Wild Barley Introgression

Searching for runs of indentity by state (IBS) in introgressed wild barley

• Wild barley lines often show introgression from cultivated barley. However it is not clear
  how large the regions of introgression are or if they occur randomly across the genome.

• We have BOPA1 & BOPA2 and genotype by sequencing (GBS) data for all 318 lines in the sample
  the Wild Barley Diversity Collection. There is exome capture resequencing for ~100 lines.

• Lines thought to be introgressed: WBDC027 WBDC045 WBDC172 WBDC182 WBDC190 WBDC227 WBDC311 WBDC344

• Introgressed lines in Liana's Population (Nice et al. 2016)

  Update 2018-04-02: finished realigning remaining 2 bam files below

  We have exome capture resequencing data for these lines. 5 out of 7 of the lines
  below have already been read mapped and realigned. The 2 samples that still need
  to be read mapped are in bold. The *finished_realigned_reheader.bam files are located in
  /home/morrellp/liux1299/Shared/Projects/Introgressed/sequence_handling/LianaPop_introgressed/realigned

  • WBDC_016
  • WBDC_092
  • WBDC_172
  • WBDC_173
  • WBDC_182
  • WBDC_227
  • WBDC_350

• It would also be worth looking for high IBS to cultivated lines in wild barley from
  Azerbaijan and similar regions where the phenotype is most similar to cultivated barley.
  This would include: WBDC150 WBDC205 WBDC217 WBDC227 WBDC228 WBDC229 WBDC231 WBDC232

Barley iSelect 9K SNP positions

• Physical positions from BLAST search
• Genetic map positions from the iSelect 2013 Consensus map
  • These are available on T3, on this page, under
    "iSelect_2013Consensus_AllSNPs"