Copy Number Variants (CNV) are modifications affecting the genome sequence of DNA, for instance, they can be duplications or deletions of a considerable number of base pairs (i.e., greater than 1000 ...bp and up to millions of bp). Their impact on the variation of the phenotypic traits has been widely demonstrated. In addition, CNVs are a class of markers useful to identify the genetic biodiversity among populations related to adaptation to the environment. The aim of this study was to detect CNVs in more than four thousand Holstein cows, using information derived by a genotyping done with the GGP (GeneSeek Genomic Profiler) bovine 100K SNP chip. To detect CNV the SVS 8.9 software was used, then CNV regions (CNVRs) were detected. A total of 123,814 CNVs (4,150 non redundant) were called and aggregated into 1,397 CNVRs. The PCA results obtained using the CNVs information, showed that there is some variability among animals. For many genes annotated within the CNVRs, the role in immune response is well known, as well as their association with important and economic traits object of selection in Holstein, such as milk production and quality, udder conformation and body morphology. Comparison with reference revealed unique CNVRs of the Holstein breed, and others in common with Jersey and Brown. The information regarding CNVs represents a valuable resource to understand how this class of markers may improve the accuracy in prediction of genomic value, nowadays solely based on SNPs markers.
Abstract Scrapie is a transmissible spongiform encephalopathy affecting sheep and goats. The prion protein-encoding gene ( PRNP ) plays a crucial role in determining susceptibility and resistance to ...scrapie. At the European level, surveillance of scrapie is essential to prevent the spread of the disease to livestock. According to the Regulation EU 2020/772 polymorphisms K222, D/S146 could function as resistance alleles in the genetic management of disease prevention. In Italy, a breeding plan for scrapie eradication has not been implemented for goats. However, surveillance plans based on the PRNP genotype have been developed as a preventive measure for scrapie. This research aimed to describe the polymorphisms at 7 positions within the PRNP gene in 956 goats of the Alpine, Saanen and mixed populations farmed in the Lombardy Region in Italy. PRNP polymorphisms were detected using single nucleotide polymorphism markers included in the Neogen GGP Goat 70 k chip. The K222 allele occurred in all populations, with frequencies ranging from 2.1 to 12.7%. No animals carried the S/D146 resistance allele. However, it has been demonstrated that polymorphisms in the other positions analysed could influence resistance or susceptibility to scrapie outbreaks in different ways. Ten potentially distinct haplotypes were found, and the most prevalent of the three populations was H2, which differed from the wild type (H1) in terms of mutation (S vs P) at codon 240. This study provided additional information on the genetic variability of the PRNP gene in these populations in the Lombardy region of Italy, contributing to the development of genetic control measures for disease prevention.
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.
In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its ...farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K.
CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database.
This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.
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.
In this study we investigated the genetic variability, the inbreeding and allele frequencies of monogenic traits in seven herds of Holstein breed and provided insight to farmers on the value of ...genomic management of reproduction in their herds. A total of 3,953 Holstein cows were sampled and genotyped with the Neogen GGP Bovine 100K SNP chip within the activities of the Regione Lombardia funded GO-PEI project ‘GENOmic tool for the management of reproduction in dairy cattle and for the control of inbreeding – GENORIP’. Principal component analysis was applied for analysing the genetic variability within and among farms using the SVS software of Golden Helix. Run of Homozygosity (ROH) and the genomic inbreeding were obtained with the detectRUNS package of the R software. Genotype frequencies for mendelian disease, fertility and production traits were also obtained. A total of 458,267 ROH were identified and ROH were distributed on all autosomes with an average length of 2,703,811 bp covering 12.7% of the genome. Several genomic regions appear under selection, while a specific region on BTA4 was identified in one herd, harbouring genes mainly related to the specific selection strategy of the farmer. The FROH values obtained considering ROH greater than 16 Mb, varied from 0.004 to 0.325, with the highest FROH average value of 0.136. Among mendelian heritable diseases, the Haplotype Cholesterol Deficiency was the one with the largest proportion of carrier animals, i.e. 5.6%. A herd-tailored process to assist farmers in genomic management of reproduction was released. The ROH distribution within herd, together with the genotype frequencies for disease, fertility and production mendelian traits, suggest that similar directional selection is occurring across herds. This study released to each farmer the genomic make-up of their herd used jointly with the gEBV estimated by their national breeders’ association (ANAFIBJ) for herd reproductive management.
Mastitis is one of the most significant diseases affecting dairy cattle profitability. A genome wide association study (GWAS) was performed using the selective genotyping approach to identify ...Quantitative Trait Loci (QTL) associated with mastitis susceptibility. According to the received antibiotic treatments in all their productive life, 52 lactating cows have been classified in resistant (no therapy and low SCC) and susceptible (more than one treatment and high SCC) to mastitis. Genotyping of animals was performed using the NEOGEN's GGP Bovine 100K SNP chip and QTL were identified comparing the SNPs allelic frequencies between the two groups. 26 SNPs related to mastitis susceptibility were identified in 9 chromosomes. The use of treatment data, coupled with SCC from milk recording, improved cow's classification accuracy in resistant and susceptible individuals. For this reason, the mandatory recording of treatments active from January 2022, could be a new source of information to improve the genetic selection for mastitis resistance.
Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and ...positions around the animal’s trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world’s animals.
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
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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.
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs ...often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.
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