Mitochondrial D-loop sequence variation among Italian horse breeds

The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano) was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits

Genome-wide association studies using copy number variants in Brown Swiss Dairy cattle.

Detecting Copy Number Variation (CNV) in cattle provides the opportunity to study their association with quantitative traits (Winchester et al., 2009; Zhang et al., 2009; Hou et al., 2011; Clop et al., 2012; de Almeida et al., 2016;). The aim of this study was to map CNVs in 1,410 Brown Swiss males and females using Illumina BovineHD Genotyping BeadChip data and to perform a genome-wide association analysis for production functional and health traits. After quality control, CNVs were called with the GoldenHelix SVS 8.3.1 and PennCNV software and were summarized to CNV regions (CNVRs) at a population level, using BEDTools. Additionally, common CNVRs between the two software were set as consensus. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7.The quality control filtered out 294 samples. The GoldenHelix SVS 8.3.1 software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 127 CNVRs were identified to be significantly associated with one or more of the evaluated traits. The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for quantitative traits considered in selection programs of the Brown Swiss breed

A high-resolution CNV map across Brown Swiss cattle populations.

Genomic studies and their use in selection programs are having a strong impact in dairy cattle selection (E. Liu et al., 2010). The first aim was to create a high resolution map of CNV regions (CNVRs) in Brown Swiss cattle and the characterization of identified CNVs as markers for quantitative and population genetic studies. CNVs were called in a set of 164 sires with PennCNV and genoCN. PennCNV identified 2,377 CNVRs comprising 1,162 and 1,131 gain and loss events, respectively, and 84 regions of complex nature. GenoCN detected 41,519 CNVRs comprising 3,475 and 34,485 gain and loss events, respectively, and 3,559 regions of complex ones. Consensus calls between algorithms were summarized to CNVRs at the population level. GenoCN was also used to identify total allelic content in consensus CNVRs. Moreover, population haplotype frequencies were calculated. Linkage disequilibrium (LD) was established between CNVs and SNPs in and around CNVRs. In this study the potential contribution of CNVs as genetic markers for genome wide association studies (GWAS) has been assessed thanks to PIC and LD values. The next aim is to investigate genomic structural variation in cattle using dense SNP information in more than 1000 samples of the Italian and Swiss Brown Swiss breed genotyped on HD Bovine BeadChips. Today there is still no CNV map available across Brown Swiss populations belonging to different countries. This study therefore expands the catalogue of CNVRs in the bovine genome, delivers an international based high-resolution map of CNVRs specific to Brown Swiss dairy cattle and will lastly provide information for GEBV estimation with CNVs

Genomic variability in Mexican chicken population using Copy Number Variation

Copy number variants (CNVs) are polymorphisms which influence phenotypic variation and are an important source of genetic variability [1]. In Mexico the backyard poultry population is a unique widespread Creole chicken (Gallus gallus domesticus) population, an undefined cross among different breeds brought to Mexico from Europe and under natural selection for almost 500 years [2-3]. The aim of this study was to investigate genomic variation in the Mexican chicken population using CNVs.A total of 256 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array were used in the analyses. The individual CNV calling, based on log-R ratio and B-allele frequency values, was performed using the Hidden Markov Model (HMM) of PennCNV software on the autosomes [4-5]. CNVs were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools.The HMM detected a total of 1924 CNVs in the genome of 256 samples resulting, at population level, in 1216 CNV regions, of which 959 gains, 226 losses and 31 complex CNVRs (i.e. containing both losses and gains), covering a total of 47 Mb of sequence length corresponding to 5,12 % of the chicken galGal4 assembly autosome. A comparison among this study and 7 previous reports about CNVs in chicken was performed, finding that the 1,216 CNVRs detected in this study overlap with 617 regions (51%) mapped by others studies. This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been never genetically characterized with SNP markers. Based on a cluster analysis (pvclust – R package) on CNV markers the population, even if presenting extreme morphological variation, does not resulted divided in differentiated genetic subpopulations. Finally this study provides a CNV map based on the 600K SNP chip array jointly with a genome-wide gene copy number estimates in Mexican chicken population.

Association Between BoLA-DRB3.2 Polymorphism and Bovine Papillomavirus Infection for Bladder Tumor Risk in Podolica Cattle

Blood samples from 260 unrelated cattle (132 animals affected by papillomavirus-associated bladder tumors and 128 healthy) were genotyped using the classic polymerase chain reaction/restriction fragment length polymorphism method to screen MHC class II bovine leukocyte antigen-DRB3. 2 polymorphism. The DRB3*22 allele was significantly (p ≤ 0.01) detected in healthy cattle, thus appearing to have a negative association (protective effect) with virus infection of the urinary bladder known to represent a bladder tumor risk for cattle living free at pasture. Considering the two sequence alleles identified in animals carrying DRB3*22, DRB3*011:01 allele from samples of animals harboring the unexpressed bovine papillomaviruses (BPV)-2 E5 gene was characterized by amino acid residues believed to have a protective effect against BPV infection such as arginine at position 71 (R71) in pocket 4, histidine at position 11 (H11) in pocket 6, and both glutamine at position 9 (Q9) and serine at position 57 (S57) in pocket 9 of the antigen-binding groove. The DRB3*011:02v allele from affected animals was characterized by amino acids believed to be susceptibility residues such as lysine (K71), tyrosine (Y11), glutamic acid (E9), and aspartic acid (D57) in these pockets. These results suggest that animals harboring the DRB3*011:01 allele may have a lower risk of BPV infection and, consequently, a reduced risk of bladder tumors

Genetic parameters of fatty acids in Italian Brown Swiss and Holstein cows

The aim of this study was to estimate the genetic parameters and to predict experimental breeding values (EBVs) for saturated (SFA), unsaturated (UFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids, the ratio of fatty acids, and the productive traits in Italian Brown Swiss (BSW) and Holstein Friesian (HOL) cattle. Test-day yields from 235,658 HOL and 21,723 BSW cows were extracted from the Italian HOL and BSW Associations databases from November 2009 to October 2012 out of 3310 herds. The milk samples collected within the routine milk recording scheme were processed with the MilkoscanTM FT 6500 Plus (Foss, Hillerød, Denmark) for the identification of SFA, UFA, MUFA and PUFA composition in milk. Genetic parameters for fatty acids and productive traits were estimated on 1,765,552 records in HOL and 255,592 records in BSW. Heritability values estimated for SFA, UFA, MUFA and PUFA ranged from 0.06 to 0.18 for the BSW breed and from 0.10 to 0.29 for HOL. The genetic trends for the fatty acids were consistent between traits and breeds. Pearson's and Spearman's correlations among EBVs for SFA, UFA, MUFA and PUFA and official EBVs for fat percentage were in the range 0.32 to 0.54 for BSW and 0.44 to 0.64 for HOL. The prediction of specific EBVs for milk fatty acids and for the ratio among them may be useful to identify the best bulls to be selected with the aim to improve milk quality in terms of fat content and fatty acid ratios, achieving healthier dairy productions for consumers

Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection

The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and FROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (FST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and FROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population

Morphological Characterization of Two Light Italian Turkey Breeds

We aimed to investigate the variability within turkeys’ phenotypical traits in two Italian heritage breeds: Brianzolo (BRZ) and Nero d’Italia (NIT), as analyzed through morphometry, morphometrical indexes, linear scoring, and colorimetric indexes. A total of 92 birds were measured, weighed, and scored (46 NIT: M/F = 19/27; 46 BRZ: M/F = 19/27). Live weight (LW), total body length (BL, excluding feathers), keel length (KL), chest circumference (BC), wingspan (WS), shank length (SL), shank diameter (SD), and shank circumference (SC). Massiveness (MASS), stockiness (STOCK), and long-leggedness (LLEG) indexes were also calculated. The body condition score (BCS) applied a linear evaluation to nutritional status and muscular development. Colorimetric indexes (L*, a*, b*) were recorded, sampling skin and shank. Data were analyzed using GLM procedures and PCA. NIT was the heaviest breed (4.89 vs. 4.07 kg; p ≤ 0.05). In both breeds, sexual dimorphism was visible in the LW trait with males (M) weighing significantly heavier than females (F) (p ≤ 0.05). NIT birds recorded the highest BL values: 58.44 vs. 57.15 cm (p ≤ 0.05). MASS was higher in NIT (8.26 vs. 7.0; p ≤ 0.05), and STOCK was higher in BRZ (82.62 vs. 85.37; p ≤ 0.05). Colorimetric indexes revealed significant differences in skin lightness (L*) and redness (a*). For shank color, the breed significantly affected differences in the indexes. This study characterizes these breeds at high risk of genetic erosion and extinction, which will help the morphological standardization of birds and the enhancement of genetic variability

Breeders management and reproductive traits in three heritage rabbit (Oryctolagus cuniculus) breeds: a preliminary study

The aim of the present research is to investigate breeders’ management strategies and their effects on reproductive performances in heritage breeds. A total of 468 litters were analysed: Belgian Hare (N = 151), Burgundy Fawn (N = 105), Californian (N = 212). Litter size (born alive), percentage of weaned kits and percentage of selected kits were analysed using a model that included the effects of breed, year of birth, litter’s origin (with three levels: both internal parents = 0, one outside parent = 1 both outside parents = 2) and their interactions (breed*year of birth, breed*litter’s origin, year of birth*litter’s origin, breed*year of birth*litter’s origin). Besides, number of litters per buck and number of litters per doe were analysed using a model with only effect of breed. All these analyses were carried out with SPSS software. No effects of breeds on litter size, percentage of weaned and percentage of selected kits were found. Year of birth presented significant effects on litter size and percentage of weaned kits (p ≤ 0.05). The inclusion of external breeders didn’t significantly influence analysed reproductive data. The number of litters per buck and per doe were not influenced by breed. The frequency of external breeders’ inclusion is breed specific. Data recording is a basic step in phenotypical characterization, our results supply some information about breeders’ management strategies and their effects on some reproductive parameters. Our results show breed specific frequencies of inclusions of external breeders and a positive effect of management procedures (genetic plus environment) on percentage of weaned kits according to the year of birth.HIGHLIGHTS Breeders management and reproductive parameters have been described The most frequent combination is a home bred doe mated to an external male A mean of 2 litters per doe and per buck have calculated in all the breeds The frequency of use of external breeders is breed specifi