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Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. We used new data from 73 WGS samples (12X) representing five turkey populations, together with previous data from 107 birds genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array from 11 populations. The PCA and Admixture show a relatively strong isolation effect between the populations. Moreover, the values of genomic inbreeding based on ROH (FROH) showed marked differences among populations and ranged from 0.096 to 0.643. Selective sweeps were identified using the integrated haplotype score (iHS) within the local group, the commercial line, and the Narragansett breed, resulting in the identification of 20, 19, and 27 regions with a total of 73, 48, and 90 candidate genes, respectively. Some of these genes such as FAM107B, MSTN, PDZRN4, HSF2 and GJA1 are associated with heat stress, growth, and carcass traits. We conclude that our results improve our understanding of the genomic architecture of the Italian turkey populations. The findings of iHS suggest that selection can play a significant role in shaping selection signatures in local turkey populations and could provide a basis for identifying gene mutations that may be beneficial in adaptation to climate change. Our results will be useful in developing and implementing conservation and selection plans for Italian turkey populations.

The determination of copy number variation (CNV) is very important for the evaluation of genomic traits in several species because they are a major source for the genetic variation, influencing gene expression, phenotypic variation, adaptation and the development of diseases. The aim of this study was to obtain a CNV genome map using the Illumina Bovine SNP50 BeadChip data of 651 bulls of the Italian Brown Swiss breed. PennCNV and SVS7 (Golden Helix) software were used for the detection of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified with PennCNV and SVS7 software, respectively. These were grouped at the population level into 1101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVR. Ten of the selected CNVR were experimentally validated with a qPCR experiment. The GO and pathway analyses were conducted and they identified genes (false discovery rate corrected) in the CNVR related to biological processes cellular component, molecular function and metabolic pathways. Among those, we found the FCGR2B, PPARα, KATNAL1, DNAJC15, PTK2, TG, STAT family, NPM1, GATA2, LMF1, ECHS1 genes, already known in literature because of their association with various traits in cattle. Although there is variability in the CNVRs detection across methods and platforms, this study allowed the identification of CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones, thus producing new knowledge for association studies with traits of interest in cattle.

The aim of this work was to study the feasibility of the Food and Agriculture Organization (FAO) microsatellite panel developed for chickens to assess genetic variability in turkeys. Genomic DNA was extracted from a total of 37 blood samples collected from turkey of different breeds [15 Brianzolo (BR); 12 Colli Euganei (EU); 10 Nero d’Italia (NI)], and all 31 chicken microsatellite markers recommended by the FAO were tested. The results show that 22 chicken markers out of 31 suggested by FAO guidelines can be applied to turkey populations. In particular, the multiplex groups confirmed in the turkey were the Multiplex Master Mix 1 (ADL0268, ADL0278, LEI0094, MCW0216, MCW0248) and the Master Mix 2 (MCW0034, MCW0069, MCW0081, MCW0222, MCW0295), whereas 13 microsatellites were amplified only under single polymerase chain reaction (PCR) conditions. No PCR products were obtained for 9 markers (LEI0166, MCW0020, MCW0078, MCW0080, MCW0104, MCW0123, MCW0248, MCW0284 and MCW0330), which is 29% of the total markers used. A panel of 22 markers was used to assess genetic diversity in three turkey breeds and a total number of 63 alleles were found. Observed (Ho) and expected (He) heterozygosity and polymorphism information content (PIC) values for each microsatellite and the relative mean values were also calculated. The mean values were 0.210, 0.250, 0.203 for Ho; 0.301, 0.348, 0.228 for He; and 0.265, 0.313, 0.199 for PIC in NI, BR and EU, respectively.