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Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed

Objective Braque Français, type Pyrénées is a French hunting-dog breed whose origin is traced back to old pointing gun-dogs used to assist hunters in finding and retrieving game. This breed is popular in France, but seldom seen elsewhere. Despite the ancient background, the literature on its genetic characterization is surprisingly scarce. A recent study looked into the...

The use of genetic markers to estimate relationships between dogs in the course of criminal investigations

Objective Attacks on humans by dogs in a pack, though uncommon, do happen, and result in severe, sometimes fatal, injuries. We describe the role that canine genetic markers played during the investigation of a fatal dog-pack attack involving a 50-year-old male truck driver in a parking lot in Tuscany (Italy). Using canine specific STR genetic markers, the local authorities, in...

The effect of mislabeled phenotypic status on the identification of mutation-carriers from SNP genotypes in dairy cattle

Background Statistical and machine learning applications are increasingly popular in animal breeding and genetics, especially to compute genomic predictions for phenotypes of interest. Noise (errors) in the data may have a negative impact on the accuracy of predictions. The effects of noisy data have been investigated in genome-wide association studies for case–control...

Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations

Background SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific mutations. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we compared – through cross...

A new polymorphism on chromosome 6 associated with bolting tendency in sugar beet

Background Premature flowering or bolting is an undesirable characteristic that causes severe sugar yield losses and interferes with harvesting. Vernalization is a prerequisite for the floral induction, achieved by exposure to low temperatures for 10–14 weeks. This process is also controlled by other environmental factors, such as long daylight photoperiods and a combination of...

Genome-enabled predictions for binomial traits in sugar beet populations

Background Genomic information can be used to predict not only continuous but also categorical (e.g. binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait of agronomic importance. In this paper, a panel of 192 SNPs...

Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis

Stefano Biffani 0 Corrado Dimauro Nicol Macciotta Attilio Rossoni Alessandra Stella 0 Filippo Biscarini 0 0 Department of Bioinformatics , PTP, Via Einstein - Loc. Cascina Codazza, 26900 Lodi

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

Background In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A...

Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection

Marco Milanesi Riccardo Negrini Giordano Mancini Filippo Biscarini Alessandra Stella Alessio Valentini Paolo Ajmone-Marsan Background: A number of methods are available to scan a genome for selection

Across-line SNP association study for (innate) immune and behavioral traits in laying hens

Background An association study between single nucleotide polymorphism markers (SNP) and (innate and adaptive) immune parameters but also feather condition score on the back, rump and belly of laying hens was performed. The immune parameters measured in blood samples were natural and acquired antibody titers and complement activity. Feather condition score as a measure of feather...