Citrus CAPS Marker Database

Locus name: Ov0104

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1200
Comment on PCR:
F-primer: CCATACCTGCCCATCCC
R-primer: AAATTTACGCTTGACGCAAAA

EST info

EST Accession number 1: AU186385
EST Accession number 2: DC893808

sequence-tagged site (STS seq)

STS:
GCNNACATCTTTGCTAACATCATCACTTCCCGTAAATGTGCNGCAAAGTCAGAGAATGAC
ATGTTGCAGTCCTTCATTGACTCAAAGTACAAAGATGGCCGGCCCACAACTGAGTCTGAG
GTCACTGGTTTACTCATTGCCGCTCTTTTTGCTGGGCAGCACACCAGCTCAATCACCTCC
ACTTGGACTGGGGCCTATCTCCTCAAATACAAGGAGTGTCTATCTGCTGTGCAGGAGGAA
CAAAAAANCCTGATGAAAAAACACGGGAAAAGGGTTGATCATGATATCTTAGCTGAGATG
GATGTCCTCTATCGATGCATTAAGGAAGCCCTGAGACTACACCCTCCACTGATCATGCTT
TTGCGAAGCTCACACAGTGATTTTACTGTGCAGACCCGTGAAGGTAAAGAATACGACATA
CCAAAGGGACACATAGTTGGAACATCACCAGCNTTTGCAAACCGGCTTCCTCATATTTAC
AAGAATCCAGACAGTTACGATCCTGATAGGTTTGCTCCTGGAAGAGAAGAAGATAAGGCN
GCTGGGGCNTTCTCATATATTTCGTTTGGTGGGGGTAGGCATGGATGTCTTGGTGAGCCT
TTTGCATATCTGCAGATAAAGGCAATATGGAGCCATTTGTTAGAAATTTTGAATTTGAGC
TGATATCTCCTTTCCCTGAGATTGATTGGAATGCAATGGTTGTTGGTGT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AGAGAATGACATGTTGCAGTCCTTCATTGACTCAAAGTACAAAGATGGCCGGCCCACAAC
TGAGTCTGAGGTCACTGGTTTACTCATTGCCGCTCTTTTTGCTGGGCAGCACACCAGCTC
AATCACCTCCACTTGGACTGGGGCCTATCTCCTCAAATACAAGGAGTGTCTATCTGCTGT
GCAGGAGGAACAAAAAAACCTGATGAAAAAACACGGGAAAAGGGTTGATCATGATATCTT
AGCTGAGATGGATGTCCTCTATCGATGCATTAAGGAAGCCCTGAGACTACACCCTCCACT
GATCATGCTTTTGCGAAGCTCACACAGTGATTTTACTGTGCAGACCCGTGAAGGTAAAGA
ATACGACATACCAAAGGGACACATAGTTGGAACATCACCAGCATTTGCAAACCGGCTTCC
TCATATTTACAAGAATCCAGACAGTTACGATCCTGATAGGTTTGCTCCTGGAAGAGAAGA
AGATAAGGC
STS source:
STS Forward / Reverse: Foward read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
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

Rsetriction enzyme: Hae3
Comment:
Figure legend:
CV (No.1 Top) 101 Tahiti, 100 Rangpurlime, 102 Limonia, 104 LisbonL, 99 SweetLime, 92 Hirado, 87 MGF, 85 Kinukawa, 84 Hassaku, 83 Yamamikan, 78 Natsudaidai, 58 Rokugatu, Tr Trovita, 50 WNV, 44 Tankan, 42 Iyo,
(No.1 Bottom) 39 HgNt, 36 Ujukitsu, 32 Kawabata, 30 Shunkokan, 70 Yuzu, 54 Henka, 53 Ichang lemon, 37 Kunenbo, Mg Miyagawa, 31 Yatsushiro, 27 Kabuchii, 26 Ponkan, 25 Medet. 22. Dancy, 14 Tachibana, 11 Hirakishu (26' Ohta ponkan)
(No.2 Top) 6 Cleopatra, 4 CQ, 2 Fukuremikan, FD Hiryuu, 124 Largeleaf, 125 Small leaf, 141 CTV-S, 136 Rubidoaux,
(No.2 Bottom) FD, Hassaku, Km, F1, RP94, SA, 02, 04, 05, 06, 07, 08, 09, 10, 11, 13
BDZ BenDi Zao, SO Shuto, BP Banpeiyu
Rsetriction enzyme: Hinf1
Comment:
Figure legend:
CV (No.1 Top) 101 Tahiti, 100 Rangpurlime, 102 Limonia, 104 LisbonL, 99 SweetLime, 92 Hirado, 87 MGF, 85 Kinukawa, 84 Hassaku, 83 Yamamikan, 78 Natsudaidai, 58 Rokugatu, Tr Trovita, 50 WNV, 44 Tankan, 42 Iyo,
(No.1 Bottom) 39 HgNt, 36 Ujukitsu, 32 Kawabata, 30 Shunkokan, 70 Yuzu, 54 Henka, 53 Ichang lemon, 37 Kunenbo, Mg Miyagawa, 31 Yatsushiro, 27 Kabuchii, 26 Ponkan, 25 Medet. 22. Dancy, 14 Tachibana, 11 Hirakishu (26' Ohta ponkan)
(No.2 Top) 6 Cleopatra, 4 CQ, 2 Fukuremikan, FD Hiryuu, 124 Largeleaf, 125 Small leaf, 141 CTV-S, 136 Rubidoaux,
(No.2 Bottom) FD, Hassaku, Km, F1, RP94, SA, 02, 04, 05, 06, 07, 08, 09, 10, 11, 13
BDZ BenDi Zao, SO Shuto, BP Banpeiyu

Experiments: Segregation pattern

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hae3
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: Hae3
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 Miyagawa-wase
Restriction enzyme: Hae3
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
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: Ciclev10004850m
Scaffold: scaffold_9
Start: 13440332
End: 13442904

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_02379:mRNA_2.1
Scaffold: C_unshiu_02379
Start: 22906
End: 25482
Gene function: Obtusifoliol 14-alpha demethylase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 56.724

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-08
JtTr cM: 28.207

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

Km/O41 LG:
Km/O41 cM:

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:

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

SNP1: SI216
DNA sequence around SNP1:
GACCCGTGAAGGTAAAGAATACGACATACCAAAGGGACACATAGTTGGAACATCACCAGC
[A/T]TTTGCAAACCGGCTTCCTCATATTTACAAGAATCCAGACAGTTACGATCCTGATA
GGTTT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: