Citrus CAPS Marker Database

Locus name: Ov0509

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 750
Comment on PCR:
F-primer: CGGGGCCATAATAATG
R-primer: AATAGTACCTACCAGCCAAAA

EST info

EST Accession number 1: DC894046
EST Accession number 2: DC894047

sequence-tagged site (STS seq)

STS:
TTGTGATCAACAATTCTTCATTTTGCTTCAATGTTTCAGAGTATGATCGAAGCCTGTATA
ATGAGATTCAATTAAACTAGGCATAGTTCTTCATAGTTATACCGTATGAAGAATCTGTCT
AATATTAAATGGCGGGCAGTAGTCAACTTTTCTTAGCATGCTTTATCCTTGCTAGGGCAA
CTTAACATGGTNTCAGNGCTAAATTGACTTAATCTTGTGTTCAGTCTCCTTGTTGAATTA
ATTAATTTATGAAATTGGGGAATGGTAAAATTGTGCNAGCCACTTAAAAGAAAGTGATGG
AGAAATTGTGTAAGACTGGCAGCCTCAAAGCTGTAAGAATTCAGGAGTATTTGGGGGCTA
TATATATGAAGAGAAAACCT
STS source: Consensus seuqence of 12 cvs.
STS Forward / Reverse: Foward read
STS:
CTCCACCTNACAATTTGTNACTGCTTTCCNCCTAATAAGAGGTTTTNTCTTCATATATAT
AGCCCCCAAATACTCCTGAATTCTTACAGCTTTGAGGCTGCCAGTCTTACACAATTTCTC
CATCACTTTCTTTTAAGTGGCTGGCACAATTTTACCATTCCCCAATTTCATAAATTAATT
AATTCAACAAGGAGACTGAACACAAGATTAAGTCAATTTAGCTCTGANACCATGTTAAGT
TGCCCTAGCAAGGATAAAGCATGCTAAGAAAAGTTGACTACTGCCCGCCATTTAATATTA
GACAGATTCTTCATACGGTATAACTATGAAGAACTATGCCTAGTTTAATTGAATCTCATT
ATACAGGCTTCGATCATACTCTGAAACATTGAAGCAAAATGAAGAATTGTTGATCACAAG
CAGACATAAACCAGAGACAAATGACTCAAATCAGATAAAAGAGTCTTGGAAGATAACTTT
AAAAAAAAAAACATTAATTAATTCNTTATCCAAGGCATCTGACTTCAAGCTTTTTGCATT
GCACANATTAACTTCATGAATATTATTGATTCCATCAAACAACATTAACATGTTGCGCTA
TCAATCTCAAATATATTACCAGCTCGATATGCACATTTCTCAAATAAAGAACCGCTTCCT
GTGGTTAATTATCAAATTGACTCAGTTATCTTATCATACTTTTGGCGGGNAAGGTACTAT
TAAA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TCATATATATAGCCCCCAAATACTCCTGAATTCTTACAGCTTTGAGGCTGCCAGTCTTAC
ACAATTTCTCCATCACTTTCTTTTAAGTGGCTGGCACAATTTTACCATTCCCCAATTTCA
TAAATTAATTAATTCAACAAGGAGACTGAACACAAGATTAAGTCAATTTAGCTATGAAAC
CATGTTAAGTTGCCCTAGCAAGGATAAAGCATGCTAAGAAAAGTTGACTACTGCCCGCCA
TTTAATATTAGACAGATTCTTCATACGGTATAACTATGAAGAACTATGCCTAGTTTAATT
GAATCTCATTATACAGGCTTCGATCATACTCTGAAACATTGAAGCAAAATGAAGAATTGT
TGATCACAAGCAGACATAAACCAGAGACAAATGACTCAAATCAGATAAAAGAGTCTTGGA
AGATAACTTT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CAAATGACTCAAATCAGATAAAAGAGTCTTGGAAGATAACTTTAAAAAAAAAAACATTAA
TTAATTCATTATCCAGAGGCATCTGACTTCAAGCTTTTTGCATTGCACAGATTAACTTCA
TGAATATTATTGATTCCATCAAACAACATTAACATGTTGCGCTATCAATCTCAAATATAT
TACCAGCTCGATATGCACATTTCTCAAATAAAGAACCGCTTCCTGTGGNAANTANC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase/Poncirus
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Shiamese acidless/RP-94
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Sty1
Rank as CAPS marker: Less informative for main cultivars
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: 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
Rsetriction enzyme: Sty1
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: Dra1
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: Dra1
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: Dra1
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: Sty1
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: Sty1
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:
Scaffold:
Start:
End:

Target on C. unshiu (v1.0)

Transcript ID: No
Scaffold:
Start:
End:
Gene function:

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 102.28

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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-09
Rp/Sa cM: 21.445

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:
DNA sequence around SNP1:
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: