Citrus CAPS Marker Database

Locus name: Ov0002

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1400
Comment on PCR:
F-primer: GAAGAAGACCGGCAAGGTGTT
R-primer: TCTTCCAGGTTGGCGTTGAG

EST info

EST Accession number 1: AU186184
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GATGTCGGGATGAAGAAGAAAGGCGTCGACGAGTTCCCCTTCTGCGTTCACCTCGTCAGT
TGGGAGAAGGAGAACGTGTCGAGCGAGGCCTTGGAAGCTGCCCGTATCGCTTGCAACAAG
TACATGGCCAAGTACGCCGGCAAGGATGCTTTCCATTTGCGAGTGAGGGTGCACCCCTTC
CATGTTCTGCGTATTAACAAGATGCTTTCGTGTGCTGGGGCTGATAGGCTCCAGACTGGA
ATGAGGGGTGCTTTTGGAAAGCCCCAAGGAACCTGTGCTCGTGTTGCTATCGGGCAGGTC
TTGCTTTCTGTCCGTTGCAAGGATAGTAACAGCCACCATGCTCAGGAGGCCCTTCGCCGT
GCTAAGTTCAAGTTTCCTGGTCGTCAAAAGATTATTGTCA
STS source: Clementine haploid
STS Forward / Reverse: Foward read
STS:
GGCGTCGACGAGTTCCCCTTCTGCGTTCACCTCGTCAGTTGGGAGAAGGAGAACGTGTCG
AGCGAGGCCTTGGAAGCTGCCCGTATCGCTTGCAACAAGTACATGGCCAAGTACGCTGGC
AAGGATGCTTTCCATTTGCGAGTGAGGGTGCACCCCTTCCATGTTCTGCGCATTAACAAG
ATGCTTTCGTGTGCTGGGGCTGATCGGCTCCAGACTGGAATGAGGGGTGCTTTTGGAAAG
CCCCAAGGAACCTGTGCTCGTGTTGCTATCGGGCAGGTCTTGCTTTCTGTCCGTTGCAAG
GACAGTAACAGCCACCATGCTCAGGAGGCCCTTCGCCGTGCTAAGTTCAAGTTTCCTGGT
CGTCAAAAGATTATTGTCAGCAGGAAATGGTATGCGTTTTTATCCATGACTGCATTCATG
TTAAAGTTAACTCGTATTTGCTTGTATTATATGGATTGGCGTGTCACAAGATTAGCAGAT
CACATGGATTAAGTTGCCTGGTGCTGGTGTCTCTAGTAGTGAGTTTAAAAAATCTACCCT
TATTTAAATTTTTTTCTTTTTTCTTTTTTAAAGAAAAACACAATCAATTAGATGCCTGTT
GCTGGTAGTCTCTA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AGTTCCCCTTCTGCGTTCACCTCGTCAGTTGGGAGAAGGAGAACGTGTCGAGCGAGGCCT
TGGAAGCTGCCCGTATCGCTTGCAACAAGTACATGGCCAAGTACGCTGGCAAGGATGCTT
TCCATTTGCGAGTGAGGGTGCACCCCTTCCATGTTCTGCGCATTAACAAGATGCTTTCGT
GTGCTGGGGCTGATCGGCTCCAGACTGGAATGAGGGGTGCTTTTGGAAAGCCCCAAGGAA
CCTGTGCTCGTGTTGCTATCGGGCAGGTCTTGCTTTCTGTCCGTTGCAAGGACAGTAACA
GCCACCATGCTCAGGAGGCCCTTCGCCGTGCTAAGTTCAAGTTTCCTGGTCGTCAAAAGA
TTATTGTCAGCAGGAAATGGTATGCG
STS source:
STS Forward / Reverse: Foward read
STS:
ACAAGATTAGCAGTTCCCTGGATTAAGTTGCCTGGGCTGGGTCTTTAGTAGTGAGNTTAA
AAATCTNCCCTTATTAAATTTTTTCTTTTTTCTTTTTNAAGAAAAAACCCAATCAATTAG
ATGCCTGTTGCTGGTAGTCTCTAGGTTTGGGTTTAAAAAATTAACTTCAGGTAGTGTAAT
GGAGCTTTAGGGACATATGAGNGTTAGATTGAATTTCTATTTGTTTATTNTAGGCTGATC
GNGCTTTTTTTTTTTAAAATACCCATATCTATATGAATGCTCTCTTAAGATCTTGTTTGG
GTTTACTTTCTCACTATTGCATAATTATGCTTGTTTTTAGGGGATTTACCAAGTTCAGCC
GTGCTGATTATCTGAGGTGGAAGTCGGAGAACAGGATTGTCCCAGATGGTGTGAATGCCA
AGGTAACATCAAACTTTATTGGAGTTAAAACATTATTGCATTGCAATTTTGCTTTACTTG
AGTTCTTTATAAAATAGTGTTGTCAATCTCTATATTGTGTGTCGAAGCAATCTGCTTTTG
CCTCAGTCGATGCATTATTGTTCTGTTCTACTTCTGGAATTTGTTCTCTTCAATTTAGCC
TCTCGTGTCCTTTCTTGATTTAGTGTTTATGACTGATGGTATTTGC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
GAACAAATTCCAGAAGTAGAACAGAACAATAATGCATCGACTGAGGCAAAAGCAGATTGC
TTCGACACACAATATAGAGATTGACAACACTATTTTATAAAGAACTCAAGTAAAGCAAAA
TTGCAATGCAATAATGTTTTAACTCCAATAAAGTTTGATGTTACCTTGGCATTCACACCA
TCTGGGACAATCCTGTTCTCCGACTTCCACCTCAGATAATCAGCACGGCTGAACTTGGTA
AATCCCCT
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: 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
Rsetriction enzyme: Msp1
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: Kiyomi x Okitsu41gou
Restriction enzyme: Hinc2
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
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: 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10032770m
Scaffold: scaffold_4
Start: 2422861
End: 2424838

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00979:mRNA_13.2
Scaffold: C_unshiu_00979
Start: 50508
End: 52478
Gene function: 60S ribosomal protein L10

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 13.657

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 68.221

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-07
Rp/Sa cM: 82.035

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: SI110
DNA sequence around SNP1:
GGCAAGGATGCTTTCCATTTGCGAGTGAGGGTGCACCCCTTCCATGTTCTGCG[T/C]AT
TAACAAGATGCTTTCGTGTGCTGGGGCTGAT
SNP2: SI179
DNA sequence around SNP2:
AAGTAAAGCAAAATTGCAATGCAATAA[T/C]GTTTTAACTCCAATAAAGTTTGATGTTA
CCTTGGCATTCACACCATCTGGGACAATCCTG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: