Conservation of the dark bee (Apis mellifera mellifera): estimating C-lineage introgression in Nordic breeding stocks

Displacement and admixture are threatening the survival and genetic integrity of the European dark bee, Apis mellifera mellifera. Studies on the phenotype-genotype map and genotype by environment interactions in honey bees are demonstrating that variation at subspecies level exists and is worth conserving. SNP-based tools for monitoring genetic integrity in bees have been developed, but are not yet widely used by European dark bee breeders. We used a panel of ancestry informative SNP markers to assess the level of admixture in Nordic dark bee breeding stocks. We found that bee breeders falsely classified admixed stocks based on morphometry as purebred and vice versa. Even though most Nordic A. m. mellifera breeding stocks have low proportions of C-lineage ancestry, we recommend to incorporate genotyping in Nordic dark bee breeding programmes to ensure that minimal genetic diversity is lost, while the genetic integrity of the subspecies is maintained.We are greatly indebted to the participating bee breeders for allowing us to include their samples in this study and for providing the samples. We sincerely thank Dr. Stefan Fuchs for providing the morphological reference data. This project would not have been possible without the help of João Costa from the Genomics Unit of the Instituto Gulbenkian de Ciência, Portugal, who carried out the genotyping for us. We thank the two anonymous reviewers who helped greatly to improve the manuscript. This research was partly funded by the Norwegian Agriculture Agency 17/3472.info:eu-repo/semantics/publishedVersio

The status and need for characterization of Nordic animal genetic resources

acceptedVersio

Schematic representation of PRDM9 domains and allelic variation in <i>Pan</i>.

<p>The top block depicts alleles identified in this study. The second block shows the additional alleles characterized by Auton et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039064#pone.0039064-Auton1" target="_blank">[36]</a>. The four alleles common to both studies are shown in the top block, with the number of occurrences and the corresponding (sub-)species given in square brackets. Pp  =  <i>Pan paniscus,</i> Ptv  =  <i>P. troglodytes verus</i>, Ptt  =  <i>P. t. troglodytes</i>, Pts  =  <i>P. t. schweinfurthii</i>. Different ZnF repeats are coded by letters and repeats marked with a * differ from those with the same letter code by one, two, or three synonymous substitutions. The underlying nucleotide sequence, as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039064#pone-0039064-g002" target="_blank">Figure 2</a>, of O* is n or zg, D* represents q, A* is zf and U* represents w. Colors correspond to the AA residue combination at positions −1, 3 and 6 of the ZnFs, as given in the legend. Residue position 2, which also plays a role in DNA binding is fixed (serine) and therefore not shown. Human allele A is depicted for reference.</p

Self-comparison of predominant PRDM9 alleles.

<p>These diagrams depict the results of an analysis comparing PRDM9 DNA sequences to themselves with a window size of 83 and a mismatch limit of five. The main diagonal represents the alignment of a sequence to itself. The off-diagonal lines represent similar patterns within the sequences. The human allele shows a clear two-block structure, in which the repeats of the first half of the sequence are more similar to one another than to those in the second half of the sequence and vice versa. This structure is not seen in any of the <i>Pan</i> alleles.</p

Alignment of PRDM9 ZnF repeats of 52 <i>Pan</i> individuals and one human.

<p>The ZnF repeats identified in 82 <i>Pan</i> alleles of which 28 are unique DNA sequences, including data from Auton et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039064#pone.0039064-Auton1" target="_blank">[36]</a> and Oliver at al. (GU166820: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039064#pone.0039064-Oliver1" target="_blank">[19]</a>), are depicted in the top block. Pp  =  <i>Pan paniscus,</i> Ptv  =  <i>P. troglodytes verus</i>, Ptt  =  <i>P. t. troglodytes</i>, Pts  =  <i>P. t. schweinfurthii</i>. The second block depicts the ZnF repeats of the human A allele for comparison with those identified in <i>Pan</i>. For comparative purposes, we adhere to the break between repeats chosen by Oliver et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039064#pone.0039064-Oliver1" target="_blank">[19]</a>. The two conserved cysteine and histidine residues are marked at the top and positions −1, 3 and 6 of the alpha helices are identified by black frames.</p

Primers used in this study.

<p>T_a °C =  annealing temperature in degrees Celsius.</p>*<p>indicates primers used for sequencing.</p

Distribution of alleles according to subspecies/species.

<p>Alleles (p1 = A1 and p11 = B2) differ only by two synonymous substitutions, so that bonobos and eastern chimpanzees share an allele (P1) at the amino acid level. Two alleles (W11a, W11b) identified in western chimpanzees differ only by one synonymous substitution and represent one allele at the amino acid level.</p>*<p>There is one shared allele between central and eastern chimpanzees: alleles p6 and E1 are identical at the nucleotide level.</p