SNP development for genetic diversity analysis in apricot

Abstract

High-throughput DNA and RNA sequencing technologies have resulted in the successful identification of Single nucleotide polymorphisms (SNPs). In order to develop a large SNP set for wide application in apricot (Prunus armeniaca L.), we carried out RNA high-throughput sequencing (RNA-Seq) in two apricot genotypes, BRojo Pasión^and BZ506-7.^After trimming and cleaning, 70 % of RNA-Seq reads were aligned to the reference peach genome. Sequences uniquely mapped on the peach genome allowed for the discovery of 300 k SNP/INDEL variations, with a density of one SNP per 850 bp. Some 95 SNPs of the 99 tested were analyzed in a set of 37 apricot accessions using SNPlex™ genotyping technology. The results provide accurate values for nucleotide diversity in coding sequences in apricot. The combination of a highly efficient RNA-Seq approach and SNPlex™ high-throughput genotyping technology thus provide a powerful tool for apricot genetic analysis. SNP markers produced a total of 267 allelic combinations in the 37 apricot accessions assayed with a mean of 2.8 combinations per locus, an observed heterozygosity per marker ranging from 0.06 to 0.65, and a power of discrimination ranging from 0.12 to 0.66. In addition, SNP markers confirmed parentage and also determined relationships between the accessions in a manner consistent with their pedigree relationships.

Inheritance of reproductive phenology traits and related QTL identification in apricot

“…As expected, the 'Currot' maps were the longest ones because the SNPs had been previously designed from the RNASeq data of 'Z506-7' and 'Rojo Pasión' (both derived from 'Orange Red' × 'Currot'; Salazar et al 2015). In spite of the high efficiency of these markers for the discrimination of a panel of 37 apricot accessions, the percentage of those useful for mapping in both populations was about 50 %.…”

“…SSR peaks were visualised using Peak Scanner 1.0 software. The SNP design and analysis was performed according to Salazar et al (2015) from 'Rojo Pasión' and 'Z506-7' transcriptome data. 'Rojo Pasión' and 'Z506-7' were obtained from crossing 'Orange Red' × 'Currot' and have a common parent with our populations.…”

“…Furthermore, the development of new technological approaches based on next-generation sequencing (NGS) has facilitated genomics-assisted breeding through marker assisted selection (MAS), genome-wide association studies, and genomic selection (GS), as reviewed by Varshney et al (2014). In apricot, a first approach to developing SNP markers from RNA-Seq libraries has been recently described, entailing a significant decrease in the time and cost of genotyping (Salazar et al 2015). SNP markers, due to their high abundance, allow us to cover a large extension of the genome and are ideal for genetic mapping (Ball et al 2010).…”

“…The recent modern SNP genotyping platforms, which are almost completely automated, make the error rate lower than in the case of SSRs, while a higher density of SNPs is required to have equal or greater accuracy than SSRs (Salazar et al 2015). However, it has been shown that when the genotyping error rates are low, we can obtain accurate maps with both markers (Ball et al 2010).…”

Genetic mapping and QTL analysis in European hazelnut (Corylus avellana L.)

“…The development of new high-throughput sequencing technologies enable to achieve high-density linkage maps by direct analyses of sequence variations, including single nucleotide polymorphisms (SNPs) (Huang et al 2014). Markers such SNPs are more abundant and genome wide distributed and can be analysed multiplexing hundreds of markers (Salazar et al 2015). Nevertheless, SSRs are found to be more polymorphic and are considered as the best marker system for construction of framework linkage map (Jones et al 2007).…”