Sequence-Based Multi Ancestry Association Study Reveals the Polygenic Architecture of Varroa destructor Resistance in the Honeybee Apis mellifera.

Honeybees, Apis mellifera, have experienced the full impacts of globalisation, including the recent invasion by the parasitic mite Varroa destructor, now one of the main causes of colony losses worldwide. The strong selection pressure it exerts has led some colonies to develop defence strategies conferring some degree of resistance to the parasite. Assuming these traits are partly heritable, selective breeding of naturally resistant bees could be a sustainable strategy for fighting infestations.

Avenues towards reconciling wild and managed bee proponents.

Bees are crucial for food security and biodiversity. However, managed bees are increasingly considered drivers of wild bee declines, leading to stakeholder conflicts and restrictive policies. We propose avenues to reconcile wild and managed bee proponents and point out knowledge gaps that hinder the development of evidence-based policies.

Shape and joint angle data for seven European horse breeds and their repeatability.

Conformation traits are important in the selection and distinction between horse breeds, but tend to be evaluated subjectively within a breed and cannot be compared between them. The horse shape space model, using a combination of 253 landmarks and semi-landmarks, provides objective information on the shape of a horse photographed from the side that can be compared between breeds. In this dataset, we are providing the full set of 253 landmarks for 1241 horses from seven breeds, including an R code file to extract joint angle information and transform the raw data into csv files for further analysis, such as breed comparisons, heritability or genome-wide association studies (single- or multibreed).

Inertial sensor data of horses from four breeds at walk and trot in hand on a straight line.

Horses have been used and bred for centuries for their movements. However, specific breeds are expected to have different movement capabilities. We have measured 425 horses from four different breeds at walk and trot on a straight line using an inertial measurement unit (IMU) system (EquiMoves®).

Increased heterozygosity in low-pass sequencing data allows identification of blood chimeras in cattle.

In about 90% of multiple pregnancies in cattle, shared blood circulation between fetuses leads to genetic chimerism in peripheral blood and can reduce reproductive performance in heterosexual co-twins. However, the early detection of heterosexual chimeras requires specialized tests. Here, we used low-pass sequencing data with a median coverage of 0.

New genomic insights into the conformation of Lipizzan horses.

Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses.

Identification of runs of homozygosity in Western honey bees () using whole-genome sequencing data.

Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole-genome queen genotypes, from a pool-seq data experiment including 265 Western honeybee colonies from and .

Determining Objective Parameters to Assess Gait Quality in Franches-Montagnes Horses for Ground Coverage and Over-Tracking - Part 2: At Trot.

In gait quality assessments of horses, stride length (SL) is visually associated with spectacular movements of the front limbs, and described as ground coverage, while the movement of the hind limb under the body is supposedly essential to a longer over-tracking distance (OTD). To identify movement patterns with strong associations to SL and OTD, limb and body kinematics of 24 Franches-Montagnes (FM) stallions were measured with 3D optical motion capture (OMC) on a treadmill during an incremental speed test at trot (3.3-6.

Estimates of Genetic Parameters for Shape Space Data in Franches-Montagnes Horses.

Conformation traits such as joint angles are important selection criteria in equine breeding, but mainly consist of subjective evaluation scores given by breeding judges, showing limited variation. The horse shape space model extracts shape data from 246 landmarks (LM) and objective joint angle measurements from triplets of LM on standardized horse photographs. The heritability was estimated for 10 joint angles (seven were measured twice with different LM placements), and relative warp components of the whole shape, in 608 Franches-Montagnes (FM) horses (480 stallions, 68 mares and 60 geldings born 1940-2018, 3-25 years old).

Determining Objective Parameters to Assess Gait Quality in Franches-Montagnes Horses for Ground Coverage and Over-Tracking - Part 1: At Walk.

Ground coverage and over-tracking are two gait quality traits describing the forward movement of the front respectively the hind limbs in relation to stride length and over-tracking distance. To investigate the complex interplay of different movement patterns in ground coverage and over-tracking, limb and body kinematics of 24 Franches-Montagnes (FM) stallions were measured with 3D optical motion capture (OMC) on a treadmill during an incremental speed test at the walk (1.4-2.

Gait quality scoring data of Franches-Montagnes stallions at walk and trot on a treadmill by experts of the breed and their reliability.

This article presents the data obtained from the scoring of 24 stallions of the Franches-Montagnes (FM) horse breed by six experts of this breed. The experts scored six traits at walk and eight at trot from the video recordings of these stallions walking and trotting on a treadmill during an incremental speed test. The scores were given on a scale of one to nine.

Two quantitative trait loci are associated with recapping of Varroa destructor-infested brood cells in Apis mellifera mellifera.

Recapping of Varroa destructor-infested brood cells is a trait that has recently attracted interest in honey bee breeding to select mite-resistant Apis mellifera colonies. To investigate the genetic architecture of this trait, we evaluated a sample of A. mellifera mellifera colonies (N = 155) from Switzerland and France and performed a genome-wide association study, using a pool of 500 workers per colony for next-generation sequencing.

A Novel QTL and a Candidate Gene Are Associated with the Progressive Motility of Franches-Montagnes Stallion Spermatozoa after Thaw.

The use of frozen-thawed semen is an important reproduction tool to preserve the biodiversity of small, native horse breeds such as the Franches-Montagnes (FM). However, not all stallions produce cryotolerant semen with a progressive motility after thaw ≥ 35%. To improve our understanding of the genetic background of male fertility traits in both fresh and frozen-thawed semen, we performed genome-wide association studies (GWAS) on gel-free volume, sperm cell concentration, total sperm count, and progressive motility in fresh and frozen-thawed semen from 109 FM stallions using 335,494 genome-wide single nucleotide polymorphisms (SNPs).

Identification of quantitative trait loci associated with calmness and gentleness in honey bees using whole-genome sequences.

The identification of quantitative trait loci (QTL) through genome-wide association studies (GWAS) is a powerful method for unravelling the genetic background of selected traits and improving early-stage predictions. In honey bees (Apis mellifera), past genetic analyses have particularly focused on individual queens and workers. In this study, we used pooled whole-genome sequences to ascertain the genetic variation of the entire colony.

Exploring Two Honey Bee Traits for Improving Resistance Against : Development and Genetic Evaluation.

For the development of novel selection traits in honey bees, applicability under field conditions is crucial. We thus evaluated two novel traits intended to provide resistance against the ectoparasitic mite and to allow for their straightforward implementation in honey bee selection. These traits are new field estimates of already-described colony traits: brood recapping rate ('') and solidness ('').

Advances and perspectives in selecting resistance traits against the parasitic mite Varroa destructor in honey bees.

Background: In spite of the implementation of control strategies in honey bee (Apis mellifera) keeping, the invasive parasitic mite Varroa destructor remains one of the main causes of colony losses in numerous countries. Therefore, this parasite represents a serious threat to beekeeping and agro-ecosystems that benefit from the pollination services provided by honey bees. To maintain their stocks, beekeepers have to treat their colonies with acaricides every year.

A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color.

The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3).

Should We Agree to Disagree? An Evaluation of the Inter-Rater Reliability of Gait Quality Traits in Franches-Montagnes Stallions.

Gait quality, that is, the way horses move according to functional and aesthetic principles, englobes many traits that are scored by experts during breeding competitions. The experts can score a trait on a subjective valuating (SV) scale or on a linear profiling (LP) scale representing the biological extremes of the population. However, the reliability of the appraisal of gait quality traits has not been extensively evaluated.

Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds.

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated.

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size.

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses.

Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses.

The evaluation of conformation traits is an important part of selection for breeding stallions and mares. Some of these judged conformation traits involve joint angles that are associated with performance, health, and longevity. To improve our understanding of the genetic background of joint angles in horses, we have objectively measured the angles of the poll, elbow, carpal, fetlock (front and hind), hip, stifle, and hock joints based on one photograph of each of the 300 Franches-Montagnes (FM) and 224 Lipizzan (LIP) horses.