Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

Kim, Sung-Ryul; Ramos, Joie; Ashikari, Motoyuki; Virk, Parminder S.; Torres, Edgar A.; Nissila, Eero; Hechanova, Sherry Lou; Mauleon, Ramil; Jena, Kshirod K.

doi:10.1186/s12284-016-0084-7

Rice

Table 2 Primer information of the allele-specific markers for eight yield-enhancing genes

From: Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

Marker	DNA polymorphism	Primer	Primer sequence (5' to 3')^a
Gn1a-17SNP	G/A SNP in promoter	Gn1a-17SNP-OPF	TCGCAGGCACTGCACTTCA
		Gn1a-17SNP-OPR	GCCACCCTAGGTTTGATTCC
		Gn1a-17SNP-AF	CATACCTAGCGTTCTATGCtGA
		Gn1a-17SNP-GR	GGAAGATAAAGAAATTTCACATaCC
Gn1a-indel3	~70-bp indel near the 3'UTR	Gn1a-indel3-F	GATCTAGATGCTCCAAAGTCC
		Gn1a-indel3-R	CTGTACGTACGTGCACGTAG
Gn1a-indel1	16-bp indel in the 5'UTR	Gn1a-indel1-F	GCCACCTTGTCCCTTCTACA
		Gn1a-indel1-R	TGCCATCCTGACCTGCTCT
SPL14-04SNP	C/T SNP in promoter	SPL14-04SNP-F	TAGCCATAGCTTCTGCGTGA
		SPL14-04SNP-CR	ACCGTGCTTACCGCCtGG
		SPL14-04SNP-TR	ACCGTGCTTACCGCCtGA
SPL14-12SNP	C/A SNP on the third exon	SPL14-12SNP-R	CAAGTGAGACTTCATGTGGT
		SPL14-12SNP-CF	ACCGACTCGAGCTGTGtTC
		SPL14-12SNP-F	GTTCAGAAGCTTTACGTTGGA
		SPL14-12SNP-AR	GCTGGGTTGACAGAAGAGAtAT
SCM2-indel1	12-bp indel in promoter	SCM2-indel1-F	GGAAATGATGAACACTGTCCA
		SCM2-indel1-R	GTTTGTCTCAGCTCTGATCTG
Ghd7-05SNP	A/T SNP on the second exon	Ghd7-05SNP-F	TGCTTATGCGTACATCTGGAT
		Ghd7-05SNP-AR	TGGGTTCAAGCTCTCCaCAT
		Ghd7-05SNP-TR	TGGGTTCAAGCTCTCCaCAA
DEP1-indel1P		DEP1-indel1-F	GCAAGTGCTCACCCAAGTG
	625-bp indel on the fifth exon	DEP1-indel1-R	GTTCGAACTTAATCAAAGGCCT
		DEP1-indel1-625F	CACGACGCAGTGCTTCAGCT
SPIKE-01SNP	G/A SNP on the third exon	SPIKE-01SNP-GF	GGTTGGTTTCCTCACTAAaCG
		SPIKE-01SNP-AF	GGTTGGTTTCCTCACTAAaCA
		SPIKE-01SNP-R	ATGGGAACTAGGAAGCAGGA
SPIKE-03SNP	G/A SNP on the fifth exon	SPIKE-03SNP-F	CTACTCGACCGTCTGGAAC
		SPIKE-03SNP-GR	TGGCTCGAAGATCTCTTCtAC
		SPIKE-03SNP-AR	TGGCTCGAAGATCTCTTCtAT
SPIKE-indel3	~20-bp indel in promoter	SPIKE-indel3-F	GGAGAGACATGGACGGCT
		SPIKE-indel3-R	TGGTGGCGATCATGCTGC
GS5-indel1	4-bp indel in promoter	GS5-indel1-F	CTAACTCCCATGGAATTACTAG
		GS5-indel1-R	GGAAAGCGAAACTGATTGACA
GS5-03SNP	T/C SNP in promoter	GS5-03SNP-OPF	ACTTTCAACTAAAGTGATATTACCTC
		GS5-03SNP-OPR	TCTATATATCCATCGTCCATGGTG
		GS5-03SNP-TF	CGCAGCCTAACTACCTAAGTAGcT
		GS5-03SNP-CR	ACATGCGTGCCAATATTCCTGTAtTG
TGW6-1d	1-bp indel on the first exon	TGW6-1d-F	GCCAACTGATCAGACTGAG
		TGW6-1d-NR	CGTGGGGAGAGTCGATtCC
		TGW6-1d-PR	CGTGGGGAGAGTCGATtCG

^aLower case nucleotide near the 3' end of allele-specific primer represents the artificial mismatched nucleotide for increasing allele specificity during primer annealing step of PCR.

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