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Table 1 Primer information on the 21 functional markers targeting 14 grain size genes

From: Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

Primer Names

Primers sequence (5′-3′)

Enzyme sites

Amplicon size (Digested) bp

GW2_SNP-F

AAAACCAAAACCTAACACGTGGATACAACA

NspI

115 (84)

GW2_SNP-R

GGCGGTGAAGATAGATGTACT

GW2_InDel-F

CTCACACTGCTCAGCCTACA

PstI

158 (127)

GW2_InDel-R

CACGATACTCCACAGCATAACTGGGAGTCT

GS2_SNP-F

GAGCGCCACATGCACCGCGGCCGCATACGT

SnaBI

287 (255)

GS2_SNP-R

TTGCCTGTTCCACCACCAACAGC

qLGY3_InDel-F

GGGTATTCTTCTTTTCTTCCA

StyI

448 (371)

qLGY3_InDel-R

TGTCTGCTGCTTCATTGCT

GS3_SNP1-F

CGAAGGGATCCACGCTGCCTCCAGATGATT

HinfI

170 (140)

GS3_SNP1-R

AGTTGCTTAAAAAGATAACGGTCAAA

GS3_SNP2-F

CAAACATGAAAACCTTGTCT

HaeIII

186 (155)

GS3_SNP2-R

AAATAAAACGTGTGATTTAATCGTTAACGGC

GL3.1_SNP-F

TGCACGATTCTATCTGGTTCAGTGGTCGA

SalI

224 (193)

GL3.1_SNP-R

CTAAACAAACAGGTTTTCTTAC

TGW3_SNP-F

TGCACTGCCAAAATCACATATTTTGAGCCG

HpaII

299 (269)

TGW3_SNP-R

TCAACTACCACTAGGTCCAC

GS5_InDel-F

ACTCCCATGGAATTACTAGAGAAGCCAAGC

AluI

262 (205/172)

GS5_InDel-R

AGGAGAAGAAAAGGTGAAAAGT

GW5_InDel-F

TGCGTCGGTCGTTGGAGG

 

419/1631

GW5_InDel-R

GCGAGCGAGCGTGTGTAGG

GS6_InDel-F

TCTTCTTCCCTTCCCTTCCAC

 

113/125

GS6_InDel-R

TGCCTCACCATTACCACTCCT

TGW6_InDel-F

AGCCCCAGCTACACGAAAAACAAGTGCCCG

HpaII

154 (104/72)

TGW6_InDel-R

GACCAACTCGCATCAATCCC

TGW6_SNP-F

ATGCGAGTTGGTCCAAAAGG

SacI

296 (266)

TGW6_SNP-R

GCAACGATCAGATGTGTTCGGTCAGAGCT

GW6a_InDel1-F

TGCACCTCTCTCGTGTTTCT

BclI

147 (117)

GW6a_InDel1-R

TTATTTTCGTTCAATTTTTCTATGGCTGAT

GW6a_InDel2-F

ATTACTCTTGATTTTTGTCTGTT

 

186/161

GW6a_InDel2-R

GAGTTTGCATGTTCGTTCT

GLW7_InDel-F

CTCGAGCTCGAGCTCATG

 

107/101/98

GLW7_InDel-R

TCCCTTTCAACCTTTTCCA

GLW7_InDel_dCaps-F

CCTCCTCCTCCTCCGCCTTCCACTTCGACT

HinfI

133 (101)

GLW7_InDel_dCaps-R

TGCTACTGTGTGCTGTGTGCT

GL7_Dup-F

GATGAGCTGACAAGAGCAAAG

 

0/314

GL7_Dup-R

AGAGGATGGGGATGAAAGAAT

GL7_InDel1-F

CAGCTCACGCACATCCAAC

 

112/101

GL7_InDel1-R

ACCATACCACATCTCATCTCAC

GL7_InDel2-F

GGACGCGTGAGATGAGATGTG

 

118/100

GL7_InDel2-R

CTCCCGCTTATTTCAACCCC

GW8_InDel-F

GTGCGTGCGTCAACACACAG

 

88/98

GW8_InDel-R

TGAGATCCCACTCCATGGCC