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Abstract Background Understanding the molecular underpinnings of phenotypic variations is critical for enhancing poultry breeding programs. The Brazilian broiler (TT) and laying hen (CC) lines exhibit striking differences in body weight, growth potential, and muscle mass. Our work aimed to compare the global transcriptome of wing and pectoral tissues during the early development (days 2.5 to 3.5) of these chicken lines, unveiling disparities in gene expression and regulation. Results Different and bona-fide transcriptomic profiles were identified for the compared lines. A similar number of up- and downregulated differentially expressed genes (DEGs) were identified, considering the broiler line as a reference. Upregulated DEGs displayed an enrichment of protease-encoding genes, whereas downregulated DEGs exhibited a prevalence of receptors and ligands. Gene Ontology analysis revealed that upregulated DEGs were mainly associated with hormone response, mitotic cell cycle, and different metabolic and biosynthetic processes. In contrast, downregulated DEGs were primarily linked to communication, signal transduction, cell differentiation, and nervous system development. Regulatory networks were constructed for the mitotic cell cycle and cell differentiation biological processes, as their contrasting roles may impact the development of distinct postnatal traits. Within the mitotic cell cycle network, key upregulated DEGs included CCND1 and HSP90, with central regulators being NF-κB subunits (RELA and REL) and NFATC2. The cell differentiation network comprises numerous DEGs encoding transcription factors (e.g., HOX genes), receptors, ligands, and histones, while the main regulatory hubs are CREB, AR and epigenetic modifiers. Clustering analyses highlighted PIK3CD as a central player within the differentiation network. Conclusions Our study revealed distinct developmental transcriptomes between Brazilian broiler and layer lines. The gene expression profile of broiler embryos seems to favour increased cell proliferation and delayed differentiation, which may contribute to the subsequent enlargement of pectoral tissues during foetal and postnatal development. Our findings pave the way for future functional studies and improvement of targeted traits of economic interest in poultry.

The antibodies produced in the first days of vertebrate life and are called natural antibodies (NAb). Other antibodies, produced in response to restricted contact with the antigen, are called specific antibodies (SpAb). To evaluate the production of NAb studies have used rabbit red blood cells (RRBC). On the other hand, evaluation of the production of specific antibodies can be performed with the use of sheep red blood cells (SRBC), a cell type that results in high production of SpAb. The aim of this study was to evaluate the production of NAb and SpAb in chicken lines developed by EMBRAPA Suínos e Aves. Animals of laying and poultry lines were inoculated intramuscularly with 5% of SRBC. The titers of NAb and SpAb were higher in laying hens than in broiler lines. The same results were obtained with anti-RRBC, the exception was males of the LLc lines, with lower antibody production compared to the other lines and females of the same line. These data show that the production of natural and specific antibodies is higher in laying hens compared to broilers, and that there is an effect of sex on antibody production.

Abstract Introduction White Striping (WS) and Wooden Breast (WB) pectoral myopathies are relevant disorders for contemporary broiler production worldwide. Several studies aimed to elucidate the genetic components associated with the occurrence of these myopathies. However, epigenetic factors that trigger or differentiate these two conditions are still unclear. The aim of this study was to identify miRNAs differentially expressed (DE) between normal and WS and WB-affected broilers, and to verify the possible role of these miRNAs in metabolic pathways related to the manifestation of these pectoral myopathies in 28-day-old broilers. Results Five miRNAs were DE in the WS vs control (gga-miR-375, gga-miR-200b-3p, gga-miR-429-3p, gga-miR-1769-5p, gga-miR-200a-3p), 82 between WB vs control and 62 between WB vs WS. Several known miRNAs were associated with WB, such as gga-miR-155, gga-miR-146b, gga-miR-222, gga-miR-146-5p, gga-miR- 29, gga-miR-21-5p, gga-miR-133a-3p and gga-miR-133b. Most of them had not previously been associated with the development of this myopathy in broilers. We also have predicted 17 new miRNAs expressed in the broilers pectoral muscle. DE miRNA target gene ontology analysis enriched 6 common pathways for WS and WB compared to control: autophagy, insulin signaling, FoxO signaling, endocytosis, and metabolic pathways. The WS vs control contrast had two unique pathways, ERBB signaling and the mTOR signaling, while WB vs control had 14 unique pathways, with ubiquitin-mediated proteolysis and endoplasmic reticulum protein processing being the most significant. Conclusions We found miRNAs DE between normal broilers and those affected with breast myopathies at 28 days of age. Our results also provide novel evidence of the miRNAs role on the regulation of WS and in the differentiation of both WS and WB myopathies. Overall, our study provides insights into miRNA-mediated and pathways involved in the occurrence of WS and WB helping to better understand these chicken growth disorders in an early age. These findings can help developing new approaches to reduce these complex issues in poultry production possibly by adjustments in nutrition and management conditions. Moreover, the miRNAs and target genes associated with the initial stages of WS and WB development could be potential biomarkers to be used in selection to reduce the occurrence of these myopathies in broiler production.

White striping (WS) is a myopathy characterized by the appearance of white stripes parallel to the muscle fibers in the breast of broiler chickens, composed of adipose and connective tissues. This condition causes economic losses and, although common, its etiology remains poorly understood. Hence, the objective was to identify genes and biological mechanisms involved in the early stages of WS using a paternal broiler line that grows slightly slower than commercial ones, at 35 days of age, through the RNA sequencing of the pectoralis major muscle. Thirty genes were differentially expressed between normal and WS-affected chickens, with 23 upregulated and 7 downregulated in the affected broilers. Of these, 14 genes are novel candidates for WS and are implicated in biological processes related to muscle development (CEPBD, DUSP8, METTL21EP, NELL2, and UBE3D), lipid metabolism (PDK4, DDIT4, FKBP5, DGAT2, LIPG, TDH, and RGCC), and collagen (COL4A5 and COL4A6). Genes related to changes in muscle fiber type and the processes of apoptosis, autophagy, proliferation, and differentiation are possibly involved with the initial stage of WS development. In contrast, the genes linked to lipid metabolism and collagen may have their expression altered due to the progression of the myopathy.

Ca and P homeostasis across the egg-laying cycle is a complex process involving absorption in the small intestine, reabsorption/excretion in the kidneys, and eggshell gland secretion. Diets with inadequate calcium and phosphorus can interfere with their absorption and digestibility, resulting in eggshell quality losses and reduced productive life, affecting egg production and welfare. A better understanding of gene expression profiles in the kidneys of laying hens during the late egg-laying period could clarify the renal role in mineral metabolism at this late stage. Therefore, the performance, egg quality and bone integrity-related traits, and expression profiles of kidney candidate genes were evaluated in 73-week-old laying hens receiving different Ca and P ratios in their diet: a high Ca/P ratio (HR, 22.43), a low ratio (LR, 6.71), and a medium ratio (MR, 11.43). The laying hens receiving the HR diet had improved egg production and eggshell quality traits compared to the other two groups. Humerus length was shorter in the HR than in the other groups. The CYP24A1 and TRPC3 genes were differentially expressed (p.adj ≤ 0.05) among the groups. Therefore, their expression profiles could be involved in calcium and phosphate transcellular transport in 73-week-old laying hens as a way to keep mineral absorption at adequate levels.

Abstract Background Umbilical Hernia (UH) is characterized by the passage of part of the intestine through the umbilical canal forming the herniary sac. There are several potential causes that can lead to the umbilical hernia such as bacterial infections, management conditions and genetic factors. Since the genetic components involved with UH are poorly understood, this study aimed to identify polymorphisms and genes associated with the manifestation of umbilical hernia in pigs using exome and transcriptome sequencing in a case and control design. Results In the exome sequencing, 119 variants located in 58 genes were identified differing between normal and UH-affected pigs, and in the umbilical ring transcriptome, 46 variants were identified, located in 27 genes. Comparing the two methodologies, we obtained 34 concordant variants between the exome and transcriptome analyses, which were located in 17 genes, distributed in 64 biological processes (BP). Among the BP involved with UH it is possible to highlight cell adhesion, cell junction regulation, embryonic morphogenesis, ion transport, muscle contraction, within others. Conclusions We have generated the first exome sequencing related to normal and umbilical hernia-affected pigs, which allowed us to identify several variants possibly involved with this disorder. Many of those variants present in the DNA were confirmed with the RNA-Seq results. The combination of both exome and transcriptome sequencing approaches allowed us to better understand the complex molecular mechanisms underlying UH in pigs and possibly in other mammals, including humans. Some variants found in genes and other regulatory regions are highlighted as strong candidates to the development of UH in pigs and should be further investigated.

Abstract Locomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR

Femoral head separation (FHS) is characterized by the detachment of growth plate (GP) and articular cartilage, occurring in tibia and femur. However, the molecular mechanisms involved with this condition are not completely understood. Therefore, genes and biological processes (BP) involved with FHS were identified in 21-day-old broilers through RNA sequencing of the femoral GP. 13,487 genes were expressed in the chicken femoral head transcriptome of normal and FHS-affected broilers. From those, 34 were differentially expressed (DE; FDR ≤0.05) between groups, where all of them were downregulated in FHS-affected broilers. The main BP were enriched in receptor signaling pathways, ossification, bone mineralization and formation, skeletal morphogenesis, and vascularization. RNA-Seq datasets comparison of normal and FHS-affected broilers with 21, 35 and 42 days of age has shown three shared DE genes (FBN2, C1QTNF8, and XYLT1) in GP among ages. Twelve genes were exclusively DE at 21 days, where 10 have already been characterized (SHISA3, FNDC1, ANGPTL7, LEPR, ENSGALG00000049529, OXTR, ENSGALG00000045154, COL16A1, RASD2, BOC, GDF10, and THSD7B). Twelve SNPs were associated with FHS (p < 0.0001). Out of those, 5 were novel and 7 were existing variants located in 7 genes (RARS, TFPI2, TTI1, MAP4K3, LINK54, and AREL1). We have shown that genes related to chondrogenesis and bone differentiation were downregulated in the GP of FHS-affected young broilers. Therefore, these findings evince that candidate genes pointed out in our study are probably related to the onset of FHS in broilers.

Abstract Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.

Abstract Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

Abstract Background Bacterial chondronecrosis with osteomyelitis (BCO) develops in the growth plate (GP) of the proximal femur and tibia and is initiated by damage to the less mineralized chondrocytes followed by colonization of opportunistic bacteria. This condition affects approximately 1% of all birds housed, being considered one of the major causes of lameness in fast growing broilers. Although several studies have been previously performed aiming to understand its pathogenesis, the molecular mechanisms involved with BCO remains to be elucidated. Therefore, this study aimed to generate a profile of global differential gene expression involved with BCO in the tibia of commercial broilers, through RNA sequencing analysis to identity genes and molecular pathways involved with BCO in chickens. Results Our data showed 192 differentially expressed (DE) genes: 63 upregulated and 129 downregulated in the GP of the tibia proximal epiphysis of BCO-affected broilers. Using all DE genes, six Biological Processes (BP) were associated with bone development (connective tissue development, cartilage development, skeletal system development, organ morphogenesis, system development and skeletal system morphogenesis). The analyses of the upregulated genes did not indicate any significant BP (FDR

Abstract Background The proximal femoral head separation (FHS) or epiphysiolysis is a prevalent disorder affecting the chicken femur epiphysis, being considered a risk factor to infection which can cause bacterial chondronecrosis with osteomyelitis in broilers. To identify the genetic mechanisms involved in epiphysiolysis, differentially expressed (DE) genes in the femur of normal and FHS-affected broilers were identified using RNA-Seq technology. Femoral growth plate (GP) samples from 35-day-old commercial male broilers were collected from 4 healthy and 4 FHS-affected broilers. Sequencing was performed using an Illumina paired-end protocol. Differentially expressed genes were obtained using the edgeR package based on the False Discovery Rate (FDR

Abstract Background Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. Results Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. Conclusions The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.

ABSTRACT The objective of this study was to compare the antimicrobial activity of macrophages and serum in laying hen (MM, CC, and CCc) and broiler chicken lineages (TT and LL). Macrophages were evaluated for phagocytic and antimicrobial activity. Microbicidal serum activity was evaluated by the resistance test for serum and the agar test. The results showed that phagocytic activity was higher in males of the MM strain, with 13% of macrophages presenting phagocytosis, while the other lineages studied, and even female MM, presented a rate of 6% of phagocytic cells. However, antimicrobial activity in macrophages from males of CCc lineage and females of TT lineage were higher, eliminating more than 30% of the Salmonella enterica inoculum, while in the other strains, the results were similar, with inoculum reduction below 30%. In the serum resistance assay, female laying lines presented higher antibacterial activity than female broiler lines. In the trials to evaluate the microbicide activity of the serum, females of both broiler and laying lineages presented higher performance when compared with males of the same lineage. Females of laying hen lines (MM and CC) present a greater antibacterium activity than males. These results can contribute to a better understanding of the immune response in broiler chicken and laying hen lineages, to aid development of lineages of birds more resistant to pathogens.

Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.

Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.

White Striping (WS) has been one of the main issues in poultry production in the last years since it affects meat quality. Studies have been conducted to understand WS and other myopathies in chickens, and some biological pathways have been associated to the prevalence of these conditions, such as extracellular calcium level, oxidative stress, localized hypoxia, possible fiber-type switching, and cellular repairing. Therefore, to understand the genetic mechanisms involved in WS, 15 functional candidate genes were chosen to be analyzed by quantitative PCR (qPCR) in breast muscle of normal and WS-affected chickens. To this, the pectoral major muscle (PMM) of 16 normal and 16 WS-affected broilers were collected at 42 days of age and submitted to qRT-PCR analysis. Out of the 15 genes studied, six were differentially expressed between groups. The CA2, CSRP3, and PLIN1 were upregulated, while CALM2, DNASE1L3, and MYLK2 genes were downregulated in the WS-affected when compared to the normal broilers. These findings highlight that the disruption on muscle and calcium signaling pathways can possibly be triggering WS in chickens. Improving our understanding on the genetic basis involved with this myopathy might contribute for reducing WS in poultry production.

Abstract 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.

Abstract Background Natural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (FST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and FST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations. Results ROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. FST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and FST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine. Conclusions Identification of ROH and FST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits.

Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1–4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20–40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.

Femoral head separation (FHS) is usually a subclinical condition characterized by the detachment of articular cartilage from the bone. In this study, a comprehensive analysis identifying shared and exclusive expression profiles, biological processes (BP) and variants related to FHS in the femoral articular cartilage and growth plate in chickens was performed through RNA sequencing analysis. Thirty-six differentially expressed (DE) genes were shared between femoral articular cartilage (AC) and growth plate (GP) tissues. Out of those, 23 genes were enriched in BP related to ion transport, translation factors and immune response. Seventy genes were DE exclusively in the AC and 288 in the GP. Among the BP of AC, the response against bacteria can be highlighted, and for the GP tissue, the processes related to chondrocyte differentiation and cartilage development stand out. When the chicken DE genes were compared to other datasets, eight genes (SLC4A1, RHAG, ANK1, MKNK2, SPTB, ADA, C7 and EPB420) were shared between chickens and humans. Furthermore, 89 variants, including missense in the SPATS2L, PRKAB1 and TRIM25 genes, were identified between groups. Therefore, those genes should be more explored to validate them as candidates to FHS/FHN in chickens and humans.

Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR

The use of reference genes is required for relative quantification in gene expression analysis and the stability of these genes can be variable depending on the experimental design. Therefore, it is indispensable to test the reliability of endogenous genes previously to their use. This study evaluated nine candidate reference genes to select the most stable genes to be used as reference in gene expression studies with the femoral cartilage of normal and epiphysiolysis-affected broilers. The femur articular cartilage of 29 male broilers with 35 days of age was collected, frozen and further submitted to RNA extraction and quantitative PCR (qPCR) analysis. The candidate reference genes evaluated were GAPDH, HMBS, HPRT1, MRPS27, MRPS30, RPL30, RPL4, RPL5, and RPLP1. For the gene stability evaluation, three software were used: GeNorm, BestKeeper and NormFinder, and a global ranking was generated using the function RankAggreg. In this study, the RPLP1 and RPL5 were the most reliable endogenous genes being recommended for expression studies with femur cartilage in broilers with epiphysiolysis and possible other femur anomalies.

Abstract Background Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds. Results ABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs. Conclusions This study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production.

Abstract Background Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. Conclusions In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.

Abstract: The objective of this work was to estimate genetic parameters for bird carcass and meat quality traits, as well as to explore the genetic patterns of the breeding values of this population using cluster analyses. Data from 1,846 birds were used to estimate the genetic parameters of production and quality traits using the multiple-trait animal model, and cluster analyses were performed. The heritability estimates ranged from 0.08± 0.03 for meat pH measured 24 hours after slaughter to 0.85± 0.09 for body weight. The genetic correlations between production traits were high and positive. The genetic correlations between meat quality traits were low and were not informative due to the high standard errors (same magnitudes as those of the genetic correlations). The genetic correlations between meat production and quality traits were negative, except between production traits and meat lightness intensity. Based on breeding values (EBVs), the evaluated population can be divided into four groups through cluster analyses, and one group is suitable for selection because the birds presented EBVs above and around the average of the population, respectively, for production and quality traits. Therefore, it is possible to obtain genetic gains for production-related traits without decreasing meat quality.

The use of reference genes is required for relative quantification in gene expression analysis and since the stability of these genes could be variable depending on the experimental design, it has become indispensable to test the reliability of endogenous genes. Therefore, this study evaluated 10 reference candidate genes in two different experimental conditions in order to obtain stable genes to be used as reference in expression studies related to scrotal hernias in pigs. Two independent experiments were performed: one with 30 days-old MS115 pigs and the other with 60 days-old Landrace pigs. The inguinal ring/canal was collected, frozen and further submitted to real-time PCR analysis (qPCR). For the reference genes stability evaluation, four tools were used: GeNorm in the SLqPCR, BestKeeper, NormFinder and Comparative CT. A general ranking was generated using the BruteAggreg function of R environment. In this study, the RPL19 was one of the most reliable endogenous genes for both experiments. The breed/age effects influenced the expression stability of candidate reference genes evaluated in the inguinal ring of pigs. Therefore, this study reinforces the importance of evaluating the stability of several endogenous genes previous their use, since a consensual set of reference genes is not easily obtained. Here, two sets of genes are recommended: RPL19, RPL32 and H3F3A for 30-days MS115 and PPIA and RPL19 for the 60 days-old Landrace pigs. This is the first study using the inguinal ring tissue and the results can be useful as an indicative for other studies working with gene expression in this tissue.

O objetivo deste trabalho foi caracterizar genotipicamente, e construir o mapa de ligação e mapear locos associados a características quantitativas (QTL) de desempenho e carcaça no cromossomo 5 de linhagens brasileiras galinhas. Utilizou-se uma população F2 CTCT, resultante do acasalamento entre machos da linhagem de postura CC e fêmeas da linhagem de corte TT. Um total de 356 animais foi genotipado com 11 marcadores microssatélites. A caracterização genotípica foi realizada pela estimação dos seguintes parâmetros genotípicos: conteúdo de informação polimórfica (0,45-0,69), heterozigosidades observada (0,48-1,00) e esperada (0,48-0,74), e número de alelos por loco (3-5). Empregou-se o mapeamento por intervalo combinado à modelagem fenotípica por modelo misto, no mapeamento de QTL. O comprimento do mapa de ligação foi de 174,7 cM. Não foram constatadas inversões entre o mapa obtido, o mapa consenso e o genoma. Foram mapeados nove QTL, dos quais sete foram sugestivos ("log of odds", LOD3,0). Seis destes QTL são inéditos: conversão alimentar e eficiência alimentar dos 35 aos 41 dias de idade (significativo), pesos de cabeça e fígado, e triglicerídeos e triglicerídeos+colesterol. A população CTCT apresenta variabilidade genotípica, o mapa de ligação é similar ao mapa consenso e ao genoma, e novos QTL foram mapeados.

The objective of this study was to estimate genetic and phenotypic correlations of body weight at 6 weeks of age (BW6), as well as final carcass yield, and moisture, protein, fat and ash contents, using data from 3,422 F2 chickens originated from reciprocal cross between a broiler and a layer line. Variance components were estimated by the REML method, using animal models for evaluating random additive genetic and fixed contemporary group (sex, hatch and genetic group) effects. The heritability estimates (h²) for BW6, carcass yield and percentage of carcass moisture were 0.31 ± 0.07, 0.20 ± 0.05 and 0.33 ± 0.07, respectively. The h² for the percentages of protein, fat and ash on a dry matter basis were 0.48 ± 0.09, 0.55 ± 0.10 and 0.36 ± 0.08, respectively. BW6 had a positive genetic correlation with fat percentage in the carcass, but a negative one with protein and ash contents. Carcass yield, thus, appears to have only low genetic association with carcass composition traits. The genetic correlations observed between traits, measured on a dry matter basis, indicated that selection for carcass protein content may favor higher ash content and a lower percentage of carcass fat.

This study aimed at mapping QTL (quantitative trait loci) using linear combinations of characteristics of economical interest in Gallus gallus. A total of 350 F2 chickens from an initial crossing among males from a broiler line (TT) with females from a layer line (CC) were used. It was conducted a QTL mapping in chromosomes of Gallus gallus (GGA1, GGA3, GGA5, GGA8, GGA11, and GGA13) for 20 performance and carcass traits. For detecting QTL, it was used the likelihood ratio test between a reduced model (including fixed effects of sex, hatch and random effect of infinitesimal genetic value) and a full model (including all the previous effects plus QTL effects). When original characterists were analyzed, that is, before the formation of linear combinations, six significant QTLs were mapped at 1% in the genome, four in the GGA1 (live weight at 35 days of age and at 42 days of age, abdominal fat and heart weight); and two on GGA3 (live weight at 35 and 42 days of age); three significant QTLs at 5% in the genome, one on GGA1 (head weight), one on GGA3 (wings weight), and one on GGA8 (gizzard weight); besides seven suggestive linkages for several traits. When QTLs were mapped for principal components, many mapped QTLs were confirmed for original traits, in addition to finding three QTLs and eight suggestive linkages not mapped for the original traits.Este estudo teve por objetivo mapear QTL (quantitative trait loci) utilizando combinações lineares de características de interesse econômico em Gallus gallus. Foram estudadas 350 aves F2 oriundas de um cruzamento inicial entre machos de uma linhagem de corte (TT) e fêmeas de uma linhagem de postura (CC). Foi conduzido mapeamento de QTL nos cromossomos Gallus gallus (GGA1, GGA3, GGA5, GGA8, GGA11 e GGA13), para 20 características de desempenho e de carcaça. Para detectar QTL foi utilizado o teste da razão de verossimilhanças entre um modelo reduzido (incluindo efeitos fixos de sexo, incubação e o efeito aleatório de valor genético infinitesimal) e um completo (incluindo todos os efeitos anteriores mais os efeitos de QTL). Ao analisar as características originais, ou seja, antes da formação das combinações lineares, foram mapeados seis QTLs significativos a 1% no genoma, quatro no GGA1 (peso vivo aos 35 dias, peso vivo aos 42 dias, gordura abdominal e peso do coração) e dois no GGA3 (peso vivo aos 35 e aos 42 dias de idade); três QTLs significativos a 5% no genoma, sendo um no GGA1 (peso da cabeça), um no GGA3 (peso das asas), e um no GGA8 (peso da moela); além de sete ligações sugestivas para diversas características. Ao mapear QTLs para os componentes principais, foram confirmados vários QTLs mapeados para as características originais, além de encontrar três QTLs e oito ligações sugestivas não mapeadas para as características originais.

Total RNA isolated from Pectoralis major muscle from PSE (L*24h>53.0, pH"53) meats of two phenotypically distinct chicken lines, broiler and layer, was used to investigate the α-ryr and β-ryr gene expression by real-time RT-PCR approach. Mean relative quantification (RQ) values were lower (p0.05) in α-ryr gene expression regardless of line studied. The β-ryr RQ results suggested that in PSE samples an alteration might occur in the regular ratio (1:1) of α-RyR/β-RyR normally found in avian muscles. These results provided the first evidence of PSE meat occurrence as a result of the differential expression of ryanodine receptor genes which might lead to an increased in Ca2+ availability at the cell milieu.As proteínas α-RyR e β-RyR apresentam papéis distintos no mecanismo de excitação-contração com diferenças em seus mecanismos de ativação e respostas a ligantes. O RNA total de filé de peito (Pectoralis major m) com PSE (L*24h>53,0; pH 5,8) e não-PSE (4453) de duas linhagens distintas, de corte e de postura, foram utilizadas para estudar a expressão gênica dos genes α-ryr β-ryr por PCR-em-tempo-real. Os valores médios de expressão gênicas relativas (RQ) foram inferiores (p0,05) na expressão do , independentemente da linhagem estudada. Os resultados de RQ para β-ryr indicaram nas amostras PSE, uma alteração na proporção (1:1) de α-RyR/β-RyR comumente encontrada em músculos de aves. Estes resultados originam a primeira evidência da ocorrência de carnes PSE como resultado de uma disponibilidade acentuada de Ca2+ no citosol pela expressão diferenciada de proteínas receptoras de rianodina.

Chicken experimental populations have been developed worldwide for QTL mapping, but their genotypic characterizations are not usually discussed. The objective of this study was to characterize genotypically two F1 reciprocal generations and their parental lines based on the estimation of genotypic parameters. These F1 generations originated two Brazilian reference populations to map QTL. The evaluated parameters were polymorphic information content (PIC), observed and expected heterozygosities and number of alleles at microsatellite loci on chromosomes 1, 3 and 4. All parental and F1 chickens from both populations were used totalling of 83 chickens: 14 from a broiler (TT) and 14 from a layer line (CC) and 55 from their reciprocal F1 generations. The chicken lines and the resource populations were developed at the National Research Center for Swine and Poultry (EMBRAPA), Brazil. Genotypes from all animals were obtained from 34 loci on chromosomes 1 (13), 3 (12) and 4 (9). Based on the sampling, we found that the two lines exhibited a total of 163 different alleles, of which 31 (31.1%) and 44 (33.0%) alleles were unique in CC and TT lines, respectively, with allelic frequencies ranging from 0.03 to 0.82. The observed heterozygosity was higher (0.68-0.71) in both F1 generations than in their founder lines due to linkage disequilibrium. Finally, the two chicken lines used as founders created two F1 reciprocal generations with high levels of PIC (0.50-0.52) and observed heterozygosity, as well as satisfactory number of alleles per locus (4.06-4.32). Our results will allow to compare and select families with highly informative microsatellite markers for QTL studies, reducing genotyping costs.Populações experimentais de frangos tem sido desenvolvidas pelo mundo para mapeamento de QTLs, mas a caracterização genotípica delas não é normalmente apresentada. O objetivo deste estudo foi caracterizar genotipicamente duas gerações F1 recíprocas e suas linhagens parentais com base na estimação de parâmetros genotípicos. Estas gerações F1 originaram duas populações brasileiras referências para mapear QTLs. Os parâmetros avaliados foram: conteúdo de informação polimórfica (PIC), heterozigosidades observada e esperada e número de alelos por loco nos cromossomos 1, 3 e 4. Todos os animais parentais e F1 de ambas as populações foram usados, em um total de 83 animais: 14 de uma linhagem de corte (TT) e 14 de uma linhagem de postura (CC), e 55 de suas gerações recíprocas F1. Tanto as linhagens como as populações referências foram desenvolvidas no Centro Nacional de Pesquisa de Suínos e Aves (EMBRAPA), Brasil. Os genótipos de todos os animais foram obtidos a partir de 34 marcadores microssatélites localizados nos cromossomos 1 (13), 3 (12) e 4 (9). Com base na amostragem realizada, as duas linhagens exibiram um total de 163 alelos, dos quais 31 (31,1%) e 44 (33,0%) foram oriundos exclusivamente de CC e TT, respectivamente, com freqüências alélicas que variaram de 0,03 a 0,82. A heterozigosidade observada foi maior (0,68-0,71) em ambas as gerações F1 do que em suas linhagens fundadoras devido ao desequilíbrio de ligação. Finalmente, as duas linhagens parentais possibilitaram a obtenção de gerações recíprocas F1 com valores elevados de PIC (0,50-0,52) e heterozigosidade observada, bem como com um número satisfatório de alelos por loco (4,06-4,32). Estes resultados permitirão comparar e selecionar famílias e marcadores microssatélites mais informativos em estudos de QTLs, reduzindo os custos de genotipagem.

Leptin, a polypeptide hormone secreted mainly by adipose tissue, plays an important role in feed intake regulation, energy metabolism and reproduction in several species. Its function has been intensively studied in mammals; however, in birds limited information is available. The cDNA sequence for chicken leptin has been reported, and high hepatic expression levels of leptin were associated with fat deposition in selected bird lines. However, controversies still remain concerning to the chicken leptin gene and several authors failed to amplify this gene from genomic DNA or cDNA. In view of this controversy and the importance of this gene, the present study aimed to investigate the leptin gene in a population of birds developed by Embrapa Swine and Poultry Research Center (Brazil). First of all, the sequences of Gallus gallus leptin gene (GenBank AF012727) and Mus musculus (GenBank NM_008493) were aligned with the objective of designing primers in conserved regions among the two species, since 94.6% of similarity is described in the literature in those species. For all four pairs of primers designed, several amplification tests were performed with both DNA and cDNA, but neither unique fragment nor expected band size was ever achieved. The leptin sequence in GenBank does not represent the sequence of the chicken leptin gene.A leptina, hormônio polipeptídico secretado principalmente pelo tecido adiposo, tem um papel importante na regulação da ingestão de alimentos, metabolismo de energia e reprodução em mamíferos. A função do gene da leptina tem sido intensamente estudada em mamíferos, porém, em aves, ainda é pouco conhecida. O cDNA deste gene foi identificado em galinhas, e a alta expressão hepática e os níveis de leptina no plasma foram associados à alta deposição de gordura presente em linhagens de aves selecionadas. Entretanto, permanecem controvérsias sobre o gene da leptina em galinhas, pois diversos autores não conseguiram amplificar este gene a partir de DNA genômico ou cDNA. Tendo em vista essas controvérsias e a importância desse gene, o presente trabalho teve como objetivo amplificar o gene da leptina numa população de aves desenvolvida pela Embrapa Suínos e Aves (Brasil). Primeiramente, as seqüências do gene da leptina de Gallus gallus (GenBank AF012727) e Mus musculus (GenBank NM_008493) foram alinhadas com o objetivo de desenhar os primers em regiões conservadas nas duas espécies, pois como descrito na literatura, esses genes apresentam 94,6% de similaridade. Para os quatro pares de primers desenhados, foram realizados diversos testes de amplificação utilizando DNA e cDNA, mas não foi obtido um fragmento único ou a banda esperada. A seqüência do gene da leptina depositada no GenBank não representa a seqüência do gene da leptina de galinhas.

A linkage map is essential not only for quantitative trait loci (QTL) mapping, but also for the organization and location of genes along the chromosomes. The present study is part of a project whose major objective is, besides from construction the linkage maps, the whole genome scan for mapping QTL for performance traits in the Brazilian experimental chicken population. Linkage maps of chicken chromosomes 6 to 8, 11 and 13 were constructed based on this population. The population was developed from two generations of crossbreeding between a broiler and a layer line. Fifty-one microsatellite markers were tested, from which 28 were informative: 4, 8, 7, 4 and 5 for chromosomes 6, 7, 8, 11 and 13, respectively. A SNP located in the leptin receptor gene was included for chromosome 8. Ten parental, 8 F1 and 459 F2 chickens from five full-sib families were genotyped with these markers. The number of total informative meioses per locus varied from 232 to 862, and the number of phase-known informative meioses from 0 to 764. Marker orders in the chromosomes coincided with those of the chicken consensus map, except for markers ADL0147 and MCW0213, on chromosome 13, which were inverted. The reduced number of phase-known informative meioses for ADL0147 (150) may be pointed out as a possible cause for this inversion, apart from the relative short distance between the two markers involved in the inversion (10.5 cM).O mapa de ligação além de ser fundamental no mapeamento de locos de características quantitativas (QTLs) é importante na organização e localização de genes distribuídos ao longo dos cromossomos. O presente estudo é parte de um trabalho cujo objetivo maior, é a análise de mapeamento de QTLs para características de desempenho no genoma de uma população experimental desenvolvida no Brasil. Com base nesta população foram construídos os mapas de ligação dos cromossomos 6 a 8, 11 e 13 da galinha. A população foi desenvolvida a partir de duas gerações de cruzamentos entre uma linhagem de corte e uma de postura. Foram testados 51 marcadores microssatélites, dos quais 28 foram informativos: 4, 8, 7, 4 e 5 dos cromossomos 6, 7, 8, 11 e 13, respectivamente. Um SNP localizado no gene do receptor da leptina foi incluído no cromossomo 8. Os 10 parentais, 8 F1 e um total de 459 aves F2 de cinco famílias de irmãos completos foram genotipados com estes marcadores. O número de meioses informativas totais por loco variou de 232 a 862 e o de meioses informativas de fase conhecida de 0 a 764. A ordem dos marcadores nos cromossomos coincidiu com a do mapa consenso da galinha, com exceção dos marcadores ADL0147 e MCW0213 do cromossomo 13 que tiveram sua ordem invertida. O número reduzido de meioses informativas de fase conhecida para o marcador ADL0147 (150) pode ser apontado como uma possível causa para a inversão, além da relativa proximidade entre os dois marcadores envolvidos na inversão (10,5 cM).

Brazilian poultry industry has reached a high level of development in both meat and egg production as a result of constant technological modernization. Further improvements can be achieved through genomics, but before this can be accomplished, a better understanding of gene expression profiles and nucleotide polymorphisms is necessary. Since animal physiology is directly or indirectly controlled by the pituitary and hypothalamus, the aim of the present work was to identify and analyze genes expressed in these tissues in chicken lines with different growth potential. Two pituitary and hypothalamus cDNA libraries from 21 day broiler (TT) and layer (CC) chickens lines were constructed and allowed identification of 3,074 unique sequences and 77 single nucleotide polymorphisms (SNPs). The collection of expressed sequence tags (ESTs) and SNPs identified in this study represents an important resource for future studies aimed at identifying genes responsible for growth in chicken.

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers.

Selective genotyping for a certain trait in individuals with extreme phenotypes contributes sufficient information to determine linkage between molecular markers and quantitative trait loci (QTL). In this experiment an F2 population, developed by crossing males from a broiler line with females from a layer line, was employed to detect QTL on chromosomes 3 and 5. Twenty-eight performance and carcass traits were measured in F2 offspring, and phenotypic correlations between traits were calculated. Body weight at 42 days (BW42) presented the greatest positive correlations with most other traits, with correlation between body weights at 35 and 41 days, weight gain between birth and 35, 41 and 42 days, as well as weights of carcass and some body parts superior to 0.8. One hundred-and-seventy F2 offspring, representing the top (4.5%) and the bottom (4.5%) of a normal distribution curve of BW42, were selected with equal proportions of males and females, and within dam family. Samples were genotyped for 19 informative markers on chromosome 3, and 11 markers on chromosome 5. Marker allelic frequencies of phenotypic groups with high and low BW42 were compared with a chi-square test. Four regions on chromosome 3 and three regions on chromosome 5 had markers that were suggestively associated with BW42 (P < 0.10), confirming and expanding previous studies.

A genetic map provides insight into genome organization and chromosomal location of markers and genes, and is important for quantitative trait loci (QTL) mapping. The objective of this study was to use a Brazilian resource population to construct a linkage map for chicken chromosome 1. Eighty microsatellite markers were tested and 26 informative markers were typed in an experimental F2 population developed by two generations of crossbreeding between a broiler sire line and a layer line. A total of 649 F2 individuals from seven full-sib families with about 95 F2 offspring each were genotyped. Multi-locus linkage analysis resulted in a chromosome 1 map of 26 ordered markers. Locus order was in general agreement with other published linkage maps, except for two discrepancies: 1) order of loci MCW10 and MCW208 was reversed in this map relative to the Wageningen linkage map, 2) markers ADL234 and LEI68, that were mapped to the same position in Compton, East Lansing and Wageningen populations, were separated by a distance of 5.9 centimorgans in our population. The higher number of informative meioses from our population could explain these differences. This map is an important first step in our effort to map QTL in the Brazilian chicken resource population, and complements the international consensus map information.Um mapa genético proporciona o entendimento da organização do genoma e da localização cromossômica de marcadores e genes, e é importante para o mapeamento de locos controladores de características quantitativas (QTL). O objetivo deste estudo foi utilizar uma população brasileira para construir um mapa de ligação do cromossomo 1 da galinha. Oitenta marcadores microssatélites foram testados e 26 marcadores informativos foram genotipados em uma população F2 experimental, desenvolvida em duas gerações de um cruzamento entre uma linha macho de corte e uma linhagem de postura. Foram genotipados um total de 649 indivíduos F2 de sete famílias de irmãos completos com cerca de 95 F2 cada uma. A análise de ligação Multi-locus gerou um mapa do cromossomo 1 com 26 marcadores ordenados. A ordem dos locos foi em geral semelhante àquela de outros mapas de ligação publicados, exceto por duas discrepâncias: 1) a ordem entre os marcadores MCW10 e MCW208 foi invertida no presente mapa quando comparado com o mapa de ligação de Wageningen, 2) Os marcadores ADL234 e LEI68 que foram mapeados na mesma posição nas populações de Compton, East Lansing e Wageningen foram separados por uma distância de 5,9 centimorgans na presente população. O maior número de meioses informativas desta população pode explicar esta diferença. Este mapa é o primeiro passo no esforço de mapear QTL na população brasileira o qual pode também ser usado para complementar a informação do mapa consenso internacional da galinha.

O presente trabalho teve por objetivo estimar herdabilidades (h²) e correlações genéticas (r g) dos caracteres seminais, da motilidade espermática (MOT), do volume de sêmen (VOL) e da concentração de espermatozóides (CON) de aves White Leghorn. Foram utilizados 698 machos White Leghorn da linhagem DD1, desenvolvida na EMBRAPA - CNPSA, com ejaculados coletados às 24, 26 e 28 semanas de idade. As estimativas de herdabilidades e seus erros-padrão, respectivamente, para as 24, 26 e 28 semanas de idade, foram, para VOL, 0,30 (0,18), 0,27(0,17) e 0,32(0,18); para MOT, 0,08(0,16), 0,34(0,18) e 0,26 (0,17); e para CON, 0,29 (0,18), 0,31 (0,17) e 0,34 (0,19). Os valores obtidos para correlações genéticas e seus erros-padrão, às 24 semanas foram: -0,11 (0,56) entre MOT e VOL, -1,77 (3,45) entre MOT e CON e 0,51 (0,37) entre VOL e CON. As estimativas r g às 26 semanas foram de -0,15 (0,32) entre MOT e VOL, -0,61 (0,36) entre MOL e CON e 0,65 (0,26) entre VOL e CON. As estimativas DE r g às 28 semanas foram de -0,13 (0,35) entre MOL e VOL, -0,86 (0,42) entre MOL e CON e 0,16 (0,29) entre VOL e CON. Com base nestes resultados, sugere-se a utilização dos caracteres volume de sêmen e/ou concentração de espermatozóides, medidos a partir das 26 semanas de idade, na pré-seleção de reprodutores White Leghorn. A motilidade espermática não seria recomendada, por apresentar correlações negativas com os caracteres volume e concentração de espermatozóides.The objective of this work was to estimate heritabilities (h²) and genetic correlations (r g) of semen motility (MOT), semen volume (VOL) and spermatozoa concentration (CON) of White Leghorn strain. Six hundred and ninety-eight DD1 strain roosters, developed at CNPSA/EMBRAPA, were used with the ejaculated collected at 24, 26 and 28 wk of age. The heritabilities estimates and standard deviation, respectively for the 24, 26 and 28 weeks of age, were for VOL, .30 (.18), .27(.17) and .32(.18), for MOT, .08(.16), .34 (.18) and .26 (.17), and for CON, .29 (.18), .31 (.17) e .34 (.19). The genetic correlations and standard deviation at 24 weeks of age were -.11 (.56) between MOT and VOL, -1.77 (3.45) between MOT and CON, and .51 (.37) between VOL and CON. At 26 weeks of age the r g estimates were -.15 (.32) between MOT and VOL, -.61 (.36) between MOT and CON, and .65 (.26) between VOL and CON. The r g estimates at 28 weeks of age were -.13 (.35) between MOT and VOL, -.86 (.42) between MOT and CON, and .16 (.29) between VOL and CON. The results suggest that both character semen volume and/or concentration of spermatozoa, measured at 26 weeks of age and on, can be used in pre-selection of White Leghorn males. Sperm motility is not recommended because of the negative correlation with volume and concentration characters.

O objetivo do presente trabalho foi estimar correlações genéticas entre caracteres de sêmen (volume de sêmen, motilidade espermática e concentração de espermatozóides) e de postura (produção de ovos, períodos parciais e total, peso médio de ovo) de aves White Leghorn. Para obtenção dos caracteres de sêmen, foram usados 698 machos da linhagem DD1, desenvolvida na EMBRAPA-CNPSA. O sêmen foi coletado às 24, 26 e 28 semanas de idade e, para obtenção dos caracteres de postura, foram usadas suas irmãs inteiras (média de duas irmãs por macho). De acordo com os resultados obtidos, sugere-se que, para a seleção com vistas ao aumento da produção total de ovos (r g = 0,44±0,09) e peso do ovo (r g = 0,67±0,04), seja usado o caráter concentração de espermatozóides, medido respectivamente, às 24 e 28 semanas de idade.

O objetivo deste trabalho foi avaliar as mudanças genéticas ocorridas no desempenho, na composição da carcaça e no tamanho e resistência dos ossos, em linhagens experimentais, após seis gerações de seleção. As aves pertenciam às linhas paternas LL, LLc (controle), ZZ e LC1 (comercial), e às maternas PP, PPc (controle), KK e LC2 (comercial). As mudanças genéticas foram obtidas a partir dos desvios entre cada linha selecionada e a respectiva linha controle (LL-LLc e PP-PPc). A seleção para peso corporal resultou em respostas correlacionadas na conversão alimentar, mas não nas características de carcaça. As mudanças genéticas no ganho de peso não estão sendo acompanhadas por mudanças correlacionadas na resistência dos ossos. A ênfase de seleção diferenciada entre linhas puras paternas e maternas está alterando o conteúdo de Ca, água e de gordura das carcaças de frango de corte.An experiment was carried out to determine the genetic changes in performance, carcass composition and measures of bone size and resistancy of paternal (LL, LLc, ZZ and LC1) and maternal lines (PP, PPc, KK and LC2). The genetic changes were estimated as deviations between selected and control lines (LL-LLc and PP-PPc). The body weight selection improved feed:gain ratio, but did not cause any correlated response in the carcass traits. The genetic changes in the weight gain are not acompanied by correlated changes in the bone resistancy. Diferent selection emphasis in the selection of paternal and maternal pure lines is altering the Ca, water and fat content of the carcass.