Articles
Ploidy screening in apple germplasm using flow cytometry to improve GWAS accuracy
Article number
1449_8
Pages
57 – 62
Language
English
Abstract
In 2020, the apple core collection of Bosnia and Herzegovina (B&H) was genotyped with the Axiom® Apple 480 K SNP array to perform genome wide association studies (GWAS). The core collection was previously created by merging Simple Sequence Repeats (SSR) profiles of traditional apple accessions conserved ex-situ in B&H into a single database.
The database was then used to identify a subset of 52 genotypes that best represent the overall genetic diversity of the apple accessions analyzed.
A key feature of B&H’s traditional apple germplasm is the high incidence of triploids, which can negatively affect the quality of the SNP genotype data analyses and lead to false marker-locus-trait associations.
The identification and consequent exclusion of triploid genotypes from genome wide association studies in apples has so far been based mainly on previously published SSRs.
Thus, accessions that have more than two different alleles on SSR loci are referred to as putative triploids.
A more accurate method to determine the ploidy level is the use of flow cytometry.
In this study, we compare the use of both methods (SSRs and flow cytometry) for ploidy screening of accessions in the B&H’s apple core collection and discuss the impact of unrecognized triploids on SNP quality parameters such as call and heterozygosity rate.
The database was then used to identify a subset of 52 genotypes that best represent the overall genetic diversity of the apple accessions analyzed.
A key feature of B&H’s traditional apple germplasm is the high incidence of triploids, which can negatively affect the quality of the SNP genotype data analyses and lead to false marker-locus-trait associations.
The identification and consequent exclusion of triploid genotypes from genome wide association studies in apples has so far been based mainly on previously published SSRs.
Thus, accessions that have more than two different alleles on SSR loci are referred to as putative triploids.
A more accurate method to determine the ploidy level is the use of flow cytometry.
In this study, we compare the use of both methods (SSRs and flow cytometry) for ploidy screening of accessions in the B&H’s apple core collection and discuss the impact of unrecognized triploids on SNP quality parameters such as call and heterozygosity rate.
Publication
Authors
A. Konjić, A. Okić, J. Grahić, F. Bogunić, A. Hajrudinović-Bogunić, N. Pojskić, F. Gai
Keywords
flow cytometry, SNP array, SSR markers, Malus domestica, ploidy
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