Genetic variability of Akhal-Teke horses bred in Italy

Background. The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods. Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences ofAKH(56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results. Nucleic markers showed a high degree of polymorphism (Ho D 0.642; He D 0.649) and a low inbreeding level (FIS D 0.016) in Italian horses, compared to other AKH populations (ranged from 0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity () and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy

A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations

Copy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina's 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized

Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus)

Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered

Genomic variability in Mexican chicken population using copy number variants

Background: Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. Results: The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom\uc2\uae Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. Conclusions: 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 genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population

Copy number variation in cattle breeds

Detecting all classes of genetic variation in livestock species, such as cattle, is a pre-requisite to studying their association to traits of interest. Copy Number Variations (CNVs) are classes of polymorphic DNA regions including deletions, duplications and insertions of DNA fragments of at least 0.5 kb to several Mb, that are copy number variable when compared to a reference genome. CNVs can be identified using various approaches, among those the SNP array data are low cost, dense coverage, and high throughput. The aim of this study was to obtain a consensus genome map of Copy Number Variable Regions (CNVRs) in the Brown Swiss (dataset of 192 bulls), Red Pied Valdostana (dataset of 143 bulls) and Finnish Ayrshire (dataset of 243 bulls) cattle breeds all genotyped on the Illumina Bovine HD BeadChip, and two SNP based CNV calling algorithms. Brown Swiss cattle originated in the Swiss Alps, kept as a triple purpose breed. Once imported in the US, it was mainly selected for increased milk production. The Valdostana Red Pied cattle is the most common autochthonous dual purpose breed in the region Valle d\u2019Aosta in Italy (13,000 animals in 2013, almost all of them registered in the Herd Book). The Finnish Ayrshire is the most common cattle in Finland. CNVs were called with the PennCNV and SVS7 software and were summarized to CNVRs at the population level as overlapping CNV calls within breed. PennCNV identified 2,377, 1,723 and 1,689 for the Italian Brown Swiss, the Red Pied Valdostana and the Finnish Ayrshire, respectively. SVS7 detected 370, 235 and 2,063 for the three cattle breeds. These regions were annotated with Ensembl v78 Bos taurus gene set (UMD3.1) and genomic regions harboring QTL for production and functional traits. The comparison among CNVRs here identified provided common regions in the breeds. The results of this study are a comprehensive genomic analysis of cattle CNVs derived from SNP data, which will be a valuable genomic variation resource and will enrich the bovine CNV map in the cattle genome, providing new information for association studies with traits included in the selection programs