Recipient Organization
PENNSYLVANIA STATE UNIVERSITY
208 MUELLER LABORATORY
UNIVERSITY PARK,PA 16802
Performing Department
Entomology
Non Technical Summary
The beekeeping industry is facing serious challenges to maintaining the high numbers of colonies necessary to supply the national demands for crop pollination and honey production. The primary challenge is that posed by pests and pathogens that cause colony-declines nationwide. Among the many pests and pathogens attacking honey bees,Varroamites and a number of viruses (e.g. Deformed Wing Virus, DWV) they vector are among their deadliest enemies. These mites have developed resistance to chemical treatments overtime, leaving beekeepers with very few options to manage this pest and associated diseases. Our recent studies of feral honey bees--surviving colonies that live in wild conditions without miticide treatments--have indicated that, on average, feral colonies have higher DWV pressures but also higher overwintering survival than managed, treated, colonies. Through gene expression studies, we have identified an immunological pathway that, when upregulated, is linked to higher survival in honey bee colonies. Given that immune gene expression in honey bees is highly heritable, these results suggest the presence of genetic variants that may confer tolerance to DWV among honey bee colonies of Pennsylvania. Identifying the genetic basis of this type of immunological trait could facilitate genomic assisted selection of disease tolerant honey bees in the US. The goal of this project is to combine genomic approaches with a strong community science (a.k.a. citizen science) participation to (1) identify the genetic basis of traits associated with disease tolerance, (2) quantify other phenotypes of interest to beekeepers (survival and honey production) from these colonies, and (3) establish queens with these genetics in multiple apiaries across the state. Funds for this project will facilitate the characterization of traits linked to mite resistance and DWV tolerance, and facilitate the implementation of these traits in the apiaries of beekeepers in Pennsylvania. We will develop a methodology that can be implemented regionally and across North America through partnerships between researches and experienced beekeepers. We aim to assist local queen rearing programs to use information from marker-assisted selection for effective breeding of more resilient honey bees.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Goals / Objectives
*Objective 1: Identify genetic variants associated with Varroa mite and DWV tolerance across different honey bee lines.We predict that genes associated with immunological traits that confer tolerance toVarroamite and DWV will show signatures of strong positive selection. This objective will provide critical information about the genetic basis of traits that we have previously found to be associated with tolerance to viruses.*Objective 2: Quantify traits of beekeeping interest (survival and honey production).We will work with 10 beekeepers in Pennsylvania to collect data on phenotypes of the colonies that we will genotype in objective 1. The colonies will be established in different environments across the PA. López-Uribe, Underwood, and Harpur have worked with the beekeepers from the PA Queen Improvement Project for several years on multiple NE-SARE funded projects related to selecting and breeding disease-resistant local stocks. We will work with a select group of beekeepers from this organization to collect high-quality phenotypic data from colonies included in this project. This methodological approach--combining scientists and beekeepers for genotype-phenotype studies--could be applied to other regions of the country.*Objective 3: Graft queens from colonies with desirable tolerance traits and introduce them in apiaries across Pennsylvania.We aim to successfully establish colonies with disease tolerant traits by grafting queens from colonies that have been genotyped and phenotypes in this study. This objective will determine whether these traits can be successfully established in multiple regions across the state where environmental conditions significantly vary.
Project Methods
Objective 1: Identify genetic variants associated with DWV tolerance across Pennsylvania.Sampling design: We will use two types of genetic lines (feral Pennsylvania and Purdue mite biters) and one control (Georgia packages) for our genomic studies. Pennsylvania ferals will be obtained from the honey bee breeder Devon Paderewski who reports overwintering survival of over 80% despite high levels of mites in his colonies. Purdue mite biters will be obtained from Harpur who currently advises on the breeding program at Purdue University. Finally, Georgia colonies will be sourced from several suppliers. These colonies are commonly used as a source of bees among Pennsylvania beekeepers. We will purchase at least 7 queens from each genetic line and establish them in our apiary at University Park (Spring 2021).Sampling protocol: Co-PD Underwood will establish colonies and will sample 50-80 foragers from each colony included in the study (~21 colonies total: 7 feral PA + 7 Purdue biters + 7 Georgia). All individuals will be collected in alcohol in the field to preserve DNA quality.Genome Sequencing: PD López-Uribe and collaborator Harpur will resequence the genomes of the 21 targeted colonies by sampling a total of 50 individuals per colony that will be pooled for full-genome re-sequencing using the Nova-Seq 6000 S4 for 2x150-bp reads. Each sequencing run will yield 80M reads (average of 46X coverage) for each colony included in our study.Selection Scans:The sequencing data generated will allow us to compare allele frequencies between and among the 3 different lines for traits associated with the expression ofHymenoptaecinandAmNrx-1(neurexin:one of the genes over-expressed in the Purdue mite biter line; Morfin et al. 2019). Through the use of comparative genomic scans between colonies, we also aim to identify areas where the genomes of these lines are differentiated (suggesting other regions under positive selection). Each pooled sample will be aligned to the most recent version of the honey bee genome version (Amel_HAv3.1) using BWA (Li and Durbin 2010) and re-aligned around high-complexity regions using STAMPY (Lunter and Goodson 2011). We will then identify high-quality sequence variants within every sample by taking the intersection set of two pooled-sequencing genotypes using CRISP (Bansal 2010), a fast and accurate pooled-sequencing genotype caller (Huang et al. 2015). We can then identify significant differences in allele frequency between each population at high-quality sites across the genome using POPOOLATION2 (Kofler et al. 2011). We will use this genomic information to associate tolerance to disease and honey production that will be characterized in objective 3.Objective 2: Quantify phenotypic traits of beekeeping interest (survival and honey production).Colony establishment:Co-PD Underwood will work with 10 beekeepers in Pennsylvania to establish 7 colonies of each genetic line mentioned in objective 1 in 10 different regions of the state and collect phenotypic data from these colonies.Beekeeping management: We will purchase 70 new queens from each genetic line and establish them in ten apiaries. Each beekeeper will follow a standardized protocol to manage their colonies throughout the 2 years of the experiment. The beekeeping management protocol will include organic management forVarroamites to facilitate the maintenance of the selected tolerance traits as advantageous in these colonies.Data collection:Beekeepers will collect data about 4 traits in these colonies: (1) mite loads using alcohol washes; (2) mite biting behavior; (3) overwintering survival, and (4) pounds of honey produced per colony by weighing colonies before and after honey extraction. The data collected by experienced beekeepers will provide information about phenotype-genotype associations across different environments.Objective 3: Graft queens from colonies with identified traits and establish them in apiaries across Pennsylvania.Grafting protocol: Co-PD Underwood will work with beekeepers to use grafting to produce queens from the colonies that havehighoverwintering survival and honey production results (from objective 1). Grafting is a common method of queen rearing where worker bee larvae from the colony of interest are transferred from cells in the comb into queen cell cups. These cups will be placed in a colony that is in the right condition to convert them into queen cells. Upon emergence, the queens will be open-mated.Establishment of queens in new apiaries: Once the queens reach maturity, we will requeen 10 colonies with genetics from successful colonies per line (as per objectives 1 and 2) and establish these colonies in nearby locations. This process will be implemented in the apiaries of 10 beekeeper participants (for a total of 200 colonies = 10 colonies x 10 beekeepers x 2 lines). As controls, we will use 10 colonies with queens that have unselected genetics. Control and selected colonies will be followed for 1 year (until Spring 2023) to quantify productivity and health following the protocol in objective 2. The established protocols will be included in an extension publication--written by PD López-Uribe, Co-PD Underwood, and Collaborator Harpur--detailing a queen breeding guide that would inform beekeepers on the considerations for using marker-assisted selective breeding and how to best do it. The results of this project will be disseminated in a combination of peer-reviewed and extension publications.