diff --git a/assays/biparental_mapping/dataset/eam7_introgression_area.md b/assays/biparental_mapping/dataset/eam7_introgression_area.md new file mode 100644 index 0000000000000000000000000000000000000000..61ee91ea2920489932050459ab7650e3830634be --- /dev/null +++ b/assays/biparental_mapping/dataset/eam7_introgression_area.md @@ -0,0 +1,6 @@ +## reduced *eam7* introgression: + + +| marker start | marker end | Mbp start | Mbp end | size (Mbp) | +| - | - | - | - | - | +| JHI-Hv50k-2016-390119 | JHI-Hv50k-2016-401705 | 96.64 | 382.8 | 286.16 | \ No newline at end of file diff --git a/assays/biparental_mapping/isa.assay.xlsx b/assays/biparental_mapping/isa.assay.xlsx index a11ccc3a8bf7854c4a1d4877534bb4332dc2d5d7..2b205909b10a6e3792348865a54aac9c70c78057 100644 Binary files a/assays/biparental_mapping/isa.assay.xlsx and b/assays/biparental_mapping/isa.assay.xlsx differ diff --git a/assays/biparental_mapping/protocols/CAPS_marker_analysis.md b/assays/biparental_mapping/protocols/CAPS_marker_analysis.md index cf942a5f21fd0baf48feca5f371ac0c4c0de3aec..0f84933595bd017380d7608e88b2dc8eab482006 100644 --- a/assays/biparental_mapping/protocols/CAPS_marker_analysis.md +++ b/assays/biparental_mapping/protocols/CAPS_marker_analysis.md @@ -28,3 +28,7 @@ | ------ | ------ | ------ | ------ | ------ | ------ | ------ | | M-PPD-H1 | F | ACGTGAATGGTGGATCGGC | BstUI | 60°C | 506 | 433, 73 | | | R | TATAGCTAGGTGCGTGGCG | + +**Analysis:** + +- based on observed recombinations in combination with flowering time data, the eam7 introgression area can be redefined \ No newline at end of file diff --git a/assays/biparental_mapping/protocols/target_gene_identification.md b/assays/biparental_mapping/protocols/target_gene_identification.md index dc8e78740c541e3af14df29ed1e61efc88177d5d..d440b73a36580b9c7539e182979be4d8455d009c 100644 --- a/assays/biparental_mapping/protocols/target_gene_identification.md +++ b/assays/biparental_mapping/protocols/target_gene_identification.md @@ -1,16 +1,6 @@ ## *eam7* target gene identification -- based on the CAPS marker results, the introgression area could be reduced to 2.98 cM/286 Mbp (Morex V3, Mascher et al. 2021) - -Flanking markers: - -| marker | position in MorexV3 (bp) | -| - | - | -| JHI-Hv50k-2016-390119 | 96639872 | -| JHI-Hv50k-2016-401705 | 382834297 | - - -- this region contains 1084 high confidence (HC) genes +- the reduced introgression area contains 1084 high confidence (HC) genes - Arabidopsis (Araport11, Cheng et al. 2017) homologs were indentified via BLASTP - 10 of the genes genes were homologous to Arabidopsis genes with functions in the circadian clock -> target_genes - 4 of these genes were associated with early flowering in barley or Arabidopsis -> target genes