Citrus CAPS Marker Database

Locus name: If0208

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 600
Comment on PCR:
F-primer: AATATTTCTGCGAATCACTGA
R-primer: GCAAACCACACCAAGGA

EST info

EST Accession number 1: DC893504
EST Accession number 2: DC893505

sequence-tagged site (STS seq)

STS:
TATCACAGGGCTCAGGGGATACTTGACTTCTGCTTTCTTCACGACGGGCTTAAAGGTTGT
TGCCCCTCTCTTTGCCGTCTATGTAACTTGGCCAGTGCTTCGACTGCCAGCCTTGGTTGC
AGTGCTTCCATTTCTGGTTGGTTGTGCGGCTCAACTTGCATTTGAGACCAATCTTGACAA
GCGTGGGTCATCATGTTGGCCCTTAATTCCTATCATCTTTGAGGTTGTTTCTTGACTCAT
ATTTATCTTTCTCAGGCCAAAATCAAGGATTTATTAACTTTATTTTAAAATCAAGGATTT
TAATGACTTTATTTTATTGGCAGGTATACAGACTTTATCAGTTGAGCAAAGCTGCTAATT
TCATTGAGAGATTGATGTTCTCAATGAAAGATCTTCCGAGATCTCCGGAATTGCTGGAAA
GAGGCAGTGCAATGGTTTCCATGGTAGTGATTTTCCAA
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read
STS:
GGTGGGGTCTTATCACAGGGCTCAGGGGATACTTGACTTCTGCTTTCTTCACGACGGGCT
TAAAGGTTGTTGCCCCTCTCTTTGCCGTCTATGTAACTTGGCCNGTGCTTCGACTGCCAG
CCTTGGTTGCAGTGCTTCCATTTCTGGTTGGTTGTGCGGCTCAACTTGCATTTGAGACCA
ATCTTGACAAGCGTGGGTCNTCATGTTGGCCCTTAATTCCTATCATCTTTGAGGTTGTTT
CTTGACTCATATTTNTCTTTCTCAGGCCAAAATCAAGGATTTNTTAACTTTATTTTAAAA
TCAAGGATTTTAATGACTTTATTTTATTGGCAGGTATACAGACTTTATCAGTTGAGCAAA
GCTGCTAATTTCATTGAGAGATTGATGTTCTCAATGAAAGATCTTCCGAGATCTCCGGAA
TTGCTGGAAAGAGGCAGTGCAATGGTTTCCATGGTAGTGATTTTCCAA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CTCGGAAGATCTTTCATTGAGAACATCAATCTCTCAATGAAATTAGCAGCTTTGCTCAAC
TGATAAAGTCTGTATACCTGCCAATAAAATAAAGTCATTAAAATCCTTGATTTTAAAATA
AAGTTAATAAATCCTTGATTTTGGCCTGAGAAAGAAAAATATGAGTCAAGAAACAACCTC
AAAGATGATAGGAATTAAGGGCCAACATGATGACCCACGCTTGTCAAGATTGGTCTCAAA
TGCAAGTTGAGCCGCACAACCAACCAGAAATGGAAGCACTGCAACCAAGGCTGGCAGTCG
AAGCACTGGCCAAGTTACATAGACGGCAAAGAGAGGGGCAACAACCTTTAAGCCCGTCGT
GAAGAAAGCAGAAGTCAAGTATCCCCTGAGCCCTGTGATAAGACCCCACCTCTTTGGGCT
GAATTGTAAA
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Reverse read
STS:
AATATTTCTGCCAATCACTGATCGAGTTCAGAGGCCATATTTACAATTCAGCCCAAAGAG
GTGGGGTCTTATCACAGGGCTCAGGGGATACTTGACTTCTGCTTTCTTCACGACGGGCTT
AAAGGTTGTTGCCCCTCTCTTTGCCGTCTATGTAACTTGGCCAGTGCTTCGACTGCCAGC
CTTGGTTGCAGTGCTTCCATTTCTGGTTGGTTGTGCGGCTCAACTTGCATTTGAGACCAA
TCTTGACAAGCGTGGGTCNTCATGTTGGCCCTTAATTCCTATCATCTTTGAGGTTGTTTC
TTGACTCATATTTNTCTTTCTCAGGCCAAAATCAAGGATTTATTAACTTTATTTTAAAAT
CAAGGATTTTAATGACTTTATTTTATTGGCAGGTATACAGACTTTATCAGTTGAGCAAAG
CTGCTAATTTCATTGAGAGATTGATGTTCTCAATGAAAGATCTTCCGAGATCTCCGGAAT
TGCTGGAAAGAGGCAGTGC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
GGTGGGGTCT TATCACAGGG CTCAGGGGAT ACTTGACTTC TGCTTTCTTC ACGAC
GGGCT TAAAGGTTGT TGCCCCTCTC TTTGCCGTCT ATGTAACTTG GCCTGTGCTT
CGACTGCCAG CCTTGGTTGC AGTGCTTCCA TTTCTGGTTG GTTGTGCGGC TCAA
CTTGCA TTTGAGACCA ATCTTGACAA GCGTGGGTCATCATGTTGGC CCTTAATTC
C TATC
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinf1
Rank as CAPS marker: Available marker
Comment:
Figure legend:
CVName 1. Nagami, 2. Budha's, 3. Miyagawa, 4. Trovita, 5. Kiyomi, 6. Tachibana, 7. Koji, 8. Kinokuni (8' Hirakishu), 9. Mato pumello, 10. Kunip,
11. King, 12. Ponkan (12' Ohta ponkan), 13. Dancy, 14. Willowleaf, 15. Clementine, 16. C-haploid, 17. Encore, 18. Amaka, 19. Youkou, 20. Shiranuhi,
21. Harumi, 22. Nishinokaori, 23. Duncan GF, 24. Mineola, 25. Seminol, 26. Seihou, 27. Akemi, 28. Tsunokaori, 29. Ariake, 30. Nankou,
31. Mihocore, 32. Hareyaka, 34. Harehime, 35. Hayaka, 36. Southern Red, 37. Amakusa, 38. Setoka, *. Flying Dragon, SY(Southern Yellow), 40(MK, Mukakukishu)

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Hinf1
Comment:
Figure legend:
A: A255 (Okitu46gou), G: G434 (Kankitsu Chuukanbohon Nou5gou),
K or Km: Kiyomi, M or Mg: Miyagawa-wase, MK: Mukaku kisyu,
LE: Lee, O: Okitsu41gou, RP or RP94: Kankitsu Chukanbohon Nou6gou,
Sacd or SA: Siamese Acidless, SW: Sweet spring, T or Tr: Trovita orange,
X: meaningless
Population name: Jutaro unshu x Trovita orange
Restriction enzyme: Hinf1
Comment:
Figure legend:
A: A255 (Okitu46gou), G: G434 (Kankitsu Chuukanbohon Nou5gou),
K or Km: Kiyomi, M or Mg: Miyagawa-wase, MK: Mukaku kisyu,
LE: Lee, O: Okitsu41gou, RP or RP94: Kankitsu Chukanbohon Nou6gou,
Sacd or SA: Siamese Acidless, SW: Sweet spring, T or Tr: Trovita orange,
X: meaningless
Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hinf1
Comment:
Figure legend:
A: A255 (Okitu46gou), G: G434 (Kankitsu Chuukanbohon Nou5gou),
K or Km: Kiyomi, M or Mg: Miyagawa-wase, MK: Mukaku kisyu,
LE: Lee, O: Okitsu41gou, RP or RP94: Kankitsu Chukanbohon Nou6gou,
Sacd or SA: Siamese Acidless, SW: Sweet spring, T or Tr: Trovita orange,
X: meaningless
Population name: Kiyomi x Okitsu41gou
Restriction enzyme: Hinf1
Comment:
Figure legend:
A: A255 (Okitu46gou), G: G434 (Kankitsu Chuukanbohon Nou5gou),
K or Km: Kiyomi, M or Mg: Miyagawa-wase, MK: Mukaku kisyu,
LE: Lee, O: Okitsu41gou, RP or RP94: Kankitsu Chukanbohon Nou6gou,
Sacd or SA: Siamese Acidless, SW: Sweet spring, T or Tr: Trovita orange,
X: meaningless

Target on C. clementina (v1.0)

Transcript ID: Ciclev10001680m
Scaffold: scaffold_5
Start: 40628244
End: 40630241

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00234:mRNA_9.1
Scaffold: C_unshiu_00234
Start: 94988
End: 99176
Gene function: TRNA-processing ribonuclease BN

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 39.296

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-09
KmMg cM: 72.036

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-09S
JtTr cM: 115.15

Km/O41 map info (Nakano et al. 2003)

Km/O41 LG: NAT-09
Km/O41 cM: 89.867

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG:
Rp/Sa cM:

CAPS genotyping (Hybrid cv/Citrus collection)

CAPS genotyping: Hb

Cultivar identification (M: Cultivar identification manual / T: Ninomiya et al. 2015/ K: Nonaka et al. 2017)

Cultivar identification M/T/K: M,K

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI083
DNA sequence around SNP1:
AGTCAAGAAACAACCTCAAAGATGATAGGAATTAAGGGCCAACATGA[T/C]GACCCACG
CTTGTCAAGATTGGTCTCAAATGCAAGTTGAGCCGCACAACCAACCAGAAAT
SNP2: SI317
DNA sequence around SNP2:
TTTCTTCACGACGGGCTTAAAGGTTGTTGCCCCTCTCTTTGCCGTCTATGTAACTTGGCC
[A/T]GTGCTTCGACTGCCAGCCTTGGTTGCAGTGCTTCCATTTCTGGTTGGTTGTGCGG
CTCAA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: