Citrus CAPS Marker Database

Locus name: Ov0020

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 2200
Comment on PCR:
F-primer: AGCTGAGATGGCACTGGT
R-primer: TGGACATAAGATTTGGCAACT

EST info

EST Accession number 1: AU186345
EST Accession number 2: DC893762

sequence-tagged site (STS seq)

STS:
TGTGAAACCTAATGTAAGATCTTGAATTGCATGCTAAATGTGTTTTTATAAGTCGCATGA
CATAAAGGATACTTTTCTAGGTATCAGTAAGTTCATATATTCTTCTCCTGATAATTTCAT
AATTGTTCCTGCAGGTGTATGTCACAATGTATCTCAATGACTGCCAGCGTACTGCTTTCT
ATGAGGGCATTGGACTAGACACCAAAGAATTTGACATGCATGTCATCATTGAGGTTAGTC
TGTGGCTGAGCTTGTTAGTGTGCTTTTTACAGAAGTTTATGAAGATTTCTGTGCTGCNAA
TCAATTGTCAATATGTAGAACTTGACAGCACATTGTGTACCAGCCAAGTGAGCCAACNAA
GCTCACTTTAACAATATCCTGCTTTTCTTCATTTGCATTTTNAGTTTTAGTAAGACATCT
AACAGTGTCAGTGTCATATCTATATGACCTAGGAAAAGAGGACAGAATTACCATTTTTTA
TGATACTTGAACTTGTGTATCTGAAATTCTTTTTCTACAGACCAATCGCACAACGGCTAG
AATTTTCCCTGCTGTGCTGGATGTTGAAAACCCAGAGTTCAAGAGGAGGTTGGATCGGAT
GGTAGAGATCAACGAGAGGCTTCTTGCTGTAGGGGCGACCGATTNGACA
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CGGTCGCCCCTACAGCAAGAAGCCTCTCGTTGATCTCTACCATCCGATCCAACCTCCTCT
TGAACTCTGGGTTTTCAACATCCAGCACAGCAGGGAAAATTCTAGCCGTTGTGCGATTGG
TCTGTAGAAAAAGAATTTCAGATACACAAGTTCAAGTATCATAAAAAATGGTAATTCTGT
CCTCTTTTCCTAGGTCATATAGATATGACACTGACACTGTTAGATGTCTTACTAAAACTA
AAAATGCAAATGAAGAAAAGCAGGATATTGTTAAAGTGAGCTTTGTTGGCTCACTTGGCT
GGTACACAATGTGCTGTCAAGTTCTACATATTGACAATTGATTTGCAGCACAGAAATCTT
CATAAACTTCTGTAAAAAGCACACTAACAAGCTCAGCCACAGACTAACCTCAATGATGAC
ATGCATGTCAAATTCTTTGGTGTCT
STS source:
STS Forward / Reverse: Reverse 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: 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

Rsetriction enzyme: Hind3
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: NC
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Hind3
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: 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: 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: Ciclev10011842m
Scaffold: scaffold_6
Start: 21598429
End: 21600967

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00037:mRNA_7.2
Scaffold: C_unshiu_00037
Start: 37719
End: 40241
Gene function: Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 55.145

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 22.465

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-04
Km/O41 cM: 3.806

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

Rp/Sa LG: RP-04
Rp/Sa cM: 40.905

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: SI055
DNA sequence around SNP1:
GTTGGCTCACTTGGCTGGTACACAATGTGCTGTCAAGTTCTACATATTGACAATTGATT[
T/C]GCAGCACAGAAATCTTCATAAACTTCTGTAAAAAGCACACTAACAAGCTCAGCCAC
AGAC
SNP2: SI143
DNA sequence around SNP2:
ACTGACACTGTTAGATGTCTTACTAAAACT[A/G]AAAATGCAAATGAAGAAAAGCAGGA
TATTGTTAAAGTGAGCTT
SNP3: SI213
DNA sequence around SNP3:
ATCCAACCTCCTCTTGAACTCTGGGTTTTCAACATCCAGCACAGCAGGGAAAATTCTAGC
[T/C]GTTGTGCGATTGGTCTGTAGAAAAAGAATTTCAGATACACAAGTTCAAGTATCAT
AAAAA
SNP4:
DNA sequence around SNP4: