Citrus CAPS Marker Database

Locus name: Ov0403

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 900
Comment on PCR:
F-primer: CTGTCAAATCCACTCCCCAGA
R-primer: CATAAGCCCAGGCATTGTTG

EST info

EST Accession number 1: DC893934
EST Accession number 2: DC893935

sequence-tagged site (STS seq)

STS:
AGCTTGCTTGTGTTGTTGCTTCTTTATCGAGCGTGGCATGCATGTTTGATTTTGGTTACC
GATATGCCATTAGTTTTCAGCTTATGTAAAAATAAATAAAGAGATCAGACATAACTTCAA
TTTAAAACAAAAAGCTCTAGGCGCAAGAAAANTTGTAATTCTAGCGTAAGCAGTCTCAAG
TATCTGATCAAAGAAACCTGTAATCGACAAACAGGTACGGCCCAGACCGCCCAAAGTACT
TGGGACCATTCTCTGAGCAAACACCATCATACTTGACTGGTGAGTTCCCTGGTGACTANG
GCTGGGATACCGCTGGTTTATCAGCAGACCCCGAGACATTTGCTAAGAACCGTGAGCTAG
AGGTGATCCACAGCAGATGGGCAATGCTTGGAGCTCTTGGCTGCGTCTTCCCTGAAATCC
TCTCCAAGAATGGAGTGAAGTTCGGCGAAGCAGTTTGGTTCAAGGCTGGCGCTCAAATCT
TCTCTGAAGGTGGCCTTGACTATCTTGGCAACCCCAACCTCATTCATGCTCAGAGCATTT
TGGCTATCTGGGCCTGCCAGGTTGTGCTCATGGGTTTTGTTGAAGGATACAGAATTGGTG
GCGGTCCTCTTGGTGAAGGACTTGACCCACTTTACCCTGGTGGTGCTTTTGACCCACTTG
GTTTGGCTGATGACCCCGATCAATTTGCTGAGTTGAAGGTCAAGGAGCTCAAGAATGGCC
GTCTGGCTATGTTCTCCATGGTTGGATTCT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AGCGTGGCATGCATGTTTGATTTTGGTTACCGATATGCCATTAGTTTTCAGCTTATGTAA
AAATAAATAAAGAGATCAGACATAACTTCAATTTAAAACAAAAAGCTCTAGGCGCAAGAA
AAATTGTAATTCTAGCGTAAGCAGTCTCAAGTATCTGATCAAAGAAACCTGTAATCGACA
AACAGGTACGGCCCAGACCGCCCAAAGTACTTGGGACCATTCTCTGAGCAAACACCATCA
TACTTGACTGGTGAGTTCCCTGGTGACTAAGGCTGGGATACCGCTGGTTTATCAGCAGAC
CCCGAGACATTTGCTAAGAACCGTGAGCTAGAGGTGATCCACAGCAGATGGGCAATGCTT
GGAGCTCTTGGCTGCGTCTTCCCTGAAATCCTCTCCAAGAATGGAGTGAAGTTCGGCGAA
GCAGTTTGGTTCAAGGCTGGCGCTCAAATCTTCTCTGAAGGTGGCCTTGACTATCTTGGC
AACCCCAACCTCATTCA
STS source:
STS Forward / Reverse: Foward read
STS:
AGCGTGNCATGCATGTTTGATTTTGGTTACCGATATGCCATTAGTTTTCAGCTTATGTAA
AAATAAATAAAGAGATCAGACATAACTTCAAGTTAAAACAAAAAGCTCTAGGCGCAAGAA
AAATTGTAATTCTAGCGTAAGCAGTCTCAAGTATCTGATCAAAGAAACCTGTAATCGACA
AACAGGTACGGCCCAGACCGCCCAAAGTACTTGGGACCATTCTCTGAGCAAACACCATCA
TACTTGACTGGTGAGTTCCCTGGTGACTANGGCTGGGATACCGCTGGTTTATCAGCAGAC
CCCGAGACATTTGCTAAGAACCGTGAGCTAGAGGTGATCCACAGCAGATGGGCAATGCTT
GGAGCTCTTGGCTGCGTCTTCCCTGAAATCCTCTCCAAGAATGGAGTGAAGTTCGGCGAA
GCAGTTTGGTTCAAGGCTGGCGCTCAAATCTTCTCTGAAGGTGGCCTTGACTATCTTGGC
AACCCCAACCTCATTCATGCTCAGAGCATTTTGGCTATCTGGGCCTGCCAGGTTGTGCTC
ATGGGTTTTGTTGAAGGATACAGAATTGGTGGCGGTCCTCTTGGTGAAGGACTTGACCCA
CTTTACCCTGGTGGTGCTTTTGACCCACTTGGTTTGGCTGATGACCCCGATCAATTTGCT
GNTTTGAAGGTCAAGGAGCTCAAGAA
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CAAAAGCACCACCAGGGTAAAGTGGGTCAAGTCCTTCACCAAGAGGACCGCCACCAATTC
TGTATCCTTCAACAAAACCCATGAGCACAACCTGGCAGGCCCAGATAGCCAAAATGCTCT
GAGCATGAATGAGGTTGGGGTTGCCAAGATAGTCAAGGCCACCTTCAGAGAAGATTTGAG
CGCCAGCCTTGAACCAAACTGCTTCGCCGAACTTCACTCCATTCTTGGAGAGGATTTCAG
GGAAGACGCAGCCAAGAGCTCCAAGCATTGCCCATCTGCTGTGGATCACCTCTAGCTCAC
GGTTCTTAGCAAATGTCTCGGGGTCTGCTGATAAACCAGCGGTATCCCAGCCATAGTCAC
CAGGGAACTCACCAGTCAAGTATGATGGTGTTTGCTCAGAGAATGGTCCCAAGTACTTTG
GGCGGTCTGGGCCGTACCTGTTTGTCGATTACAGGTTTCTTTGATCAGATACTTGAGACT
STS source:
STS Forward / Reverse: Reverse read
STS:
TACCGATATG CCATTAGTTT TCAGCTTATG TAAAAATAAA TAAAGAGATC AGACA
TAACT TCAANTTAAA ACAAAAAGCT CTAGGCGCAA GAAAAATTGT AATTCTAGCG
TAAGCAGTCT CAAGTATCTG ATCAAAGAAA CCTGTAATCG ACAAACAGGT ACGG
CCCAGA CCGCCCAAAG TACTTGGGAC CATTCTCTGA GCAAACACCA TCATACTTG
A CTGGTGAGTT CCCTGGTGAC TATGGCTGGG ATACCGCTGG TTTATCAGCA GAC
CCCGAGA CATTTGCTAA GAACCGTGAG CTAGAGGTGA TCCACAGCAG ATGGGCAA
TG CTTGGAGCTC TTGGCTGCGT CTTCCCTGAA
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): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hha1
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: Hha1
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Rsa1
Comment: PCR_condition: 56C aneal
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: Rsa1
Comment: PCR_condition: 56C aneal
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: Rsa1
Comment: PCR_condition: 56C aneal
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: Ciclev10016280m
Scaffold: scaffold_2
Start: 23891814
End: 23893095

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00081:mRNA_50.1
Scaffold: C_unshiu_00081
Start: 296655
End: 297936
Gene function: Chlorophyll a/b binding protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 61.779

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-06
KmMg cM: 12.61

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
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/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: SI136
DNA sequence around SNP1:
CTTGGGACCATTCTCTGAGCAAACACCATCATACTTGACTGGTGAGTTCCCTGGTGACTA
[A/T]GGCTGGGATACCGCTGGTTTATCAGCAGACCCCGAGACATTTGCTAAGAACCGTG
AGCTA
SNP2: SI298
DNA sequence around SNP2:
GATATGCCATTAGTTTTCAGCTTATGTAAAAATAAATAAAGAGATCAGACATAACTTCAA
[T/G]TTAAAACAAAAAGCTCTAGGCGCAAGAAAA
SNP3: SI325
DNA sequence around SNP3:
CGTCGATCGGGAAGGTCACCCTGTTTGCTACAACATTTATGGGGTGTTTGAGAGTGATGA
[A/G]CTTTATCAGAAGACTTTTGGTACTGAGGAGAAGCGTGGCCAGTTCTTGAGATGGA
GGCTG
SNP4:
DNA sequence around SNP4: