Novel Candidate Genes Involved in an Initial Stage of White Striping Development in Broiler Chickens.

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.

Key co-expressed genes correlated with blood serum parameters of pigs fed with different fatty acid profile diets.

This study investigated how gene expression is affected by dietary fatty acids (FA) by using pigs as a reliable model for studying human diseases that involve lipid metabolism. This includes changes in FA composition in the liver, blood serum parameters and overall metabolic pathways. RNA-Seq data from 32 pigs were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA). Our aim was to identify changes in blood serum parameters and gene expression between diets containing 3% soybean oil (SOY3.0) and a standard pig production diet containing 1.5% soybean oil (SOY1.5). Significantly, both the SOY1.5 and SOY3.0 groups showed significant modules, with a higher number of co-expressed modules identified in the SOY3.0 group. Correlated modules and specific features were identified, including enriched terms and pathways such as the histone acetyltransferase complex, type I diabetes mellitus pathway, cholesterol metabolism, and metabolic pathways in SOY1.5, and pathways related to neurodegeneration and Alzheimer's disease in SOY3.0. The variation in co-expression observed for HDL in the groups analyzed suggests different regulatory patterns in response to the higher concentration of soybean oil. Key genes co-expressed with metabolic processes indicative of diseases such as Alzheimer's was also identified, as well as genes related to lipid transport and energy metabolism, including CCL5, PNISR, DEGS1. These findings are important for understanding the genetic and metabolic responses to dietary variation and contribute to the development of more precise nutritional strategies.

Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

BACKGROUND: Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. RESULTS: The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. CONCLUSIONS: After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.

Transcriptome profile of skeletal muscle using different sources of dietary fatty acids in male pigs.

Pork is of great importance in world trade and represents the largest source of fatty acids in the human diet. Lipid sources such as soybean oil (SOY), canola (CO), and fish oil (FO) are used in pig diets and influence blood parameters and the ratio of deposited fatty acids. In this study, the main objective was to evaluate changes in gene expression in porcine skeletal muscle tissue resulting from the dietary oil sources and to identify metabolic pathways and biological process networks through RNA-Seq. The addition of FO in the diet of pigs led to intramuscular lipid with a higher FA profile composition of C20:5 n-3, C22:6 n-3, and SFA (C16:0 and C18:0). Blood parameters for the FO group showed lower cholesterol and HDL content compared with CO and SOY groups. Skeletal muscle transcriptome analyses revealed 65 differentially expressed genes (DEG, FDR 10%) between CO vs SOY, and 32 DEG for CO vs FO, and 531 DEG for SOY vs FO comparison. Several genes, including AZGP1, PDE3B, APOE, PLIN1, and LIPS, were found to be down-regulated in the diet of the SOY group compared to the FO group. The enrichment analysis revealed DEG involved in lipid metabolism, metabolic diseases, and inflammation between the oil groups, with specific gene functions in each group and altered blood parameters. The results provide mechanisms to help us understand the behavior of genes according to fatty acids.

Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil.

BACKGROUND: The high similarity in anatomical and neurophysiological processes between pigs and humans make pigs an excellent model for metabolic diseases and neurological disorders. Lipids are essential for brain structure and function, and the polyunsaturated fatty acids (PUFA) have anti-inflammatory and positive effects against cognitive dysfunction in neurodegenerative diseases. Nutrigenomics studies involving pigs and fatty acids (FA) may help us in better understanding important biological processes. In this study, the main goal was to evaluate the effect of different levels of dietary soybean oil on the lipid profile and transcriptome in pigs' brain tissue. RESULTS: Thirty-six male Large White pigs were used in a 98-day study using two experimental diets corn-soybean meal diet containing 1.5% soybean oil (SOY1.5) and corn-soybean meal diet containing 3.0% soybean oil (SOY3.0). No differences were found for the brain total lipid content and FA profile between the different levels of soybean oil. For differential expression analysis, using the DESeq2 statistical package, a total of 34 differentially expressed genes (DEG, FDR-corrected p-value < 0.05) were identified. Of these 34 DEG, 25 are known-genes, of which 11 were up-regulated (log2 fold change ranging from + 0.25 to + 2.93) and 14 were down-regulated (log2 fold change ranging from - 3.43 to -0.36) for the SOY1.5 group compared to SOY3.0. For the functional enrichment analysis performed using MetaCore with the 34 DEG, four pathway maps were identified (p-value < 0.05), related to the ALOX15B (log2 fold change - 1.489), CALB1 (log2 fold change - 3.431) and CAST (log2 fold change + 0.421) genes. A "calcium transport" network (p-value = 2.303e-2), related to the CAST and CALB1 genes, was also identified. CONCLUSION: The results found in this study contribute to understanding the pathways and networks associated with processes involved in intracellular calcium, lipid metabolism, and oxidative processes in the brain tissue. Moreover, these results may help a better comprehension of the modulating effects of soybean oil and its FA composition on processes and diseases affecting the brain tissue.

RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids.

Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms' variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets.

Check-All-That-Apply method for sensory characterization of pork from immunocastrated male pigs fed different oil sources

In the last decade, other quality attributes have emerged as the main aspects that impact pork consumers acceptance, such as environmentally friendly production, nutritional value, and animal welfare. This study applies a Check-All-That-Apply (CATA) questionnaire for sensory characterization of loins from genetically lean immunocastrated male pigs fed diets containing either a standard commercial diet with 1.5 % soybean oil (control) or 3 % oil from either soybean oil (SO), canola oil (CO), or fish oil (FO) during the growing-finishing phases. Twenty CATA attributes for loin samples were generated. We interviewed 101 consumers to select all the CATA terms that they considered suitable to characterize sensory attributes of longissimus lumborum muscle samples of pigs from each dietary treatment. The CATA results indicated differences among pork loin samples depending on the source and inclusion level of dietary oil. Loins from pigs fed 3 % SO were characterized by a higher frequency of the "juicy texture" attribute (p < 0.05) and a lower frequency of the "dry texture" attribute (p < 0.05) compared to loins from 3 % FO-fed pigs. Moreover, loins from pigs fed 3 % SO had a lower citation frequency of the "tasteless" attribute (p < 0.05) compared to loins from 3 % FO-fed pigs. The attributes "cooked pork meat-like taste", "juicy texture", "tender texture", and "brightness" were placed close to the overall liking. "Tender texture", "juicy texture", "pork meat-like" (odor and taste), and "cooked pork meat-like taste" attributes were considered drivers of liking. Feeding genetically lean immunocastrated male pigs with diets containing 3 % SO may be advisable from a pork sensory quality perspective.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness.

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs.

The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.

Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases.

Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science.

SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens.

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.

A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens.

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.

Genome-wide detection of CNVs and their association with performance traits in broilers.

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.

Exploring the genetic architecture of feed efficiency traits in chickens.

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.

Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach.

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.

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

BACKGROUND: Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs. RESULTS: Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes. CONCLUSIONS: The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.

Identification of selection signatures involved in performance traits in a paternal broiler line.

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.

Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken.

Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle.

Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer's palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens.

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.