From d72f6a79fea1d6df25a30365ba94d95dcc7f04f0 Mon Sep 17 00:00:00 2001 From: Gesa Helmsorig <gesa.helmsorig@hhu.de> Date: Wed, 13 Nov 2024 12:51:09 +0000 Subject: [PATCH] Update 2 files - /assays/biparental_mapping/protocols/target_gene_identification.md - /assays/biparental_mapping/dataset/target_genes_results.md --- .../dataset/target_genes_results.md | 13 ++++++++++--- .../protocols/target_gene_identification.md | 5 +++-- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/assays/biparental_mapping/dataset/target_genes_results.md b/assays/biparental_mapping/dataset/target_genes_results.md index 9e25344..f92cc6a 100644 --- a/assays/biparental_mapping/dataset/target_genes_results.md +++ b/assays/biparental_mapping/dataset/target_genes_results.md @@ -1,4 +1,6 @@ -**related to the circadian clock:** +## Results: target gene identification for *eam7* + +**Candidates related to the circadian clock:** | MorexV3 gene ID | pident | evalue | Araport11 gene ID | Gene name | SNP positions | Changes in aa sequence | | ------ | ------ | ------ | ------ | ------ | ------ | ------ | @@ -15,11 +17,16 @@ -**associated with early flowering:** +**Candidates associated with early flowering:** | gene name | MoresV3 gene ID | | - | - | | 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 +| LIGHT-REGULATED WD 1 (LWD1) | HORVU.MOREX.r3.6HG0583670 | + + +**Candidates with consistent mutations across *eam7* / *EAM* genotypes:** + +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.md b/assays/biparental_mapping/protocols/target_gene_identification.md index e71e905..dc8e787 100644 --- a/assays/biparental_mapping/protocols/target_gene_identification.md +++ b/assays/biparental_mapping/protocols/target_gene_identification.md @@ -1,7 +1,8 @@ +## *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: +Flanking markers: | marker | position in MorexV3 (bp) | | - | - | @@ -13,4 +14,4 @@ flanking markers: - 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 +- 1 had a consistent mutations in *eam7* vs *EAM7* plants \ No newline at end of file -- GitLab