Mapping populations

Approximately 330 barley unigenes were mapped in three mapping populations using sequence polymorphisms.

  • Oregon Wolfe Barley Dominant x Recessive (Costa et al. TAG, 2001, 103:415)

  • Steptoe x Morex (Kleinhofs et al. TAG, 1993, 86:705)

  • Lina x HS92 (Ramsay et al. Genetics, 2000, 156:1997)

  • Mapping techniques

    While SNP discovery strategy is based entirely on de novo sequencing, the detection of polymorphisms in doubled haploid lines of mapping populations was achieved by a number of techniques. Cost of detection platform, time required to develop an assay for each individual gene and the information content provided by detection platform all need to be taken into account. In general, we are looking for a system that does not require optimization of SNP detection for each individual gene.

    The following SNP detection techniques have been successfully used at SCRI:

  • denaturing HPLC of DNA heteroduplexes

  • restriction enzyme digestion

  • Cel I digestion (Surveyor mutation detection kit from Transgenomic)

  • PCR fragment length polymorphism

  • sequencing of PCR products from doubled haploid lines

  • Pyrosequencing
  • allele-specific PCR amplification

  • Mapping data

    Linkage data is managed and analyzed using Map Manager QTX and JoinMap.