Mapping SNP-anchored genes using high-resolution melting analysis in almond

Abstract

Peach and almond have been considered as model species for the family Rosaceae and other woody plants. Consequently, mapping and characterisation of genes in these species has important implications. High-resolution melting (HRM) analysis is a recent development in the detection of SNPs and other markers, and proved to be an efficient and cost-effective approach. In this study, we aimed to map genes corresponding to known proteins in other species using the HRM approach. Prunus unigenes were searched and compared with known proteins in the public databases. We developed single-nucleotide polymorphism (SNP) markers, polymorphic in a mapping population produced from a cross between the cloned cultivars Nonpareil and Lauranne. A total of 12 SNP-anchored putative genes were genotyped in the population using HRM, and mapped to an existing linkage map. These genes were mapped on six linkage groups, and the predicted proteins were compared to putative orthologs in other species. Amongst those genes, four were abiotic stress-responsive genes, which can provide a starting point for construction of an abiotic resistance map. Two allergy and detoxification related genes, respectively, were also mapped and analysed. Most of the investigated genes had high similarities to sequences from closely related species such as apricot, apple and other eudicots, and these are putatively orthologous. In addition, it was shown that HRM can be an effective means of genotyping populations for the purpose of constructing a linkage map. Our work provides basic genomic information for the 12 genes, which can be used for further genetic and functional studies.

RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

“…HRM profiles of the fragments and evaluation techniques were established and the resulting SNP data were used to cluster the accessions of wild almond species. HRM is a novel, homogenous and closed-tube post-PCR method that can be applied to analyse the genetic variations as well as SNPs, polymorphism length and methylations of DNA in PCR amplicons 40, 41 . HRM requires an additional step, the melting process following cycling, and an additional reagent, a specific generic DNA fluorescence dye, to complete the assay compared to conventional PCR.…”

Evaluation of High-Resolution Melting for Gene Mapping in Rice

“…Because of these benefits, HRM has already been used in many investigations including the detection of SNP mutations (Margraf et al 2006;Wu et al 2008), RNA editing (Chateigner-Boutin and Small 2007), identification of transgenic plants (Akiyama et al 2009), varietal identification (Mackay et al 2008), and food traceability (Ganopoulos et al 2010;Jaakola et al 2010). HRM analysis has also been successfully used for genetic mapping in white lupin, barley, apple, and almond (Chagné et al 2008;Croxford et al 2008;Lehmensiek et al 2008;Wu et al 2009). It has also been used to develop a genetic map of SNP markers in Cryptomeria japonica (Ujino-Ihara et al 2010).…”

SNP development for genetic diversity analysis in apricot

“…More recently, Bielsa et al (2014) used SNP markers to characterize different Prunus rootstocks. In almond, Wu et al (2009) andTavassolian et al (2010) created the first genetic maps combining SNP markers with other markers, including RAPDs and SSRs. Later, Eduardo et al (2013) and Martínez-García et al (2013a, b) identified the first SNPs linked to quantitative trait loci (QTL) in highly saturated peach linkage maps.…”