Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species
Authors: Karim Sorkheh
Sezai Ercisli
Júlia Halász
Attila Hegedus
Mehrana Koohi Dehkordi
Journal: Scientific Reports (2017)
Discipline: Multidisciplinary
Keywords: Wild almond species; genetic variation; retrotransposon markers; Ty3-gypsy; Ty1-copia-elements
Affiliations: Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Ahvaz, Iran. ., Department of Agronomy, Faculty of Agriculture, Payame-Noor University, P.O. Box 19395-3697, Tehran, Iran., Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey., Department of Genetics and Plant Breeding, Szent István University, H-1118, Budapest, Villányiút 29-43, Hungary.

Abstract:  Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity. 

Retracted: Yes

PubPeer comments:
 Unfortunately, I had serious difficulties in understanding the outputs of this paper. Part of the comments displayed in the results section are not supported by figures and some other sections of the results are not even referring to any figure or table. For exemple in the population genetic structure inference part, authors are claiming that .... the populations from Spartioides section were placed into the second cluster (red).... but the ARA population is grouping with cluster 3 (Figure 5). Similarly, they say ....while population of Lycioides section were placed into the third cluster (green colour) . In Figure 5, only the Lycoides ERI, EBU and URU are clustering in group III. The REU and LYC populations are missing (and grouping elsewhere) while the Spartioides ARA population is placed in group III. Those discrepancies between figures and comments in the text are highly confusing and happen all over the paper. Some other sections such as Genetic relatedness of the accessions of Prunus spp based on SNP-HRM are referring to no figure or table and I did not understand could not assess the results commented here. I do have the strong feeling that this paper requires serious reviewing and proofreading and do not understand why how Scientific Reports published it as it is. Data appears highly intersting but the layout of the paper is arguable, together with the results discussion sections. One last question: why did the authors not perform a Structuration diversity analysis based on the SSR data ? They performed such analysis for all other markers except those microsatellites, in consequence I do not understand what this part is doing here... , 
 There are a few queries about two supplementary figures in this paper that involve IRAP and REMAP data, which affects most of the core conclusions of this paper. Since the published images are quite blurred, perhaps the authors could post the high-resolution files of the original gel images that might offer some clarification into these queries. Arrows indicate possible splicing between lanes. In particular, in Suppl. Fig 2, several bands appear to have been erased, others duplicated, or even lanes appear to have been duplicated, sometimes in reverse direction, or sometimes even triplicated. Only high-resolution images of the original blots can bring clarity. Suppl. Fig 1 https: imgur.com a FyznVdP Suppl. Fig 2 https: imgur.com a Y4fQGGB , 
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 https: www.nature.com articles s41598-020-72522-5  The Editors have retracted this article. After publication concerns were raised that there were anomalies in Supplementary Figures 1 and 2. However, the authors were unable to provide higher resolution images to allow the veracity of these data to be confirmed. Additionally the graph showing the genetic diversity of the wild almond species, which is a part of Figures 1, 2, 3 and 5, appears to be a duplication of a graph showing the genetic diversity of the liquorice species in Figure 2 in Hakimi et al.1, of the barley species in Figure 2 in Rouhain et al.2, and of olive species in Figures 1 and 2 in Khaleghi et al.3. The Editors therefore no longer have confidence in the validity of the results and conclusions reported in this article. All authors agree with the retraction. , 
 https: retractionwatch.com 2020 10 05 almond-no-joy-plant-geneticist-in-iran-up-to-at-least-six-retractions ,