Citrus CAPS Marker Database

Locus name: Ov0105

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 1200
Comment on PCR:
F-primer: ACATGTGCCGAAAGCCTTAC
R-primer: GGCGGTGATTTATCGTGATTT

EST info

EST Accession number 1: AU186386
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GGATTCCCATGGACATCCGCCATCTTTTTCTGGCTACCATATCAGCAACATCCCATGGAT
TTAGCATGGACATCCCCCATCAGATTCATCTTCTCCGACCGAAAGCCGGTTCCCGGAACA
ACGATGTTCCCGGCTTGTCCTGCCTGAGTTGGCGACTCGGAGTGGAAACTAATAACGTTA
TAGGATGGGCGACTGTTCCCGAAAAATGTGCAGGCTACGTGGGGCATTACATGTTAGGCC
AGCAGTACCGCATGGACTCTGAAGTGGTAGCTAATGAGGCCATTCTCTATGCGCAGAGCC
TCAAGCTTGCTGGCGACGGCAAGAACATTTGGGTTTTCGACATAGATGAAACCTCGCTAT
CTAATTTGCCATATTATGCTAAGAATGGATTCGGGTACGTCCGTGACCGTAAATTAACTT
AAACTTCACTTTGTCACCTATATAATTTGGACTTGAGATATATGCCATGATATGTATAGT
TTTTAATTTNTTTTTTTT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CAGCAACATCCCATGGATTTAGCATGGACATCCCCCATCAGATTCATCTTCTCCGACCGA
AAGCCGGTTCCCGGAACAACGATGTTCCCGGCTTGTCCTGCCTGAGTTGGCGACTCGGAG
TGGAAACTAATAACGTTATAGGATGGGCGACTGTTCCCGAAAAATGTGCAGGCTACGTGG
GGCATTACATGTTAGGCCAGCAGTACCGCATGGACTCTGAAGTGGTAGCTAATGAGGCCA
TTCTCTATGCGCAGAGCCTCAAGCTTGCTGGCGACGGCAAGAACATTTGGGTTTTCGACA
TAGATGAAACCTCGCTATCTAATTTGCCATATTATGCTAAGAATGGATTCGGGTACGTCC
GTGACCGTAAATTAACTTAAACTTCACTTTGTCACCTATATAATTTGGACTTGAGATATA
TGCCATGATATGTATAGTTTTTAATTT
STS source:
STS Forward / Reverse: Foward read
STS:
TTTTTTTTCAGGGTGAAGCCATACAACCCTACTTTGTTTAATGAATGGGTGAACACCGGA
AAAGCACCACCGCTGCCAGAGAGCCTTAAGCTTTACAAAAAATTATTATTGCTTGGAATT
AAGATTGTATTCCTCACGGGAAGACCAGAAGATCAGAGAAANGTTACAGAAGCTAATTTA
AAGCATGCTGGATTCGACACCTGGGAGAAGCTCATCCTCAAGTAATTAATGATGCGTGTT
TTCATCACGTTTATTTTAATGTTTATATGTCAACTAATTAATAACAAGTAAAAATTAATA
AATTGGCTGCAGGGGATCATCTCACTCAGGAGAAACAGCAGTGGTGTACAAATCAAGTGA
AAGAAAGAAGCTTGAGATGAAAGGGTACAGAATTATTGGAAACATAGGTGATCAATGGAG
CGATCTCCTGGGCACCAACGCCGGCAATCGGACGTTCAAGCTGCGGNCCC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CGTTGGTGCCCAGGAGATCGCTCCATTGATCACCTATGTTTCCAATAATTCTGTACCCTT
TCATCTCAAGCTTCTTTCTTTCACTTGATTTGTACACCACTGCTGTTTCTCCTGAGTGAG
ATGATCCCCTGCAGCCAATTTATTAAATTTTTACTTGTTATTAATTAGTTGACATATAAA
CATTAAAATAAACGTGATGAAAACACGCATCATTAATTACTTGAGGATGAGCTTCTCCCA
GGTGTCGAATCCAGCATGCTTTAAATTAGCTTCTGTAACATTTCTCTGATCTTCTGGTCT
TCCCGTGAGGAATACAATCTTAATTCCAAGCAATAATAATTTTTTGTAAAGCTTAAGGCT
CTCTGGCAGCGGTGGTGCTTTTCCGGTGTTCACCCATTCATTAAACAAAGTAGGGTTGTA
TGGCTTCACCCTGAAAAAAAATTAATT
STS source:
STS Forward / Reverse: Reverse read
STS:
TAATGCCAAGCTCTCGGACTTCGGACTTGCAAAAGATGGTCCTGAGGGTGATAAAACCCA
TGTATCAACCCGTGTGATGGGGACTTATGGCTATGCAGCCCCAGAATATGTAATGACAGG
TACGTGTAACTAAAGTAAAACTCATTTGAATTCTCTCTTCTCCTTTTTCTTCCCATTTTC
AATTTAATTTGAAACCAAAATGTTAATGAGGAAAAGGAAGCCTCGGTCGCAGTCTGTCTG
CCTTTCACAGCCTGCATTCATTGCACGCTTTTGGTTTGTAACTTAGTAGAATACAGACTT
TTAAGGAACTTTGTGGTTCTATTAGAGCTTATCTTAAATCGGACT
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: Hae3
Rank as CAPS marker: Disagree by Marco analysis
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: 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: 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

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: Kiyomi x Okitsu41gou
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: 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10031362m
Scaffold: scaffold_4
Start: 23552856
End: 23556415

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00001:mRNA_81.1
Scaffold: C_unshiu_00001
Start: 545345
End: 548897
Gene function: Receptor-like kinase plant

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

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: NAT-07
Km/O41 cM: 36.023

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

Rp/Sa LG: RP-07
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: SI126
DNA sequence around SNP1:
ACATTTGGGTTTTCGACATAGATGAAACCTCGCTAT[C/G]TAATTTGCCATATTATGCT
AAGAATGGATTCGGGTACGTCCGTGACCGTAAATTAACTTA
SNP2: SI278
DNA sequence around SNP2:
CAATAATAATTTTTTGTAAAGCTTAAGGCTCTCTGGCAGCGGTGGTGCTTTTCCGGTGTT
[A/C]ACCCATTCATTAAACAAAGTAGGGTTGTATGGCTTCACCCTGAAAAAAAATTAAT
T
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: