A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)

Abstract

With a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.

Mitochondrial and nuclear diversity of colonies of varying origins: contrasting patterns inferred from the intergenic tRNAleu-cox2 region and immune SNPs

“…The finding of elevated nuclear diversity in admixed populations relative to parental populations is consistent with predictions from population genetics theory and has been confirmed by empirical data in honey bee studies (Harpur et al, 2012). Of note is that this finding is also a by-product of the biased nature of the SNP assay employed here (Henriques et al, 2021), which was tailored to include immunerelated SNPs segregating between the two most divergent lineages: M and C. This means that both alleles will co-occur in admixed populations whereas only one alternative allele is expected to be found in parental populations.…”

“…The 156 pooled samples were genotyped in the MassARRAYV R MALDI-TOF platform using a recently developed assay containing 91 immune SNPs (Henriques et al, 2021). The membership proportions (Q-values) were inferred from these SNPs with ADMIXTURE (Alexander et al, 2009) using the same settings and reference populations of Henriques et al (2021).…”

“…The 156 pooled samples were genotyped in the MassARRAYV R MALDI-TOF platform using a recently developed assay containing 91 immune SNPs (Henriques et al, 2021). The membership proportions (Q-values) were inferred from these SNPs with ADMIXTURE (Alexander et al, 2009) using the same settings and reference populations of Henriques et al (2021). GENEALEX 6.50 (Peakall & Smouse, 2006) was used to estimate the mean number of The nuclear plot displays the average Q-values inferred from 91 SNPs located in immune-related genes using ADMIXTURE (K ¼ 4).…”

Age and Season Effect the Timing of Adult Worker Honeybee Infection by Nosema ceranae

“…It would be interesting to further investigate these factors that might influence the probability of infection and parasitic load. As a matter of fact, new tools such SNPs (single nucleotide polymorphism) assays are being developed to improve our understanding of immune gene diversity in honeybees (Henriques et al, 2021a). Both the quality and quantity of the feed the bees receive and the presence of nutraceutical substances that may be present in it could modify the development of the infection.…”

A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA

“…* email: luca.fontanesi@unibo.it single nucleotide polymorphism (SNP) panels have been designed starting from whole genome resequencing datasets produced from different honey bee populations, and informative markers that can discriminate honey bee subspecies have been identified [26][27][28][29][30][31][32] . A few SNP panels have been also designed and used for several other applications in honey bee population genetic studies [33][34][35][36][37] . For example, genome-wide association analysis for varroa-specific defence behaviour in honey bees has been carried out using a SNP panel 38 .…”