added assays

assays/biparental_mapping/protocols/CAPS_marker_analysis.txt

+**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						

assays/biparental_mapping/protocols/plant-phenotyping-flowering.txt

+**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)
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