygous for the genotypes associated with resistance for both chromosomal regions were established. The MAS F2 generation was then compared to the REL line for ascites susceptibility and 25 production traits.

Results

Selection based on SNPs in the carboxypeptidase Q (CPQ, Gga2) and leucine rich repeat transmembrane neuronal 4 (LRRTM4, Gga22) gene regions resulted in a sex- and simulated altitude- dependent reduction of ascites incidence in two F2 cohorts of the MAS line. Comparisons of the F2 MAS and REL lines for production traits when reared at ambient pressure found no significant negative impacts for feed intake (FI), feed conversion ratio (FCR), or deboned part yields for either sex for two F2 cohorts. There were, however, improvements in the MAS for full-trial body weight gain (BWG), FCR, absolute and relative tender weights, and relative drumstick weight.

Conclusions

These results validate the mapping of the 28 chromosomal regions and demonstrate that fine mapping by WGR is an effective strategy for addressing a complex trait; it also stands as the first successful SNP-based selection program against a complex disease trait, such as ascites. The MAS line is comparable and, in some instances, superior, in growth performance to the REL control while being more resistant to ascites. This study indicates that MAS based on WGR can provide significant breeding potential in agricultural systems.

Evaluation of cardiac status, ascites related factors and growth performance of five commercial strains of broiler chickens

The aim of the current study was to evaluate cardiac status, ascites susceptibility, thyroid hormones, some hematological parameters and performance of five commercial broiler strains. Chicks were selected from strains of Cobb, Hubbard, Ross 308, Arbor Acres, and Arian (Iranian commercial broiler strain). Management and nutritional conditions were the same for all strains. Ascites related factors, and growth performance were measured. The highest and lowest, RV weight/live weight at 21 day of age were related to Arian and Ross 308 strains, respectively (p < 0.05). The TV weight, TV weight/live weight and the RV weight/live weight were significantly different between various strains at 49 and 54 days of age (p < 0.05). Strain had no effect on RV/TV. Performance, T3 and T4 hormones, hematological parameters, and mortalities were not significantly different among the strains (p > 0.05). Ascites mortalities in the Ross 308 was zero; however, it had no significant difference with other strains (p > 0.05). It was concluded that, based on performance and physiological status, even though considered broiler strains did not differ significantly because of the same genetic programs probably, but according to the prices and market conditions each can be selected for breeding.

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing

BACKGROUND

Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations.

RESULTS

The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype.

CONCLUSIONS

The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

Energy metabolism and sources of oxidative stress in wooden breast - a review

Modern broilers show dramatic growth over a short interval and contribute directly to the success of the poultry meat industry. The growth performance of commercial broilers is a result of genetic selection for "performance traits", such as body size, meat yield, and feed conversion rate. However, due to the rapid growth rate of modern commercial broilers, several growth-related conditions have arisen, increasing economic losses and consumer concerns. Among the most economically consequential is the muscle disorder called wooden breast. Together with associated myopathies such as white striping and spaghetti meat, wooden breast is causing losses of $200 million a year in the U.S. alone and occurs worldwide. No causative factors are known for wooden breast to date. Wooden breast can affect over 80% of broilers in a flock, yet no methods of amelioration are currently available. Overall, the evidence suggests that wooden breast is a genetic, age-dependent condition associated with fast growth rate. The primary features of wooden breast are muscle degeneration and fibrosis, high levels of oxidative stress, hypoxia, and altered energy metabolism. Recent work has also implicated reduced pectoral vessel density in the pathogenesis of wooden breast. This review examines the history of myopathies in commercial broilers and the relationship of myopathies to metabolism and oxidative performance. This review summarizes the foundational knowledge of wooden breast and provides a platform for further investigation of wooden breast.

Predicting ascites incidence in a simulated altitude-challenge using single nucleotide polymorphisms identified in multi-generational genome wide association studies

Assessing pedigreed broiler lines for ascites resistance in an industry setting is time consuming. Further, the use of sibling selection implies study subjects are not used in the breeding program, and instead, siblings take their place in pedigree systems, which reduces overall genetic accuracy. The purpose of this study is to evaluate the effectiveness of prediction models produced with SNP with the goal of predicting ascites incidence. Ascites is the manifestation of a series of adverse changes in a broiler beginning with hypoxia. Increased blood pressure, accumulation of fluid in the abdominal cavity, and death can result. Ascites results in losses estimated at $100 million/year in the USA. A multi-generational genome wide association study in an unselected line maintained at the University of Arkansas since the 1990s identified chromosomal regions associated with ascites incidence in males when challenged at high altitude. From the identified regions of significance 20 SNP were selected to construct a predictive model (8 SNP on chromosome 11, and 12 SNP on chromosome Z). Ascites phenotype and genotype data were obtained for 295 male and female individuals from the REL line. Five modeling techniques were compared for their ascites predictive ability using a 70/30 split between training and validation. For both males and females, the artificial neural network model was the best fit prediction model due to the large area under the curve value of 0.997 and 0.997, respectively, as well as a low misclassification ratio of 0.027 and 0.037, respectively. Using a parameter decreasing method, the total number of SNP inputs used to construct artificial neural network (ANN) models was reduced. A 13 SNP male ANN model and an 18 SNP female ANN model were constructed with equally high levels of prediction accuracy compared with the 20 SNP input models. The construction of predictive ANN models indicates that we have found the genetic predictors to ascites outcome in male and female broilers from an elite line of the 1990s with a high level of accuracy.

Whole genome resequencing identifies the CPQ gene as a determinant of ascites syndrome in broilers

BACKGROUND

Ascites syndrome is the most severe manifestation of pulmonary hypertension in fast-growing broilers. The disease can be attributed to increased body weights of birds, where the higher metabolic load is not matched by sufficient oxygen supply to the cells and tissues. Although there are environmental components, the disease exhibits moderate to high heritability. The current study uses high throughput whole genome resequencing (WGR) to identify genes and chromosomal regions associated with ascites.

RESULTS

The WGR data identified the CPQ gene on chromosome 2. The association was confirmed by genotyping a large collection of DNAs from phenotyped birds from three distinct broiler lines using SNPs in intron 6 and exon 8 of the CPQ gene. By combining the genotype data for these two SNP loci, we identified three different alleles segregating in the three broiler lines. Particular genotypes could be associated with resistance to ascites. We further determined that particular genotypes most associated with resistance overexpress CPQ mRNA in three tissues which might explain the role of these alleles in contributing to resistance.

CONCLUSIONS

Our findings indicate CPQ is an important determinant of pulmonary hypertension syndrome leading to ascites in broilers. We identified particular SNPs that can be used for marker-assisted selection of broilers for resistance to the disease. Our findings validate WGR as a highly efficient approach to map determinants contributing to complex phenotypic or disease-related traits. The CPQ gene has been associated with pulmonary hypertension in genome-wide association studies in humans. Therefore, ascites investigations in broilers are likely to provide insights into some forms of hypertension in humans.