Development and application of a multiplex SNP system to evaluate the mating dynamics of Pinus thunbergii clonal seed orchards

Molecular Breeding

SuharyantoMine NoseSusumu Shiraishi

Corresponding author, e-mail:

ESM1List of locus-specific primers (LSPs) and their optimized primer concentrations used to amplify DNA amplicons containing SNP targets.

Set / Marker / Sequence (5′→3′) / PCR product (bp) / Concentra- tion (M) / Primer sequence sources used in sequencing
sA / sA1 / F:
R: / TCAAGAGTGTTAGATTTCTCCATCCC
CGTGCTGCCTAAAAGCTACAACG / 202 / 0.07 / PtIFG_1584a
sA2 / F:
R: / GCTTAGGGCTTTTCCTTCTCTGAG
CTTGGTGCATTCCCTTGGTGGTT / 632 / 0.07 / AB588028e
sA3 / F:
R: / GGATTTCTGTCTGTGGCGTCTG
AGCCCTTTCCCATTGCCTCT / 401 / 0.05 / PtIFG_1643a
sA4 / F:
R: / AACTCTTTCGTGCCAGATCGTGC
TCCCAGACAAGACAAACAATTCGT / 249 / 0.07 / PpINR_AS01C7b
sA5 / F:
R: / CCAACYGGAGGAAAAGCACGAC
ATACTACATCGCATCAGTCATACTCACC / 274 / 0.07 / PtIFG_9044a
sA6 / F:
R: / TACCCTCTGATTAAGCAAACCTAAGC
GGTTGTTGGTCTGGTTGTTGGT / 380 / 0.17 / AB588029e
sB / sB1 / F:
R: / ACAAGCTCTTGGCTAAGGAAGCTC
GAGCCCCTGCAAAACAAATATC / 460 / 0.07 / AB588032e
sB2 / F:
R: / AGGATCCCTTGCTGAGTGAGAAC
GTAACCAAGATTTTCCATGCTCC / 458 / 0.09 / AB588033e
sB3 / F:
R: / GATGTTGAGTACCTCAGAATCGGACTC
GACGCAGTCTCCTTTGTTATCGC / 601 / 0.09 / AB588027e
sB4 / F:
R: / CATTGCTCGGTACTGATTCTACAGG
AGTACGAACTTTGTGGGAAGAGGCT / 150 / 0.05 / PpINR_Pp.ap9b
sB5 / F:
R: / CCCTGGAGAAAAAGAAACAAACG
AAAGAGTTGAGGACCGATTTCATC / 643 / 0.09 / AB588026e
sB6 / F:
R: / AAACAAATCCCTCTCCAATTCAAG
CCTAGGCCATGAGTGCAGCATC / 555 / 0.13 / AB588031e
sC / sC1 / F:
R: / CTCACAAACAAAGTCACAAACACTCC
GCTGCAACATGGTTCATCTACACTCTC / 558 / 0.15 / AB588030e
sC2 / F:
R: / CGCCGAAGTCCAAGTCTAAGG
GAGCACAACCCAAAACTAAACCC / 183 / 0.11 / PtIFG_8702a
sC3 / F:
R: / AACATGATAGTGCCCACATTAGAGC
CCATGGACTGATGTTTCTCATCC / 723 / 0.10 / AB588034e
sC4 / F:
R: / TGTCACTGTTCTTCACCGATCAGAG
TCTTTAAATATACTGCCCTAGACAGCAGA / 230 / 0.05 / Pt3113c
sC5 / F:
R: / GAGGCATTTATGAGGGAACGAAACA
GTTGAAAGCGACTCCAAAGGTGAA / 252 / 0.08 / PtIFG_8429d
sC6 / F:
R: / AAAGAAAGAGGAAGAAGGCACTGTTG
CTTCAGAGTCCACGACACCCTTTAC / 413 / 0.07 / Pt2763c

aTemesgen et al. (2001); bChagné et al. (2003); cMitsugi and Shiraishi(2008); dBrown et al. (2001); ethis study