An increased understanding of the turkey sector and how farmers manage flocks can help maintain and improve the health and welfare of turkeys. We conducted a cross-sectional survey among turkey farmers in Canada to gain information regarding general farm characteristics, housing aspects (incl. lighting, ventilation), litter management, feed and water management, flock characteristics, and flock health management. The survey was distributed to 500 farmers through the Turkey Farmers of Canada in April–December 2019. A total of 83 final responses (response rate approx. 20%) were used for a descriptive analysis to determine the frequency of housing and management practices (77 commercial flocks, 6 breeder flocks). Hen flocks (n = 53) had a median age of eight weeks (IQR: 7–12 weeks) and tom flocks (n = 30) had a median age of 12 weeks (IQR: 9–14 weeks). Turkey flocks within Canada are typically kept in indoor barn systems on a concrete floor (87.5%), with bedding (e.g., straw, wood shavings) provided (100%). The majority followed a brood and move growing system (68.8%), and a large proportion of farmers indicated that they raised turkeys under the ‘Raised Without Antibiotics/Antibiotic Free’ or the ‘Responsible Use of Antibiotics’ certification (70.5%). Possible room for improvement could be found in terms of litter management and biosecurity practices, however, further research is needed to make clear recommendations.

The detrimental effects of increased homozygosity due to inbreeding have prompted the development of methods to reduce inbreeding. The detection of runs of homozygosity ( ROH ), or contiguous stretches of homozygous marker genotypes, can be used to describe and quantify the level of inbreeding in an individual. The estimation of inbreeding coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of pedigree-based inbreeding coefficients ( F PED ) with genomic-based inbreeding coefficients estimated from ROH ( F ROH ) and the genomic relationship matrix ( F GRM ). A total of 2,616,890 pedigree records were available. Of these records, 6,371 genotyped animals from three purebred turkey ( Meleagris gallopavo ) lines between 2013 and 2019 were available, and these were obtained using a dense single nucleotide polymorphism array (56,452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a mean number of 84.87 ± 8.79 ROH per animal. Short ROH with lengths of 1 to 2 Mb long were the most abundant throughout the genome. Mean ROH coverage differed greatly between chromosomes and lines. Considering inbreeding coefficient means across all lines, genomic derived inbreeding coefficients (F ROH = 0.27; F GRM = 0.32) were higher than coefficients estimated from pedigree records (F PED = 0.14). Correlations between F ROH and F PED , F ROH and F GRM , and F PED and F GRM ranged between 0.19 to 0.31, 0.68 to 0.73, and 0.17 to 0.30, respectively. Additionally, correlations between F ROH from different lengths and F PED substantially increased with ROH length from -0.06 to 0.33. Results of the current research, including the distribution of ROH throughout the genome and ROH-derived inbreeding estimates, can provide a more comprehensive description of inbreeding in the turkey genome. This knowledge can be used to evaluate genetic diversity, a requirement for genetic improvement, and develop methods to minimize inbreeding in turkey breeding programs.

Runs of homozygosity (ROH) are continuous stretches of homozygous genotypes in an individual that have been passed down from a common ancestor and can be used to accurately characterize genomic data. These ROH are correlated with other measures of inbreeding and have been applied to quantify individual autozygosity. The aim of this study was to detect and describe ROH in the turkey genome and estimate and compare measures of pedigree-based inbreeding coefficients (FPED) and genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). Pedigree records (n = 2,616,890) and genotypic records (n = 6,371) were available from three purebred turkey (Meleagris gallopavo) lines. Genotypic records were collected between 2013 and 2019 and were obtained using a dense single nucleotide polymorphism array (56,452 SNP). The overall mean length of detected ROH per animal was 2.87±0.29 Mb and mean number of ROH per animal was 84.87±8.79. Short ROH with lengths of 1–2 Mb long were the most abundant throughout the genome, accounting for approximately 45% of the identified segments. Mean ROH coverage differed greatly between chromosomes and lines. Across all lines, genomic derived inbreeding coefficients (FROH=0.27; FGRM=0.32) were higher than coefficients estimated from pedigree records (FPED=0.14). Ranges of correlations between FROH and FPED (0.19–0.31), FROH and FGRM (0.68–0.73), and FPED and FGRM (0.17–0.30) were estimated. Results from the current research provide a fundamental description of inbreeding in the turkey genome which is critical considering the growing concerns of the detrimental effects of increased inbreeding on fitness and health in livestock production. The knowledge gained from this study may subsequently be used to evaluate and maintain genetic diversity that is necessary for genetic improvement and minimizing inbreeding in turkey breeding programs.