diff --git a/assays/biparental_mapping/dataset/introgression_area.xlsx b/assays/biparental_mapping/dataset/introgression_area.xlsx index 27aae1684bdcebb48999103f0973eaf1ee3c02d4..62c8a756ef535a3ab9b15229132abebded799093 100644 Binary files a/assays/biparental_mapping/dataset/introgression_area.xlsx and b/assays/biparental_mapping/dataset/introgression_area.xlsx differ diff --git a/assays/biparental_mapping/dataset/target_genes_results.md b/assays/biparental_mapping/dataset/target_genes_results.md new file mode 100644 index 0000000000000000000000000000000000000000..838ca4e835050546ec6dc135897a481a94f37dc0 --- /dev/null +++ b/assays/biparental_mapping/dataset/target_genes_results.md @@ -0,0 +1,25 @@ +**related to the circadian clock** + +MorexV3 gene ID pident evalue Araport11 gene ID Gene name SNP positions Changes in aa sequence +HORVU.MOREX.r3.6HG0592840 73.75 2.26E-40 AT2G21660 GR-RBP1 None None +HORVU.MOREX.r3.6HG0583670 69.309 0 AT1G12910 LWD1 32 bp del (1219-1250) A407F + N408S + K409F + L410* +HORVU.MOREX.r3.6HG0587680 66.082 0 AT4G08920 CRY1 None None +HORVU.MOREX.r3.6HG0595250 38.475 3.92E-106 AT5G61380 PRR1 A642G T1300C T215A + S434P +HORVU.MOREX.r3.6HG0578070 55.367 0 AT5G51200 EDS4 - - +HORVU.MOREX.r3.6HG0589220 34.855 9.66E-46 AT3G07640 PBAC5 - - +HORVU.MOREX.r3.6HG0571470 36.735 1.3 AT3G42170 DAY-SLEEPER - - +HORVU.MOREX.r3.6HG0582650 30.108 1.00E-12 AT3G42170 DAY-SLEEPER - - +HORVU.MOREX.r3.6HG0592100 29.042 1.69E-45 AT3G42170 DAY-SLEEPER - - +HORVU.MOREX.r3.6HG0571480 28.319 1.11E-13 AT3G42170 DAY-SLEEPER - - + + +**associated with early flowering** + +PSEUDO RESPONSE REGULATOR 1 (PRR1) HORVU.MOREX.r3.6HG0595250 +CRYPTOCHROME 1a (CRY1a) HORVU.MOREX.r3.6HG0587680) +GLYCIN-RICH RNA-BINDING-PROTEIN 1 (GR-RBP1) HORVU.MOREX.r3.6HG0592840) +LIGHT-REGULATED WD 1 (LWD1) HORVU.MOREX.r3.6HG0583670 \ No newline at end of file diff --git a/assays/biparental_mapping/protocols/target_gene_identification.txt b/assays/biparental_mapping/protocols/target_gene_identification.txt new file mode 100644 index 0000000000000000000000000000000000000000..35443c2f269a7df6ad32b809a28ff3525f878d71 --- /dev/null +++ b/assays/biparental_mapping/protocols/target_gene_identification.txt @@ -0,0 +1,13 @@ + +- 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: +JHI-Hv50k-2016-390119 96639872 bp +SCRI_RS_114351 382834297 bp + + +- this region 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 +- 1 had a consistent mutation in eam7 vs EAM7 plants \ No newline at end of file