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.

Research Note: Stocking density effects on production qualities of broilers raised without the use of antibiotics.

In no antibiotics ever (NAE) broilers, enteric diseases pose a threat to intestinal health and generally welfare, which can be exacerbated because of stocking density. Through knowledge of litter condition and management, disease can be minimized, and broiler welfare can be improved. To evaluate how stocking density influences NAE broilers raised in conventional housing, we evaluated production traits for broilers raised at two stocking densities within a single commercial house. Over the course of 4 flocks, 78,960 Cobb 500 broilers were raised in an industry-style tunnel ventilated house. The house was divided into four equally sized pens, each representing one of two stocking densities. An industry standard stocking density (SSD; 0.23 m2 per bird) and low stocking density (LSD; 0.27 m2 per bird) were each assigned to two pens per flock and were alternated for each subsequent flock raised. Litter moisture content, body weight, mortality, and feed conversion (FCR) were evaluated and averaged over all four flocks for both stocking densities. Data were analyzed in JMP with an ANOVA, and means were separated by Tukey's honestly significant difference. As expected, the litter moisture content was significantly larger in the more densely packed SSD pens at weeks 2, 3, 4, and 6, totaling 0.242 moisture content on average at week 6 vs. 0.217 in LSD pens at the same flock age (P = 0.035). Weekly body weight and final flock FCR were not significantly impacted by stocking density. No association was observed in mortality between the broilers raised in SSD and LSD. The results from this study indicate that the two densities examined were comparable in their growth and efficiency. Additional management pressure would exist to handle the increase in litter moisture in flocks placed at SSD in a production setting; although, raised in the same barn at the same time, the impact of SSD vs. LSD was minimal in this study.

Survey of egg quality in commercially available table eggs.

Increased demand in consumer choice has resulted in a wide variety of egg selection available in the retail market. Specialty and designer chicken eggs represent a portion of the table egg market that is increasing in size. Egg quality is known to be of great importance in all eggs as it relates to food safety, consumer preferences, and product value. In this study, egg quality characteristics were analyzed using a one-way ANOVA to evaluate 2 commercially available conventional egg brands (A and B) and 4 commercially available designer egg brands (C-F). Three hundred nine eggs were evaluated for shell and content weight, dimensional measurements, and breakage force. Calculations were completed to determine %yolk and albumen, yolk index, and Haugh units (HU), followed by an accelerated lipid oxidation study. No significant variation exists in breakage force. Brands A-E meet AA grade standard at a score of 72 HU or above, while brand F, a pasture-raised brand, meets the A grade standard, falling between 60 and 71 HU. Brand F has the highest yolk fan color value (10.41 ± 0.193, P < 0.001) and the lowest yolk index (0.523 ± 0.013, P < 0.05). In addition, brand F has the lowest albumen height (P < 0.001). As albumen height is an indication of freshness, and as all eggs were of equivalent age, it is possible that brand F exhibits overall lower quality than other brands. The conventionally raised white eggs of A experienced the greatest increase in % free fatty acids, which would likely result in off-flavors from hydrolytic rancidity. The organic cage-free D eggs have a significantly greater peroxide value (17.3 ± 2.9, P < 0.001), relative to all other brands, and is over the 10 mEg/kg threshold, which would be considered an unsuitable product for consumption. Ultimately, the measures of egg quality used in this study are essential for evaluating the delivery of the specialty market to the consumer and may indicate that improved measures of quality are needed to truly differentiate between the different egg types and their quality.

Assessing MHC-B diversity in Silkie chickens.

The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which contains numerous immune response genes, and is known to influence disease susceptibility and resistance in chickens. Variability of MHC-B haplotypes in various well-known and commercially utilized breeds has previously been identified. This study aims to understand MHC-B diversity in the Silkie breed using a high-density SNP panel that encompasses the chicken MHC-B region. DNA was obtained from 74 females and 27 males from a commercial Silkie breeder colony that is maintained through minimal genetic selection practices. A previously described panel of 90 SNPs, all located within the MHC-B region, was used to evaluate MHC-B variability in the commercial Silkie breeder colony. MHC-B haplotypes identified from the individual SNP information in the Silkie colony were compared to published haplotypes from the same region. Of the 27 haplotypes identified in the Silkie population, 8 have been previously described. Nineteen haplotypes are unique to the Silkie population and include one novel recombinant and 2 additional possible novel recombinants. Six haplotypes were found at a frequency greater than 5% of the population, of which 4 are novel. Finally, Hardy Weinberg Equilibrium (HWE) was calculated for the observed haplotypes, which were found to be in HWE. This study shows considerable MHC-B diversity in the Silkie breed and adds further information on variability of the MHC-B region in the chicken.

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.

Effects of a chromosome 9 quantitative trait locus for ascites on economically important traits in broilers.

A quantitative trait locus on chromosome 9 was previously shown to be associated with ascites in multiple experimental and commercial populations. A study to evaluate the association of the QTL, based on variable number tandem repeat genotypes, with economically important traits was carried out on a commercial male elite line. Results indicated the highest fat and the lowest fillet mean were associated with the most resistant ascites genotype. All other traits measured for this genotype showed no trend towards positive or negatively impacting production values. The results suggest that a balanced approach could be undertaken in commercial broiler breeding operations to reduce ascites susceptibility in broiler populations without compromising overall genetic progress for traits of economic importance.