Effect of Cyclic Heat Stress on Hypothalamic Oxygen Homeostasis and Inflammatory State in the Jungle Fowl and Three Broiler-Based Research Lines.

Heat stress (HS) is devastating to poultry production sustainability due its detrimental effects on performance, welfare, meat quality, and profitability. One of the most known negative effects of HS is feed intake depression, which is more pronounced in modern high-performing broilers compared to their ancestor unselected birds, yet the underlying molecular mechanisms are not fully defined. The present study aimed, therefore, to determine the hypothalamic expression of a newly involved pathway, hypoxia/oxygen homeostasis, in heat-stressed broiler-based research lines and jungle fowl. Three populations of broilers (slow growing ACRB developed in 1956, moderate growing 95RB from broilers available in 1995, and modern fast growing MRB from 2015) and unselected Jungle fowl birds were exposed to cyclic heat stress (36°C, 9 h/day for 4 weeks) in a 2 × 4 factorial experimental design. Total RNAs and proteins were extracted from the hypothalamic tissues and the expression of target genes and proteins was determined by real-time quantitative PCR and Western blot, respectively. It has been previously shown that HS increased core body temperature and decreased feed intake in 95RB and MRB, but not in ACRB or JF. HS exposure did not affect the hypothalamic expression of HIF complex, however there was a line effect for HIF-1α (P = 0.02) with higher expression in JF under heat stress. HS significantly up regulated the hypothalamic expression of hemoglobin subunits (HBA1, HBBR, HBE, HBZ), and HJV in ACRB, HBA1 and HJV in 95RB and MRB, and HJV in JF, but it down regulated FPN1 in JF. Additionally, HS altered the hypothalamic expression of oxygen homeostasis- up and down-stream signaling cascades. Phospho-AMPKThr172 was activated by HS in JF hypothalamus, but it decreased in that of the broiler-based research lines. Under thermoneutral conditions, p-AMPKThr172 was higher in broiler-based research lines compared to JF. Ribosomal protein S6K1, however, was significantly upregulated in 95RB and MRB under both environmental conditions. HS significantly upregulated the hypothalamic expression of NF-κB2 in MRB, RelB, and TNFα in ACRB, abut it down regulated RelA in 95RB. The regulation of HSPs by HS seems to be family- and line-dependent. HS upregulated the hypothalamic expression of HSP60 in ACRB and 95RB, down regulated HSP90 in JF only, and decreased HSP70 in all studied lines. Taken together, this is the first report showing that HS modulated the hypothalamic expression of hypoxia- and oxygen homeostasis-associated genes as well as their up- and down-stream mediators in chickens, and suggests that hypoxia, thermotolerance, and feed intake are interconnected, which merit further in-depth investigations.

Ileal microbial composition in genetically distinct chicken lines reared under normal or high ambient temperatures.

BACKGROUND: Heat stress (HS) has negative effects on poultry productivity, health and welfare resulting in economic losses. Broiler chickens are particularly susceptible to HS due to their high metabolic rate and rapid growth. The commensal intestinal bacterial populations have an important physiological role in the host and could ameliorate the negative effect of HS on the host. Thus, the aim of this study was to compare changes in the ileal (IL) microbiota in four different broiler lines during HS. RESULTS: Day-old broiler chicks from Giant Jungle Fowl (JF), Athens Canadian Random Bred (ACRB), 1995 Random Bred (L1995), and Modern Random Bred (L2015) lines were raised under thermoneutral (TN) conditions until day (d) 28. On d 29 birds were subjected to TN (24 °C) or chronic cyclic HS (8 h/d, 36 °C) condition till d 56. On d 56 two birds per pen were euthanized, and IL luminal content (IL-L) and mucosal scrapings (IL-M) were collected for bacterial DNA isolation. Libraries were constructed using V3-V4 16S rRNA primers and sequenced using MiSeq. DNA sequences were analyzed using QIIME2 platform and SILVA 132 database for alpha and beta diversity, and taxonomic composition, respectively. Functional property of microbiota was predicted using the PICRUSt 2 pipeline and illustrated with STAMP software. Shannon index was significantly elevated in IL-M under HS. ß-diversity PCoA plots revealed separation of microbial community of L2015-TN from JF-TN, JF-HS, ACRB-TN, and ACRB-HS in the IL-M. PERMANOVA analysis showed a significant difference between microbial community of L1995-HS compared to ACRB-HS and JF-TN, L1995-TN compared to ACRB-HS and JF-TN, L2015-HS compared to ACRB-HS and ACRB-TN, L2015-HS compared to JF-TN, L2015-TN compared to ACRB-HS and JF-TN, and ACRB-HS compared to JF-TN in the IL-L. The impact of HS on microbial composition of IL-M was more prominent compared to IL-L with 12 and 2 taxa showing significantly different relative abundance, respectively. Furthermore, differences in microbiota due to the genetic line were more prominent in IL-M than IL-L with 18 and 8 taxa showing significantly different relative abundance, respectively. Unlike taxonomy, predicted function of microbiota was not affected by HS. Comparison of L2015 with JF or ACRB showed significant changes in predicted function of microbiota in both, IL-M and IL-L. Differences were most prominent between L2015 and JF; while there was no difference between L2015 and L1995. CONCLUSIONS: These data indicate the genetic line × temperature effect on the diversity and composition of IL microbiota. Moreover, the data showcase the effect of host genetics on the composition of IL microbiota and their predicted function. These data are of critical importance for devising nutritional strategies to maintain GIT microbial balance and alleviate the negative effects of HS on broiler chickens' performance and health.

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.

Effects of Cyclic Chronic Heat Stress on the Expression of Nutrient Transporters in the Jejunum of Modern Broilers and Their Ancestor Wild Jungle Fowl.

Heat stress (HS) has been reported to disrupt nutrient digestion and absorption in broilers. These effects may be more prominent in fast-growing chickens due to their high metabolic activity. However, the underlying molecular mechanisms are not yet fully elucidated. Hence, the current study aimed to evaluate the effect of chronic HS on jejunal nutrient transport in slow- (Athens Canadian Random Bred, ACRB from 1950), moderate- (The 1995 random bred, 95RAN), rapid- (modern broilers, modern random bred, MRB) growing birds and their ancestor wild jungle fowl (JF). One-day male chicks (n = 150/line) were placed by line in environmentally controlled chambers and kept under the same industry-standard environmental conditions until d28. On d29, an 8-h daily cyclic HS (36°C) was applied to half of the chambers, which lasted until d55, while keeping the rest under thermal neutral (TN, 24°C) conditions. Jejunum tissues were collected for morphology assessment and molecular analysis of carbohydrate-, amino acid-, and fatty acid-transporters. MRB exhibited the highest body weight (BW) followed by 95RAN under both conditions. HS decreased feed intake (FI) in MRB and 95RAN, which resulted in lower BW compared to their TN counterparts; however, no effect was observed in ACRB and JF. MRB showed a greater villus height (VH) to crypt depth (CD) ratio under both environmental conditions. Molecular analyses showed that glucose transporter (GLUT) 2, 5, 10, and 11 were upregulated in MRB compared to some of the other populations under TN conditions. HS downregulated GLUT2, 10, 11, and 12 in MRB while it increased the expression of GLUT1, 5, 10, and 11 in JF. GLUT2 protein expression was higher in JF compared to ACRB and MRB under TN conditions. It also showed an increase in ACRB but no effect on 95RAN and MRB under HS conditions. ACRB exhibited greater expression of the EAAT3 gene as compared to the rest of the populations maintained under TN conditions. HS exposure did not alter the gene expression of amino acid transporters in MRB. Gene expression of CD36 and FABP2 was upregulated in HS JF birds. Protein expression of CD36 was downregulated in HS JF while no effect was observed in ACRB, 95RAN, and MRB. Taken together, these data are the first to show the effect of HS on jejunal expression of nutrient transporters in three broiler populations known to represent 70 years of genetic progress in the poultry industry and a Red Jungle Fowl population representative of the primary ancestor of domestic chickens.

Histological Analysis and Gene Expression of Satellite Cell Markers in the Pectoralis Major Muscle in Broiler Lines Divergently Selected for Percent 4-Day Breast Yield.

Muscle development during embryonic and early post-hatch growth is primarily through hyperplastic growth and accumulation of nuclei through satellite cell contribution. Post-hatch, muscle development transitions from hyperplasia to hypertrophic growth of muscle fibers. Commercial selection for breast yield traditionally occurs at ages targeting hypertrophic rather than hyperplastic growth. This has resulted in the production of giant fibers and concomitant challenges with regard to muscle myopathies. The current study investigates the impact of selection during the period of hyperplastic growth. It is hypothesized that selection for percentage breast yield during hyperplasia will result in an increased number of muscle cells at hatch and potentially impact muscle fiber characteristics at processing. This study characterizes the breast muscle histology of three broiler lines at various ages in the growth period. The lines include a random bred control (RAN) as well as lines which have been selected from RAN for high (HBY4) and low (LBY4) percentage 4-day breast yield. Post-rigor pectoralis major samples from six males of each line and age were collected and stored in formalin. The sample ages included embryonic day 18 (E18), post-hatch day 4 (d4), and day 56 (d56). The samples were processed using a Leica tissue processor, embedded in paraffin wax, sectioned, and placed on slides. Slides were stained using hematoxylin and eosin. E18 and d4 post-hatch analysis showed advanced muscle fiber formation for HBY4 and immature muscle development for LBY4 as compared to RAN. Post-hatch d56 samples were analyzed for fiber number, fiber diameter, endomysium, and perimysium spacing. Line HBY4 had the largest muscle fiber diameter (54.2 ± 0.96 µm) when compared to LBY4 (45.4 ± 0.96 µm). There was no line difference in endomysium spacing while perimysium spacing was higher for HBY4 males. Selection for percentage 4-day breast yield has impacted the rate and extent of muscle fiber formation in both the LBY4 and HBY4 lines with no negative impact on fiber spacing. The shift in processing age to later ages has exposed issues associated with muscle fiber viability. Selection during the period of muscle hyperplasia may impact growth rate; however, the potential benefits of additional satellite cells are still unclear.

Intestinal Barrier Integrity in Heat-Stressed Modern Broilers and Their Ancestor Wild Jungle Fowl.

High environmental temperature has strong adverse effects on poultry production, welfare, and sustainability and, thereby, constitutes one of the most challenging stressors. Although colossal information has been published on the effects of heat stress on poultry productivity and gut health, the fundamemntal mechanisms associated with heat stress responses and intestinal barrier function are still not well defined. The aim of the present study was, therefore, to determine the effects of acute (2 h) heat stress on growth performance, gut integrity, and intestinal expression of heat shock and tight junction proteins in slow- (broilers of the 1950's, ACRB), moderate- (broilers of 1990's, 95RAN), rapid-(modern broilers, MRB) growing birds, and their ancestor wild jungle fowl (JF). Heat stress exposure significantly increased the core body temperature of 95RAN and MRB chickens by ~0.5-1°C, but not that of JF and ACRB compared to their counterparts maintained at thermoneutral conditions. Heat stress also depressed feed intake and increased serum fluorescein isothiocyanate-dextran (FITC-D) levels (P < 0.05) in modern broilers (95RAN and MRB) but not in JF and ACRB, indicating potential leaky gut syndrome. Molecular analyses showed that heat stress exposure significantly up regulated the duodenal expression of occludin (OCLN) and lipocalin (LCN2) in ACRB, zonula occludens (ZO-2), villin1 (VIL1), and calprotectin (CALPR) in 95 RAN, and only CALPR in MRB compared to their TN counterparts. In the jejunum however, heat stress down regulated the expression of PALS1-associated tight junction protein (PATJ) in ACRB, 95RAN, and MRB, and that of cadherin1 (CDH1) in MRB. In the ileum, heat stress significantly down regulated the expression of OCLN in 95 RAN, ZO-1 in MRB, gap junction protein alpha1 (GJA1) in JF, and VIL1 in ACRB compared to their TN counterparts. In summary, this is the first report, to our knowledge, showing that tight junction protein expression is environmental-, genotype-, and intestinal segment-dependent and identifying molecular signatures, such as CDH1, CALPR, and ZO-1, potentially involved in leaky gut syndrome-induced by heat stress in MRB.

Evaluation of Intestinal Permeability and Liver Bacterial Translocation in Two Modern Broilers and Their Jungle Fowl Ancestor.

The objective of this study was to evaluate the of intestinal permeability and liver bacterial translocation (BT) across a modern commercial broiler, a commercial broiler of 1995 genetics, and an unselected Jungle Fowl line. Modern 2015 (MB2015) broiler chicken, random bred line initiated from 1995 (RB1995), and the Giant Jungle fowl (JF). Chickens were randomly allocated to four different dietary treatments. Dietary treatments were (1) a control corn-based diet throughout the trial [corn-corn (C-C)]; (2) an early phase malnutrition diet where chicks received a rye-based diet for 10 days, and then switched to the control diet [rye-corn (R-C)]; (3) a malnutrition rye-diet that was fed throughout the trial [rye-rye (R-R)]; and (4) a late phase malnutrition diet where chicks received the control diet for 10 days, and then switched to the rye diet for the last phase [corn-rye (C-R)]. Paracellular permeability was evaluated using fluorescein isothiocyanate dextran (FITC-D). Liver BT was also evaluated. MB2015 and RB1995 consuming the rye-based diet showed increase serum levels of FITC-D when compared to the corn-fed chickens (P < 0.05). Overall, MB2015 appeared to have higher enteric permeability than the JF. To our knowledge, this would be the first paper to evaluate the effect of compensatory growth on intestinal permeability and liver BT. Further studies to evaluate microbiome and inflammatory markers in these chicken models are currently being evaluated.

Further investigation of mitochondrial biogenesis and gene expression of key regulators in ascites- susceptible and ascites- resistant broiler research lines.

We have extended our previous survey of the association of mitochondrial prevalence in particular tissues with ascites susceptibility in broilers. We previously reported that in breast muscle of 22 week old susceptible line male birds had significantly higher mtDNA copy number relative to nuclear copy number (mtDNA/nucDNA), compared to resistant line male birds. The higher copy number correlated with higher expression of PPARGC1A mRNA gene. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome. We now report the mtDNA/nucDNA ratio in lung, liver, heart, thigh, and breast of both genders at 3, and 20 weeks old. At 3 weeks the mtDNA/nucDNA ratio is significantly higher in lung, breast, and thigh for susceptible line males compared to the resistant line males. Conversely, we see the opposite for lung and breast in females. At 20 weeks of age the differences between males from the two lines is lost for lung, and thigh. Although there is a significant reduction in the mtDNA/nucDNA ratio of breast from 3 weeks to 20 weeks in the susceptible line males, the susceptible males remain higher than resistant line males for this specific tissue. We assessed relative expression of five genes known to regulate mitochondrial biogenesis for lung, thigh and breast muscle from males and females of both lines with no consistent pattern to explain the marked gender and line differences for these tissues. Our results indicate clear sex differences in mitochondrial biogenesis establishing a strong association between the mtDNA quantity in a tissue-specific manner and correlated with ascites-phenotype. We propose that mtDNA/nucDNA levels could serve as a potential predictive marker in breeding programs to reduce ascites.

Whole Genome Resequencing of Arkansas Progressor and Regressor Line Chickens to Identify SNPs Associated with Tumor Regression.

Arkansas Regressor (AR) chickens, unlike Arkansas Progressor (AP) chickens, regress tumors induced by the v-src oncogene. To better understand the genetic factors responsible for this tumor regression property, whole genome resequencing was conducted using Illumina Hi-Seq 2 × 100 bp paired-end read method (San Diego, CA, USA) with AR (confirmed tumor regression property) and AP chickens. Sequence reads were aligned to the chicken reference genome (galgal5) and produced coverage of 11× and 14× in AR and AP, respectively. A total of 7.1 and 7.3 million single nucleotide polymorphisms (SNPs) were present in AR and AP genomes, respectively. Through a series of filtration processes, a total of 12,242 SNPs were identified in AR chickens that were associated with non-synonymous, frameshift, nonsense, no-start and no-stop mutations. Further filtering of SNPs based on read depth ≥ 10, SNP% ≥ 0.75, and non-synonymous mutations identified 63 reliable marker SNPs which were chosen for gene network analysis. The network analysis revealed that the candidate genes identified in AR chickens play roles in networks centered to ubiquitin C (UBC), phosphoinositide 3-kinases (PI3K), and nuclear factor kappa B (NF-kB) complexes suggesting that the tumor regression property in AR chickens might be associated with ubiquitylation, PI3K, and NF-kB signaling pathways. This study provides an insight into genetic factors that could be responsible for the tumor regression property.

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.

Assessment of a Nutritional Rehabilitation Model in Two Modern Broilers and Their Jungle Fowl Ancestor: A Model for Better Understanding Childhood Undernutrition.

This article is the first in a series of manuscripts to evaluate nutritional rehabilitation in chickens as a model to study interventions in children malnutrition (Part 1: Performance, Bone Mineralization, and Intestinal Morphometric Analysis). Inclusion of rye in poultry diets induces a nutritional deficit that leads to increased bacterial translocation, intestinal viscosity, and decreased bone mineralization. However, it is unclear the effect of diet on developmental stage or genetic strain. Therefore, the objective was to determine the effects of a rye diet during either the early or late phase of development on performance, bone mineralization, and intestinal morphology across three diverse genetic backgrounds. Modern 2015 (Cobb 500) broiler chicken, 1995 Cobb broiler chicken, and the Giant Jungle Fowl were randomly allocated into four different dietary treatments. Dietary treatments were (1) a control corn-based diet throughout the trial (corn-corn); (2) an early phase malnutrition diet where chicks received a rye-based diet for 10 days, and then switched to the control diet (rye-corn); (3) a malnutrition rye-diet that was fed throughout the trial (rye-rye); and (4) a late phase malnutrition diet where chicks received the control diet for 10 days, and then switched to the rye diet for the last phase (corn-rye). At 10 days of age, chicks were weighed and diets were switched in groups 2 and 4. At day 20 of age, all chickens were weighed and euthanized to collect bone and intestinal samples. Body weight, weight gain, and bone mineralization were different across diet, genetic line, age and all two- and three-way interactions (P < 0.05). Overall, Jungle Fowl were the most tolerant to a rye-based diet, and both the modern and 1995 broilers were significantly affected by the high rye-based diet. However, the 1995 broilers consuming the rye-based diet appeared to experience more permanent effects when compared with the modern broiler. The results of this study suggest that chickens have a great potential as a nutritional rehabilitation model in human trials. The 1995 broilers line was an intermediate genetic line between the fast growing modern line and the non-selected Jungle Fowl line, suggesting that it would be the most appropriate model to study for future studies.

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.

Identification and Differential Abundance of Mitochondrial Genome Encoding Small RNAs (mitosRNA) in Breast Muscles of Modern Broilers and Unselected Chicken Breed.

Background: Although small non-coding RNAs are mostly encoded by the nuclear genome, thousands of small non-coding RNAs encoded by the mitochondrial genome, termed as mitosRNAs were recently reported in human, mouse and trout. In this study, we first identified chicken mitosRNAs in breast muscle using small RNA sequencing method and the differential abundance was analyzed between modern pedigree male (PeM) broilers (characterized by rapid growth and large muscle mass) and the foundational Barred Plymouth Rock (BPR) chickens (characterized by slow growth and small muscle mass). Methods: Small RNA sequencing was performed with total RNAs extracted from breast muscles of PeM and BPR (n = 6 per group) using the 1 × 50 bp single end read method of Illumina sequencing. Raw reads were processed by quality assessment, adapter trimming, and alignment to the chicken mitochondrial genome (GenBank Accession: X52392.1) using the NGen program. Further statistical analyses were performed using the JMP Genomics 8. Differentially expressed (DE) mitosRNAs between PeM and BPR were confirmed by quantitative PCR. Results: Totals of 183,416 unique small RNA sequences were identified as potential chicken mitosRNAs. After stringent filtering processes, 117 mitosRNAs showing >100 raw read counts were abundantly produced from all 37 mitochondrial genes (except D-loop region) and the length of mitosRNAs ranged from 22 to 46 nucleotides. Of those, abundance of 44 mitosRNAs were significantly altered in breast muscles of PeM compared to those of BPR: all mitosRNAs were higher in PeM breast except those produced from 16S-rRNA gene. Possibly, the higher mitosRNAs abundance in PeM breast may be due to a higher mitochondrial content compared to BPR. Our data demonstrate that in addition to 37 known mitochondrial genes, the mitochondrial genome also encodes abundant mitosRNAs, that may play an important regulatory role in muscle growth via mitochondrial gene expression control.

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.

Further investigation of a quantitative trait locus for ascites on chromosome 9 in broiler chicken lines.

Previously, we reported a genome wide association study (GWAS) that had shown association of a region between 11.8 and 13.6 Mbp on chromosome 9 with ascites phenotype in broilers. We had used microsatellite loci to demonstrate an association of particular genotypes for this region with ascites in experimental ascites lines and commercial broiler breeder lines. We identified two potential candidate genes, AGTR1 and UTS2D, within that chromosomal region for mediating the quantitative effect. We have now extended our analysis using SNPs for these genes to assess association with resistance or susceptibility to ascites in these same broiler lines. Surprisingly, in contrast to our previous GWAS and microsatellite data for this region, we find no association of the SNP genotypes or haplotypes in the region suggesting that the two genes might have limited association with the disease phenotype.

Effect of feeding CLA on plasma and granules fatty acid composition of eggs and prepared mayonnaise quality.

Eggs rich in trans, trans conjugated linoleic acid (CLA) are significantly more viscous, have more phospholipids containing linoleic acid (LA), and more saturated triacylglycerol species than control eggs. However, the fatty acid (FA) composition of yolk plasma and granule fractions are unreported. Furthermore, there are no reports of mayonnaise rheological properties or emulsion stability by using CLA-rich eggs. Therefore, the objectives were (1) compare the FA composition of CLA-rich yolk granules and plasma, relative to standard control and LA-rich control yolks, (2) compare the rheological properties of mayonnaise prepared with CLA-rich eggs to control eggs and (3) compare the emulsion stability of CLA-yolk mayonnaise. CLA-rich eggs and soy control eggs were produced by adding 10% CLA-rich soy oil or 10% of control unmodified soy oil to the hen's diet. The eggs were used in subsequent mayonnaise preparation. CLA-yolk mayonnaise was more viscous, had greater storage modulus, resisted thinning, and was a more stable emulsion, relative to mayonnaise prepared with control yolks or soy control yolks.

The metabolic rate of cultured muscle cells from hybrid Coturnix quail is intermediate to that of muscle cells from fast-growing and slow-growing Coturnix quail.

Growth rate is a fundamental parameter of an organism's life history and varies 30-fold across bird species. To explore how whole-organism growth rate and the metabolic rate of cultured muscle cells are connected, two lines of Japanese quail (Coturnix coturnix japonica), one that had been artificially selected for fast growth for over 60 generations and a control line were used to culture myoblasts. In line with previous work, myoblasts from the fast growth line had significantly higher rates of oxygen consumption, glycolytic flux, and higher mitochondrial volume than myoblasts from the control line, indicating that an increase in growth rate is associated with a concomitant increase in cellular metabolic rates and that mitochondrial density contributes to the differences in rates of metabolism between the lines. We reared chicks from two hybrid lines with reciprocal parental configurations for growth rate to explore the effect of maternally inherited mitochondrial DNA on rates of growth and metabolism. Growth rates of chicks, cellular basal oxygen consumption, glycolytic flux, and mitochondrial volume in myoblasts from chicks from both reciprocal crosses were intermediate to the fast and control lines. This indicates that genes in the nucleus have a strong influence on metabolic rates at the cellular level, compared with maternally inherited mitochondrial DNA.

Transcriptomic analysis to elucidate the molecular mechanisms that underlie feed efficiency in meat-type chickens.

Feed efficiency phenotypes defined by genotypes or gene markers are unknown. To date, there are only limited studies on global gene expression profiling on feed efficiency. The objective of this study was to identify genes and pathways associated with residual feed intake (RFI) through transcriptional profiling of duodenum at two different ages in a chicken population divergently selected for low (LRFI) or high (HRFI) RFI. The global gene expression differences in LRFI and HRFI were assessed by the Affymetrix GeneChip(®) Chicken Genome Array and RT-PCR using duodenal tissue on days 35 and 42. The Ingenuity Pathway Analysis program was used to identify canonical and gene network pathways associated with RFI. A global view of gene expression differences between LRFI and HRFI suggest that RFI can be explained by differences in cell division, growth, proliferation and apoptosis, protein synthesis, lipid metabolism, and molecular transport of cellular molecules. Chickens selected for improved RFI achieve efficiency by reducing feed intake with a nominal or no change in weight gain by either up-regulating CD36, PPARα, HMGCS2, GCG or down-regulating PCSK2, CALB1, SAT1, and SGK1 genes within the lipid metabolism, small molecule biochemistry, molecular transport, cell death, and protein synthesis molecular and cellular functions. Chickens selected for reduced RFI via reduced feed intake with no change in weight gain achieve feed efficiency for growth by the up-regulation of genes that reduce appetite with increased cellular oxidative stress, prolonged cell cycle, DNA damage, and apoptosis in addition to increased oxidation of dietary fat and efficient fatty acids transported from the intestines.

Three hen strains fed photoisomerized trans,trans CLA-rich soy oil exhibit different yolk accumulation rates and source-specific isomer deposition.

Most CLA chicken feeding trials used cis,trans (c,t) and trans,cis (t,c) CLA isomers to produce CLA-rich eggs, while reports of trans,trans (t,t) CLA enrichment in egg yolks are limited. The CLA yolk fatty acid profile changes and the 10-12 days of feeding needed for maximum CLA are well documented, but there is no information describing CLA accumulation during initial feed administration. In addition, no information on CLA accumulation rates in different hen strains is available. The aim of this study was to determine a mathematical model that described yolk CLA accumulation and depletion in three hen strains by using t,t CLA-rich soybean oil produced by photoisomerization. Diets of 30-week Leghorns, broilers, and jungle fowl were supplemented with 15% CLA-rich soy oil for 16 days, and eggs were collected for 32 days. Yolk fatty acid profiles were measured by GC-FID. CLA accumulation and depletion was modeled by both quadratic and piecewise regression analysis. A strong quadratic model was proposed, but it was not as effective as piecewise regression in describing CLA accumulation and depletion. Broiler hen eggs contained the greatest concentration of CLA at 3.2 mol/100 g egg yolk, then jungle fowl at 2.9 mol CLA, and Leghorns at 2.3 mol CLA. The t,t CLA isomer levels remained at 55% of total yolk CLA during CLA feeding. However, t-10,c-12 (t,c) CLA concentration increased slightly during CLA accumulation and was significantly greater than c-9,t-11 CLA. Jungle fowl had the smallest increase in yolk saturated fat with CLA yolk accumulation.

A quantitative trait locus for ascites on chromosome 9 in broiler chicken lines.

A genome-wide SNP survey was used to identify chromosomal regions that showed linkage disequilibrium with respect to ascites susceptibility and ventricular hypertrophy in an F2 cross between previously described ascites-resistant and -susceptible lines. Variable number tandem repeats were used to obtain genotype data to further characterize these regions. A region on chromosome 9 (12 to 13 Mbp in 2011 assembly) shows association with ascites in the ascites lines and in several commercial broiler breeder lines with a significant sex effect. There are 2 candidate genes, AGTR1 (an angiotensin II type 1 receptor) and UTS2D (urotensin 2 domain containing), in this region that have been associated with hypertension and hypoxic response in mammals.