Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms

Rice

Table 2 Primers used to detect INDEL and SSR

Primer name	Chr	Genome position (nt)	Forward primer (5’-3’)	Reverse primer (5’-3’)	Remarks *(O. meridionalisis)*
rp116			AGAAATTCTACCTCTTTCTATAAG	AATTGCCTCGGTAGGATTTTCC
ORF100-INDEL			GCCGCTTTAGTCCACTCAGCCATC	TCAATGCCTTTTTTCAATGGTCTC	5 bp insert
ctDNA336			ACAGAGGCAAGAAATAACGATTG	TTTATTCTTTCTTTCCAATTTTATG	For genotyping of ctDNA insertions
mtDNA indel			GACTCTGATTCCCCCACTATGAGAGAGCTG	CAGTCCGATGCGTTTGAGCAGTAG’]	4,132 bp deletion
INDEL5	chr10	20772383	AAGTGTGCCTTGCAACCGAG	AAGCAGCAGAACACCTGAAAC	20 bp deletion
INDEL7	chr10	21653822	GTAGCTAGTCGACAGGCAGATG	TACTGGGTATGTAAACCTGCAC	92 bp deletion
INDEL8	chr5	25412945	GATATATTTGTGCTGGCATTCTC	TTCCAGTGAAAATCATATGCAC	33 bp deletion
INDEL9	chr6	28288641	GTGTTCCTAAAACTTATGCATTGTG	CTACCAATTAGCTGTATTAACAAG	60 bp deletion
INDEL10	chr3	32263786	ATTTCAACAGCAGAATGGATTTTC	GAGCAGTTATAGTAACTTGGAGG	155 bp deletion
SSR1	chr3	10541915	GCCACCGAAACTTGTACCGTC	GTAACTTTCTGGTTGTTCCTAAAC	SSR
SSR2	chr6	13061135	CTCCACCGTGAATGTACGTAAG	CGCATCACCTCCTGCAAC	SSR
SSR3	chr10	21872477	CAAAGCTAGCCACTTGCATATG	GTCGTCGACGAACTTGGATAG	SSR
SSR5	chr4	27568462	CTTGTCAACTACTGTGGCAAG	AGAAGATCAACGGTGGTATAG	SSR
SSR7	chr10	15561422	CAAGGATGCTATAAGAGCAAAAAC	TCCTAACACTCCTATTTCATC	SSR
SSR9	chr5	1913	CTGCAAGGATCGCAAACAAAG	TATGGAAATTTGTGCGAGGTG	SSR
SSR15	chr3	34182494	CCTTGGTATTGGTTTGAATIG	TAAAGGATTGCTGGAGAAAGAAG	SSR