diff --git a/assays/biparental_mapping/README.md b/assays/biparental_mapping/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/biparental_mapping/dataset/.gitkeep b/assays/biparental_mapping/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/biparental_mapping/isa.assay.xlsx b/assays/biparental_mapping/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..dcee27779ae275b46ec8e4a7eb815e932075f55c Binary files /dev/null and b/assays/biparental_mapping/isa.assay.xlsx differ diff --git a/assays/biparental_mapping/protocols/.gitkeep b/assays/biparental_mapping/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/biparental_mapping/protocols/CAPS_marker_analysis.txt b/assays/biparental_mapping/protocols/CAPS_marker_analysis.txt new file mode 100644 index 0000000000000000000000000000000000000000..292dc39508ce9f0b803c40a69fc187136fe06935 --- /dev/null +++ b/assays/biparental_mapping/protocols/CAPS_marker_analysis.txt @@ -0,0 +1,28 @@ +**CAPS marker: PCR + digest** + +PCR: +- using GoTaq® DNA Polymerase (Promega) according to the manufacturer's protocol with CAPS-marker specific PCR primers + +digest: + +- digesting 5µl of PCR fragments with the CAPS-marker specific restriction enzyme: + + +Marker Primer Sequence 5’-3’ Enzyme annealing temp (°C) EAM7 allele: fragment size (bp) eam7 allele: fragment size (bp) +M-13 F GTAATTGCCCTAGCGTTGGA MnlI 58°C 246, 98 328 + R CAGAACCCGGGAATTAGGAT +M-16 F AAAACGGTGGCATTAGCAAG HindIII 58°C 378 214, 168 + R CGGAGGCATGATCAGGTATT +M-11 F AAAGGCCCACACTAGTGCAT BstUI 58°C 209, 128 337 + R ACGCTCACTCCCTGCATCT +M-39 F CTAAATTTCAGCCCCGAACA DdeI 55°C 237,100 334 + R TGCCTGGACTTGTTCTGATG +M-PRR1 F GAGCATAGCATGGCACTTCA Hpy188I 58°C 224, 158 383 + R GCCTGCCTAACAAACTGACC +lwd1-del F TACCATCCTCCCATTGCCTG - 60°C 199 167 + R ATTGGCTTACACTGCAGGGG + + +Marker Primer Sequence 5’-3’ Enzyme annealing temp (°C) ppd-H1 allele: fragment size (bp) Ppd-H1 allele: fragment size (bp) +M-PPDH11 F ACGTGAATGGTGGATCGGC BstUI 60°C 506 433, 73 + R TATAGCTAGGTGCGTGGCG diff --git a/assays/biparental_mapping/protocols/Promega_GoTaq-DNA-Polymerase.pdf b/assays/biparental_mapping/protocols/Promega_GoTaq-DNA-Polymerase.pdf new file mode 100644 index 0000000000000000000000000000000000000000..9348cd58edf8e597ecddbe29cd3b3534bebbf658 Binary files /dev/null and b/assays/biparental_mapping/protocols/Promega_GoTaq-DNA-Polymerase.pdf differ diff --git a/assays/biparental_mapping/protocols/QIAGEN_BioSprint_96_DNA_Plant_Kit.pdf b/assays/biparental_mapping/protocols/QIAGEN_BioSprint_96_DNA_Plant_Kit.pdf new file mode 100644 index 0000000000000000000000000000000000000000..6031be2f04ff2426636a17cd2d29e00c61e78509 Binary files /dev/null and b/assays/biparental_mapping/protocols/QIAGEN_BioSprint_96_DNA_Plant_Kit.pdf differ diff --git a/assays/biparental_mapping/protocols/plant-phenotyping-flowering.txt b/assays/biparental_mapping/protocols/plant-phenotyping-flowering.txt new file mode 100644 index 0000000000000000000000000000000000000000..79a66e3cf3a6db1690c6bab53821536b79b183d9 --- /dev/null +++ b/assays/biparental_mapping/protocols/plant-phenotyping-flowering.txt @@ -0,0 +1,3 @@ +**plant phenotyping: flowering** + +- flowering was scored in days after emergence (DAE) as the period between emergence from soil and reaching Zadoks stage 49 when the awns exited the leaf sheath (Zadoks et al. 1974) \ No newline at end of file