Genetic architecture of white striping in turkeys (Meleagris gallopavo).

White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0-3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.

Detection of lymphoproliferative disease virus in Iowa Wild Turkeys (Meleagris gallopavo): Comparison of two sections of the proviral genome.

An accurate diagnostic test is an essential aspect of successfully monitoring and managing wildlife diseases. Lymphoproliferative Disease Virus (LPDV) is an avian retrovirus that was first identified in domestic turkeys in Europe and was first reported in a Wild Turkey (Meleagris gallopavo) in the United States in 2009. It has since been found to be widely distributed throughout North America. The majority of studies have utilized bone marrow and PCR primers targeting a 413-nucleotide sequence of the gag gene of the provirus to detect infection. While prior studies have evaluated the viability of other tissues for LPDV detection (whole blood, spleen, liver, cloacal swabs) none to date have studied differences in detection rates when utilizing different genomic regions of the provirus. This study examined the effectiveness of another section of the provirus, a 335-nucleotide sequence starting in the U3 region of the LTR (Long Terminal Repeat) and extending into the Matrix of the gag region (henceforth LTR), for detecting LPDV. Bone marrow samples from hunter-harvested Wild Turkeys (n = 925) were tested for LPDV with the gag gene and a subset (n = 417) including both those testing positive and those where LPDV was not detected was re-tested with LTR. The positive percent agreement (PPA) was 97.1% (68 of 70 gag positive samples tested positive with LTR) while the negative percent agreement (NPA) was only 68.0% (236 of 347 gag negative samples tested negative with LTR). Cohen's Kappa (κ = 0.402, Z = 10.26, p<0.0001) and the McNemar test (OR = 55.5, p<0.0001) indicated weak agreement between the two gene regions. We found that in Iowa Wild Turkeys use of the LTR region identified LPDV in many samples in which we failed to detect LPDV using the gag region and that LTR may be more appropriate for LPDV surveillance and monitoring. However, neither region of the provirus resulted in perfect detection and additional work is necessary to determine if LTR is more reliable in other geographic regions where LPDV occurs.

Specific expression of alternatively spliced genes in the turkey (Meleagris gallopavo) reproductive tract revealed their function in spermatogenesis and post-testicular sperm maturation.

The tissue-specific profile of alternatively spliced genes (ASGs) and their involvement in reproduction processes characteristic of turkey testis, epididymis, and ductus deferens were investigated for the first time in birds. Deep sequencing of male turkey reproductive tissue RNA samples (n = 6) was performed using Illumina RNA-Seq with 2 independent methods, rMATs and SUPPA2, for differential alternative splicing (DAS) event prediction. The expression of selected ASGs was validated using quantitative real-time reverse transcriptase-polymerase chain reaction. The testis was found to be the site of the highest number of posttranscriptional splicing events within the reproductive tract, and skipping exons were the most frequently occurring class of alternative splicing (AS) among the reproductive tract. Statistical analysis revealed 86, 229, and 6 DAS events in the testis/epididymis, testis/ductus deferens, and epididymis/ductus deferens comparison, respectively. Alternative splicing was found to be a mechanism of gene expression regulation within the turkey reproduction tract. In testis, modification was observed for spermatogenesis specific genes; the changes in 5' UTR could act as regulator of MEIG1 expression (a player during spermatocytes meiosis), and modification of 3' UTR led to diversification of CREM mRNA (modulator of gene expression related to the structuring of mature spermatozoa). Sperm tail formation can be regulated by changes in the 5' UTR of testicular SLC9A3R1 and gene silencing by producing dysfunctional variants of ODF2 in the testis and ATP1B3 in the epididymis. Predicted differentially ASGs in the turkey reproductive tract seem to be involved in the regulation of spermatogenesis, including acrosome formation and sperm tail formation and binding of sperm to the zona pellucida. Several ASGs were classified as cilia by actin and microtubule cytoskeleton organization. Such genes may play a role in the organization of sperm flagellum and post-testicular motility development. To our knowledge, this is the first functional investigation of alternatively spliced genes associated with tissue-specific processes in the turkey reproductive tract.

Genetic parameters of feather corticosterone and fault bars and correlations with production traits in turkeys (Meleagris gallopavo).

Robustness can refer to an animal's ability to overcome perturbations. Intense selection for production traits in livestock has resulted in reduced robustness which has negative implications for livability as well as production. There is increasing emphasis on improving robustness through poultry breeding, which may involve identifying novel phenotypes that could be used in selection strategies. The hypothalamic-pituitary-adrenal (HPA) axis and associated hormones (e.g., corticosterone) participate in many metabolic processes that are related to robustness. Corticosterone can be measured non-invasively in feathers (FCORT) and reflects the average HPA axis activity over the feather growing period, however measurement is expensive and time consuming. Fault bars are visible feather deformities that may be related to HPA axis activity and may be a more feasible indicator trait. In this study, we estimated variance components for FCORT and fault bars in a population of purebred turkeys as well as their genetic and partial phenotypic correlations with other economically relevant traits including growth and efficiency, carcass yield, and meat quality. The estimated heritability for FCORT was 0.21 ± 0.07 and for the fault bar traits (presence, incidence, severity, and index) estimates ranged from 0.09 to 0.24. The genetic correlation of FCORT with breast weight, breast meat yield, fillet weight, and ultimate pH were estimated at -0.34 ± 0.21, -0.45 ± 0.23, -0.33 ± 0.24, and 0.32 ± 0.24, respectively. The phenotypic correlations of FCORT with breast weight, breast meat yield, fillet weight, drum weight, and walking ability were -0.16, -0.23, -0.18, 0.17, and 0.21, respectively. Some fault bar traits showed similar genetic correlations with breast weight, breast meat yield, and walking ability but the magnitude was lower than those with FCORT. While the dataset is limited and results should be interpreted with caution, this study indicates that selection for traits related to HPA axis activity is possible in domestic turkeys. Further research should focus on investigating the association of these traits with other robustness-related traits and how to potentially implement these traits in turkey breeding.

Genetic diversity in 10 populations of domestic Turkeys by using microsatellites markers.

The domestic turkey is a native breed in danger of extinction due to the introduction of new breeds specializing in meat production and yield. Turkeys have lost some prominence in urban areas, and only certain breeds of turkeys are preserved in rural areas. Wild and domestic turkeys are different; rural or indigenous turkeys, with black plumage, were domesticated from Mexican turkeys and have been reproduced throughout Latin America. Some of them were taken to Europe in the 16th century and later arrived in North America, where they crossed with another wild species, from which the bronze turkey emerged: the ancestor of all commercial turkeys. The objective of the present work was to evaluate the genetic diversity in 10 populations of domestic turkeys worldwide by using breeds from Europe: Spain and Italy; America: Mexico, United States and Brazil; and the Near East: Iran and Egypt. A total of 522 blood samples of both sexes were collected from domestic turkey populations. Thirty-four microsatellites were used to obtain genetic parameters, and genetic diversity was evaluated. All microsatellites used were polymorphic, and a total of 427 alleles were detected across the 34 markers investigated. In this study, a mean number of 13.44 alleles was found. The four most diverse breeds were from the Andalusia, Mexico, United States, and wild populations, which had the highest mean heterozygosity expected (0.619, 0.612, 0.650, and 0.773) and heterozygosity observed (0.422, 0.521, 0.429, and 0.627), respectively. The MNT348 marker deviated from the HWE in all populations. Our study has shown that the populations close to the species origin are more diverse than those resulting from posterior expansions. Mexican birds were the most diverse, followed by the Spanish populations because Spain imported a large number of turkeys coming from America. Such information can be complementary to other genotypic data required to validate the evolutionary relationships among turkey populations.

Genomic, biochemical and expressional properties reveal strong conservation of the CLCA2 gene in birds and mammals.

Recent studies have revealed the dynamic and complex evolution of CLCA1 gene homologues in and between mammals and birds with a particularly high diversity in mammals. In contrast, CLCA2 has only been found as a single copy gene in mammals, to date. Furthermore, CLCA2 has only been investigated in few mammalian species but not in birds. Here, we established core genomic, protein biochemical and expressional properties of CLCA2 in several bird species and compared them with mammalian CLCA2. Chicken, turkey, quail and ostrich CLCA2 were compared to their mammalian orthologues using in silico, biochemical and expressional analyses. CLCA2 was found highly conserved not only at the level of genomic and exon architecture but also in terms of the canonical CLCA2 protein domain organization. The putatively prototypical galline CLCA2 (gCLCA2) was cloned and immunoblotting as well as immunofluorescence analyses of heterologously expressed gCLCA2 revealed protein cleavage, glycosylation patterns and anchoring in the plasma membrane similar to those of most mammalian CLCA2 orthologues. Immunohistochemistry found highly conserved CLCA2 expression in epidermal keratinocytes in all birds and mammals investigated. Our results suggest a highly conserved and likely evolutionarily indispensable role of CLCA2 in keratinocyte function. Its high degree of conservation on the genomic, biochemical and expressional levels stands in contrast to the dynamic structural complexities and proposed functional diversifications between mammalian and avian CLCA1 homologues, insinuating a significant degree of negative selection of CLCA2 orthologues among birds and mammals. Finally, and again in contrast to CLCA1, the high conservation of CLCA2 makes it a strong candidate for studying basic properties of the functionally still widely unresolved CLCA gene family.

Targeted detection and molecular epidemiology of turkey coronavirus spike gene variants in turkeys and chickens.

Turkey coronavirus (TCoV) is a member of the Avian coronavirus species with infectious bronchitis virus (IBV), which is considered to be the source of TCoV. These 2 viruses are highly similar in all regions of their genomes, except for the spike gene, which is necessary for virus attachment. Although TCoV causes severe enteric disease in turkey poults, it does not cause clinical disease in chickens. However, considering that TCoV can infect chickens, it is important to distinguish TCoV from IBV in chickens. This is particularly true for chickens that are housed near turkeys and thus might be infected with TCoV and serve as a silent source of TCoV for turkeys. We developed and validated a real-time PCR assay to detect the spike gene of TCoV and sequenced a portion of this gene to evaluate the molecular epidemiology of TCoV infections associated with a commercial turkey premises in the United States in 2020-2021. We identified natural infections of TCoV in chickens, and based on the molecular epidemiology of the viruses detected, these chickens may have served as a source of infection for the commercial turkey premises located nearby.

Transcriptome Response of Differentiating Muscle Satellite Cells to Thermal Challenge in Commercial Turkey.

Early muscle development involves the proliferation and differentiation of stem cells (satellite cells, SCs) in the mesoderm to form multinucleated myotubes that mature into muscle fibers and fiber bundles. Proliferation of SCs increases the number of cells available for muscle formation while simultaneously maintaining a population of cells for future response. Differentiation dramatically changes properties of the SCs and environmental stressors can have long lasting effects on muscle growth and physiology. This study was designed to characterize transcriptional changes induced in turkey SCs undergoing differentiation under thermal challenge. Satellite cells from the pectoralis major (p. major) muscle of 1-wk old commercial fast-growing birds (Nicholas turkey, NCT) and from a slower-growing research line (Randombred Control Line 2, RBC2) were proliferated for 72 h at 38 °C and then differentiated for 48 h at 33 °C (cold), 43 °C (hot) or 38 °C (control). Gene expression among thermal treatments and between turkey lines was examined by RNAseq to detect significant differentially expressed genes (DEGs). Cold treatment resulted in significant gene expression changes in the SCs from both turkey lines, with the primary effect being down regulation of the DEGs with overrepresentation of genes involved in regulation of skeletal muscle tissue regeneration and sarcomere organization. Heat stress increased expression of genes reported to regulate myoblast differentiation and survival and to promote cell adhesion particularly in the NCT line. Results suggest that growth selection in turkeys has altered the developmental potential of SCs in commercial birds to increase hypertrophic potential of the p. major muscle and sarcomere assembly. The biology of SCs may account for the distinctly different outcomes in response to thermal challenge on breast muscle growth, development, and structure of the turkey.

Describing the relationships among meat quality traits in domestic turkey (Meleagris gallopavo) populations.

The presence of meat quality defects is increasing in the turkey industry. While the main strategy for mitigating these issues is through improved housing, management, and slaughter conditions, it may be possible to incorporate meat quality into a turkey breeding strategy with the intent to improve meat quality. Before this can occur, it is important to describe the current state of turkey meat quality as well as the correlations among the different meat quality traits and important production traits. The main objective of the present study was to provide a descriptive analysis of 8 different meat quality traits for turkey breast meat from 3 different purebred lines (A, B, and C), and their correlation with a selection of production traits. Using a total of 7,781 images, the breast meat (N = 590-3,892 birds depending on trait) was evaluated at 24 h postmortem for color (L*, a*, b*), pH, and physiochemical characteristics (drip loss, cooking loss, shear force). Descriptive statistics (mean and standard deviation) and Pearson correlations were computed to describe the relationships among traits within each genetic line. A one-factor ANOVA and post hoc t-test were conducted for each trait and between each of the genetic lines. We found significant differences between genetic lines for some color traits (L* and a*), pHinitial, drip loss, and cooking loss. The lightest line in weight (line B) had meat that was the lightest (L*) in color. The heaviest line (line C) had meat that was less red (a*) with a higher pHinitial and greater cooking loss. Unfavorable correlations between production traits and meat quality were also found for each of the genetic lines where increases in production (e.g., body weight, growth rate) resulted in meat that was lighter and redder in color and in some cases (line B and C), with an increased moisture loss. The results of this study provide an important benchmark for turkey meat quality in purebred lines and provide an updated account of the relationships between key production traits and meat quality. Although the magnitude of these correlations is low, their cumulative effect on meat quality can be more significant especially with continued selection pressure on growth and yield.

In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.).

Long non-coding RNAs (lncRNAs) are transcripts not translated into proteins with a length of more than 200 bp. LncRNAs are considered an important factor in the regulation of countless biological processes, mainly through the regulation of gene expression and interactions with proteins. However, the detailed mechanism of interaction as well as functions of lncRNAs are still unclear and therefore constitute a serious research challenge. In this study, for the first time, potential mechanisms of lncRNA regulation of processes related to sperm motility in turkey were investigated and described. Customized bioinformatics analysis was used to detect and identify lncRNAs, and their correlations with differentially expressed genes and proteins were also investigated. Results revealed the expression of 863 new/unknown lncRNAs in ductus deferens, testes and epididymis of turkeys. Moreover, potential relationships of the lncRNAs with the coding mRNAs and their products were identified in turkey reproductive tissues. The results obtained from the OMICS study may be useful in describing and characterizing the way that lncRNAs regulate genes and proteins as well as signaling pathways related to sperm motility.

PCR identification and prevalence of Eimeria species in commercial turkey flocks of the Midwestern United States.

The present study used a PCR approach to characterize prevalence of coccidial species in fecal samples obtained from 40 individual Midwestern turkey flocks to characterize distribution of species in commercial flocks. Each sample was screened for 6 prominent Eimeria species using species-specific primers and was supplemented with a primary nested-PCR approach for amplification of mitochondrial cytochrome c oxidase subunit gene I where initial sample DNA concentrations were low. All samples were positive for at least one species of Eimeria, while most presented 2 (20/40) or 3 (14/40) species in total. Prevalence across farms was primarily dominated by E. meleagrimitis (97.50%), E. adenoeides (95%), and E. gallopavonis (40%). Of the samples positive for E. adenoeides and E. meleagrimitis, almost half (17/40) contained additional species. Data presented here offer insight into Eimeria species currently challenging the Midwestern US turkey industry and potential need to evaluate flocks for species prior to implementing vaccination programs.

Thermal stress and selection for growth affect myogenic satellite cell lipid accumulation and adipogenic gene expression through mechanistic target of rapamycin pathway.

Satellite cells (SCs) are multipotential stem cells having the plasticity to convert to an adipogenic lineage in response to thermal stress during the period of peak mitotic activity (the first week after hatch in poultry). The mechanistic target of rapamycin (mTOR) pathway, which regulates cellular function and fate of SCs, is greatly altered by thermal stress in turkey pectoralis major muscle SCs. The objective of the present study was to determine the effects of thermal stress, selection for growth, and the role of the mTOR pathway on SC intracellular lipid accumulation and expression of adipogenic regulatory genes. These effects were analyzed using SCs isolated from the pectoralis major muscle of 1-wk-old modern faster-growing commercial turkey line (NC) selected for increased growth and breast muscle yield as compared with SCs of a historic slower-growing Randombred Control Line 2 (RBC2) turkey. Heat stress (43 °C) of SCs during proliferation increased intracellular lipid accumulation (P < 0.001), whereas cold stress (33 °C) showed an inhibitory effect (P < 0.001) in both lines. Knockdown of mTOR reduced the intracellular lipid accumulation (P < 0.001) and suppressed the expression of several adipogenic regulatory genes: peroxisome proliferator-activated receptor-γ (PPARγ; P < 0.001), CCAAT/enhancer-binding protein-ß (C/EBPß; P < 0.001), and neuropeptide-Y (NPY; P < 0.001) during both proliferation and differentiation. The NC line SCs showed fewer reductions in lipid accumulation compared with the RBC2 line independent of temperature. Both intracellular lipid accumulation (P < 0.001) and PPARγ expression (P < 0.001) were greater at 72 h of proliferation than at 48 h of differentiation in both the RBC2 and NC lines independent of temperature. Thus, hot and cold thermal stress affected intracellular lipid accumulation in the pectoralis major muscle SCs, in part, through the mTOR pathway in wea growth-dependent manner. Altered intracellular lipid accumulation could eventually affect intramuscular fat deposition, resulting in a long-lasting effect on the structure and protein to fat ratio of the poultry pectoralis major muscle.

Turkey breast muscle growth and development are sensitive to temperatures immediately after hatch due to an immature thermoregulatory system. Meat yield or quality problems may arise from external thermal stress during this period. Modern commercial turkeys are selected for increased growth and breast muscle yield. However, with excessive enlargement of muscle fibers, there are increased incidences of muscle damage and fat deposition in the breast muscle. The breast meat can be downgraded due to the meat quality problems. Satellite cells (SCs) are the only source of cells responsible for post-hatch muscle growth in poultry, and they are sensitive to temperature. This study identifies the cellular mechanisms in regulating thermal stress-induced fat synthesis in turkey breast muscle SCs. The results of the current study provide insight into how thermal stress and selection for rapid growth affect the fat content in SCs. These results have potential application in the development of temperature manipulation strategies to control fat production by SCs, which will impact poultry breast meat quality.

Listeriosis with viral coinfections in 8 gray foxes, 8 wild turkeys, and 2 young cervids in the southeastern United States.

Listeria monocytogenes is a bacterium that can cause disease in many species, including humans, livestock, and wildlife. Increased interactions via shared habitats may promote pathogen transmission among these groups. Our objectives were to evaluate the Southeastern Cooperative Wildlife Disease Study diagnostic data to characterize and compare L. monocytogenes-induced lesions and comorbidities in gray foxes and wild turkeys, and to describe cases of listeriosis in 2 cervids. From 1991-2020, 8 gray foxes, 8 wild turkeys, a neonatal elk, and a white-tailed deer fawn from several eastern states in the United States were diagnosed with listeriosis. All 8 foxes had hepatitis and/or hepatic necrosis with intralesional gram-positive bacilli, and concurrent canine distemper virus (CDV) infection; 2 of the foxes had been vaccinated recently for CDV. L. monocytogenes was cultured from the liver (6 of 8) or lung (2 of 8) of foxes. Lesions in wild turkeys included hepatocellular necrosis (3 of 8), heterophilic hepatitis (1 of 8), heterophilic granulomas (1 of 8), intrasinusoidal gram-positive bacilli without hepatic lesions (1 of 8), granulomatous dermatitis (1 of 8), and/or granulomatous myocarditis (2 of 8). Lymphoproliferative disease viral DNA was detected in 5 of 6 turkeys tested; reticuloendotheliosis viral DNA was detected in 2 of 3 turkeys tested. Both cervids had systemic listeriosis, with L. monocytogenes isolated from liver. Immunohistochemistry for Listeria spp. on select cases revealed immunolabeling in affected organs. Listeriosis was thus established as a cause of morbidity and mortality in 3 wildlife species, which often suffered from concurrent infections and likely immunosuppression.

Selection signatures in melanocortin-1 receptor gene of turkeys (Meleagris gallopavo) raised in hot humid tropics.

Feather colours are used by avian species for defense, adaptation and signaling. Melanocortin-1 receptor (MC1R) gene is one of the genes responsible for feather colour. This study identified selection signatures in MC1R gene of Nigerian indigenous turkeys (NIT) using British United turkeys (BUT) as control breed to investigate the evolutionary processes that have shaped NIT with various feather colours. Complete MC1R gene of 146 NIT (76 males and 70 females) and 32 BUT (18 males and 14 females) were sequenced. Transition/transversion and codon usage biases were predicted using MEGA v6 software. The selective force acting on the gene was predicted using HyPhy software. The FST values were estimated using Arlequin v3.5. The highest transition/transversion bias was predicted for white BUT (1.00) while the lowest was predicted for black NIT (0.50). Negative dN-dS values, indicative of purifying selection, were observed in MC1R gene of all the turkeys. The highest pairwise FST was observed between the MC1R gene of white BUT and black NIT while the least was observed between lavender NIT and white NIT. No recombination event was observed in black NIT and white BUT. The relative synonymous codon usage was the same among different colours for some codons. Presence of purifying selection in MC1R gene of all the turkeys with different feather colours confirms that the gene plays role in many biological processes such as feather colouration, behaviour, pain perception, immunity, growth and adaptation. The results also suggested that the genetic mechanisms generating different feather colours in turkeys are conserved.

Genome-wide association study reveals candidate genes relevant to body weight in female turkeys (Meleagris gallopavo).

The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Genome-wide association studies (GWAS) is a powerful approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with 18-week body weight in a turkey population. The data included body weight observations for 24,989 female turkeys genotyped based on a 65K SNP panel. The analysis was carried out using a univariate mixed linear model with hatch-week-year and the 2 top principal components fitted as fixed effects and the accumulated polygenic effect of all markers captured by the genomic relationship matrix as random. Thirty-three significant markers were observed on 1, 2, 3, 4, 7 and 12 chromosomes, while 26 showed strong linkage disequilibrium extending up to 410 kb. These significant markers were mapped to 37 genes, of which 13 were novel. Interestingly, many of the investigated genes are known to be involved in growth and body weight. For instance, genes AKR1D1, PARP12, BOC, NCOA1, ADCY3 and CHCHD7 regulate growth, body weight, metabolism, digestion, bile acid biosynthetic and development of muscle cells. In summary, the results of our study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program and adapted in fine mapping of quantitative trait loci to enhance genetic improvement in this species.

Transcriptome analysis of inseminated sperm storage tubules throughout the duration of fertility in the domestic turkey, Meleagris gallopavo.

Sperm storage tubules (SST) are specialized invaginations of the oviductal epithelium that permit avian species to store spermatozoa for extended periods of time, without compromising sperm fertilization capacity. The molecular and physiological mechanisms behind sperm storage tubule differentiation, sperm protection, and regression remain largely unknown, but most likely have potential implications for substantially improving hen fertility, sperm storage, and semen cryopreservation in commercial poultry species. RNA sequencing was performed on sperm storage tubules isolated from the epithelium of the uterovaginal junction (UVJ) from hens at d 1, 7, 30, 60, and 90 postinsemination (n = 4 per timepoint). Read mapping and differential expression analysis were performed using CLC Genomics Workbench. A total of 2,340 differentially expressed genes were subjected to pathway analysis through Ingenuity Pathway Analysis (IPA). Through functional annotation of differentially expressed genes during early, peak, and late egg production, novel insights regarding the role of innate and acquired immune response to sperm, lipid synthesis and transfer, steroid hormone signalling, cytoskeletal reorganization, and regulation of ion homeostasis in SST were obtained. Additionally, potential pathways were identified that could be involved with suppressing sperm motility while sperm reside within the SST. Upstream analysis identified potential regulatory roles for 18 upstream regulators that could modulate sperm storage tubule function, including suppression of sperm motility. Understanding sperm storage tubule function throughout the laying cycle, especially with regards to sperm preservation may allow for the development of industry-based protocols for semen storage and cryopreservation that mimic the sperm preservation capabilities of SST and improve fertility.

Performance and processing yield comparisons of Large White male turkeys by genetic lines, sources, and seasonal rearing.

Large White male turkey genetic lines (GL) comparison in performance and processing yields under the same conditions are rare in the literature. Two rearing experiments (EXP) were conducted to accomplish 2 objectives. The first objective was to test the effects of poult source and genetic lines on performance and processing yields. The second objective was to extract season and growth patterns when comparing both EXP common treatments. In EXP 1, male poults from 5 different sources were randomly assigned to 48 concrete: litter-covered floor pens. In EXP 2, male poults from 7 different genetic lines were randomly assigned to 48 concrete: litter-covered floor pens. For both EXP, the experimental design was a completely randomized block design with a one-factor arrangement. Both EXP were placed in the same house with the same management and nutrition in two separate seasons of the same year. Bird performance and carcass processing yield were analyzed in SAS 9.4 or JMP 15.1 in a mixed model. In EXP 1 no significant difference in BW or processing yield was observed. However, a similar GL from a commercial hatchery had an improved feed conversion ratio (FCR) over the same GL sourced directly from the genetic company hatchery. In EXP 2, statistical differences were observed in performance and breast meat yield depending on the GL. A season effect was observed when comparing the two EXP. Birds raised in the fall season had a 2 kg BW increase, on average, over their spring counterparts. This difference in BW can also be observed in a statistically higher breast meat yield by the birds raised in the fall over the ones raised in the spring. In conclusion, a comparison between GL resulted in effects due to genetic line, poult source, and rearing season on bird performance and carcass yield.

Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo).

Pendulous crop (PC) in the turkey occurs when the crop distends from its normal position, thereby preventing the movement of feed and water from the crop down into the digestive system. This condition negatively impacts the turkey industry at both production and welfare levels. In this study, we estimated the genetic parameters for PC incidence and its genetic correlation with 5 production traits. Additionally, we evaluated the prediction accuracy and bias of breeding values for the selection candidates using pedigree (BLUP) or pedigree-genomic (ssGBLUP) relationships among the animals. A total of 245,783 turkey records were made available by Hybrid Turkeys, Kitchener, Canada. Of these, 6,545 were affected with PC. In addition, the data included 9,634 records for breast meat yield (BMY); 5,592 records for feed conversion ratio (FCR) and residual feed intake (RFI) in males; 170,844 records for body weight (BW) and walking score (WS) between 18 and 20 wk of age for males (71,012) and females (99,832), respectively. Among this population, 36,830 were genotyped using a 65K SNP Illumina Inc. chip. While all animals passed the quality control criteria, only 53,455 SNP markers were retained for subsequent analysis. Heritability for PC was estimated at 0.16 ± 0.00 and 0.17 ± 0.00 using BLUP and ssGBLUP, respectively. The incidence of PC was not genetically correlated with WS or FCR. Low unfavourable genetic correlations with BW (0.12 and 0.14), BMY (0.24 and 0.24) and RFI (-0.33 and -0.28) were obtained using BLUP and ssGBLUP, respectively. Using ssGBLUP showed higher prediction accuracy (0.51) for the breeding values for the selection candidates than the pedigree-based model (0.35). Whereas the bias of the prediction was slightly reduced with ssGBLUP (0.33 ± 0.05) than BLUP (0.30 ± 0.08), both models showed a regression coefficient lower than one, indicating inflation in the predictions. The results of this study suggest that PC is a heritable trait and selection for lower PC incidence rates is feasible. Although further investigation is necessary, selection for BW, BMY, and RFI may increase PC incidence. Incorporating genomic information would lead to higher accuracy in predicting the genetic merit for selection candidates.

Transcriptome and Proteome Analysis Revealed Key Pathways Regulating Final Stage of Oocyte Maturation of the Turkey (Meleagris gallopavo).

In birds, the zona pellucida (ZP) matrix that surrounds the ovulated oocyte-called the inner perivitelline layer-is involved in sperm-zona interaction and successful fertilization. To identify the important genes and proteins connected with the final step of egg development, next-generation sequencing and two-dimensional electrophoresis, combined with mass spectrometry, were used for the analysis of mature oocytes at the F1 developmental stage. A total of 8161 genes and 228 proteins were annotated. Six subfamilies of genes, with codes ZP, ZP1-4, ZPD, and ZPAX, were identified, with the dominant expression of ZPD. The main expression site for ZP1 was the liver; however, granulosa cells may also participate in local ZP1 secretion. A ubiquitination system was identified in mature oocytes, where ZP1 was found to be the main ubiquitinated protein. Analysis of transcripts classified in estrogen receptor (ESR) signaling indicated the presence of ESR1 and ESR2, as well as a set of estrogen-dependent genes involved in both genomic and nongenomic mechanisms for the regulation of gene expression by estrogen. Oxidative phosphorylation was found to be a possible source of adenosine triphosphate, and the nuclear factor erythroid 2-related factor 2 signaling pathway could be involved in the response against oxidative stress. Oocyte-granulosa cell communication by tight, adherens, and gap junctions seems to be essential for the final step of oocyte maturation.

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds.

Italian autochthonous turkey breeds are an important reservoir of genetic biodiversity that should be maintained with an in vivo approach. The aim of this study, part of the TuBAvI national project on biodiversity, was to use run of homozygosity (ROH), together with others statistical approaches (e.g., Wright's F-statistics, principal component analysis, ADMIXTURE analysis), to investigate the genomic diversity in several heritage turkey breeds. We performed a genome-wide characterization of ROH-rich regions in seven autochthonous turkey breeds, i.e., Brianzolo (Brzl), Bronzato Comune Italiano (BrCI), Bronzato dei Colli Euganei (CoEu), Parma e Piacenza (PrPc), Nero d'Italia (NeIt), Ermellinato di Rovigo (ErRo) and Romagnolo (Roma). ROHs were detected based on a 650K SNP genotyping. ROH_islands were identified as homozygous ROH regions shared by at least 75% of birds (within breed). Annotation of genes was performed with DAVID. The admixture analyses revealed that six breeds are unique populations while the Roma breed consists in an admixture of founder populations. Effective population size estimated on genomic data shows a numeric contraction. ROH_islands harbour genes that may be interesting for target selection in commercial populations also. Among them the PTGS2 and PLA2G4A genes on chr10 were related to reproduction efficiency. This is the first study mapping genetic variation in autochthonous turkey populations. Breeds were genetically different among them, with the Roma breed proving to be a mixture of the other breeds. The ROH_islands identified harboured genes peculiar to the selection that occurred in heritage breeds. Finally, this study releases previously undisclosed information on existing genetic variation in the turkey species.