Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis )

Evolutionary Applications
Dora HenriquesM Alice Pinto

Abstract

The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. T...Continue Reading

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Citations

May 28, 2019·Pest Management Science·Alberto S CorrêaCelso Omoto
Feb 27, 2020·Nature Reviews. Genetics·Christina M Grozinger, Amro Zayed
Sep 3, 2020·Genome Biology and Evolution·Melanie ParejoAndone Estonba
Jul 30, 2021·Scientific Reports·Dora HenriquesM Alice Pinto
Dec 4, 2021·Science Advances·Kathleen A DogantzisAmro Zayed

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Methods Mentioned

BETA
genotyping
Assay

Software Mentioned

Assay Design
MassARRAY
Agena
DAVID
ADMIXTURE
PLINK

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