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.

GenoTriplo: A SNP genotype calling method for triploids.

Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo.

APIS: an updated parentage assignment software managing triploids induced from diploid parents.

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents.

Uncertainty in the mating strategy of honeybees causes bias and unreliability in the estimates of genetic parameters.

Background: Breeding queens may be mated with drones that are produced by a single drone-producing queen (DPQ), or a group of sister-DPQs, but often only the dam of the DPQ(s) is reported in the pedigree. Furthermore, datasets may include colony phenotypes from DPQs that were open-mated at different locations, and thus to a heterogeneous drone population.

Methods: Simulation was used to investigate the impact of the mating strategy and its modelling on the estimates of genetic parameters and genetic trends when the DPQs are treated in different ways in the statistical evaluation model.

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss).

Background: Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines.