title: Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  Aligning 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.
  
  
  CONCLUSIONS
  High-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.
authors.affiliation: Department of Agriculture and Food, Locked Bag 4, Bentley Delivery Centre, Bentley, WA, 6983, Australia. turfs@163.com.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Australian Export Grains Innovation Centre, 3 Baron-Hay Court, South Perth, WA, 6155, Australia. zhqisen@gmail.com.
authors.forename: Qisen
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Western Barley Genetics Alliance/Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia. 32522498@student.murdoch.edu.au.
authors.forename: Cong
authors.initials: C
authors.lastname: Tan
authors.affiliation: Western Barley Genetics Alliance/Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia. xiao-qi.zhang@murdoch.edu.au.
authors.forename: Xiao-Qi
authors.initials: XQ
authors.lastname: Zhang
authors.affiliation: Western Barley Genetics Alliance/Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia. c.li@murdoch.edu.au.
authors.forename: Chengdao
authors.initials: C
authors.lastname: Li
mesh_terms: D002874:Chromosome Mapping; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D054643:INDEL Mutation / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics
chemical_list: D005819:Genetic Markers