Abstract
BackgroundDevelopment of molecular markers such as SSR (simple sequence repeat), DArT (diversity arrays technology) and SNP (single nucleotide polymorphism) is fundamental for linkage map construction and QTL mapping. However, DArT and SNP genotyping require special tools, and detection of SSR polymorphisms requires time-consuming polyacrylamide electrophoresis. Furthermore, many markers have been mapped in different populations such that their genetic positions are inconsistent. Recently, InDel (insertion and deletion) markers have become popular in genetic map construction and map-based cloning.ResultsAligning genomic DNA sequences in two barley cultivars (Morex and Barke) identified 436,640 InDels. We designed 1140 InDel markers across the barley genome with an average genetic distance of 1 cM, each having a unique location in the barley genome. High-resolution melting (HRM) technology was used to genotype 55 InDel markers; those PCR amplicons with melting temperature differences >0.3 °C were ideal for HRM genotyping. The 1140 InDel markers together with 383 SSRs, 3909 gene-based SNPs and 1544 DArT markers were integrated into single barley genetic map according to their physical map positions.ConclusionsHigh-density InDel markers with specific genome locations were developed, with 6976 molecular markers (SSRs, DArTs, SNPs and InDels) integrated into single barley genetic map. HRM genotyping of the InDel markers each with single PCR band will facilitate quick map construction and gene fine-mapping.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2027-x) contains supplementary material, which is available to authorized users.
Highlights
Development of molecular markers such as Simple sequence repeat (SSR), Diversity arrays technology (DArT) and Single nucleotide polymorphism (SNP) is fundamental for linkage map construction and Quantitative trait loci (QTL) mapping
Genetic maps consist of several types of molecular markers including Restriction fragment length polymorphism (RFLP), Amplified fragment length polymorphism (AFLP), SSR, STS, DArT and SNP
Insertion and deletion (InDel) differing by 3–100 bp accounted for 2 % of the total InDels
Summary
Development of molecular markers such as SSR (simple sequence repeat), DArT (diversity arrays technology) and SNP (single nucleotide polymorphism) is fundamental for linkage map construction and QTL mapping. Genetic maps consist of several types of molecular markers including RFLP (restriction fragment length polymorphism), AFLP (amplified fragment length polymorphism), SSR (simple sequence repeat), STS (sequence-tagged site), DArT (diversity arrays technology) and SNP (single nucleotide polymorphism). RFLP markers have been used to construct first generation genetic maps [1, 2], but such hybridization-based markers have practical disadvantages. This led to interest in PCR-based markers, in particular those based on SSRs. SSR markers were derived from sequences held in public databases including. GBS is a powerful method for developing high-density markers in species without a sequenced genome while providing a genome shotgun sequence
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