Citrus CAPS Marker Database

Locus name: Ov0305

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1250
Comment on PCR:
F-primer: CATCTGGTCCCCACAAGT
R-primer: AGCTTTAGAGAGTGCCAATCA

EST info

EST Accession number 1: AU186464
EST Accession number 2: DC893878

sequence-tagged site (STS seq)

STS:
GNATTGCGANCCGTTTGAAATATGCTCTCACATATCGTGAAGTTATTGCTATTCTGATGC
AACGACATGTTCTTGTTGATGGGAAGGTTAGGACAGATAAGACCTACCCTGCTGGTTTCA
TGGGTATGTGAACTTCTCTCTTTGCAAGTAACTAGATTTTTTTTCCTTTTTTTGGAAATG
GTATTCTGTAATCTTGATTTTAGATCTATTAGTTATATAGGAGTAGCAGTTTCTTTTCAT
TCTTCTGCCNGGCCTATTCTTTGCAGAATTGTTGGTTTGAGGTACTGAGATTGTTATGTC
CTTTTTTTT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TATGCTCTCACATATCGTGAAGTTATTGCTATTCTGATGCAACGACATGTTCTTGTTGAT
GGGAAGGTTAGGACAGATAAGACCTACCCTGCTGGTTTCATGGGTATGTGAACTTCTCTC
TTTGCAAGTAACATGATTTTTTTTCCTTTTTTTGGAAATGGTATTCTGTAATCTTGATTT
TAGATCTATTAGTTATATAGGAGTAGCAGTTTCTTTTCATTCTTCTGCCTGGCCTATTCT
TTGCAGAATTGTTGGTTTGAGGTACTGAGATTGTTATGTCCTTTTTTTT
STS source:
STS Forward / Reverse: Foward read
STS:
CAGAGATGAGGAGGCAAAAGTATGTCTATAACTTATAGTTGATTCTCTTTGTACTCTCTG
GGTTTTTAATATTAATTTGCTGTGAAATTGCTTGTTTGAATCAAGAATTATTACTGCTGA
TAACTTATCATTATGCATGTATGTAGTTGGTNTCTCCAATTCTCTTACAAACTTGTAGTG
CATATTTTCCATTNTTTGCATATTCATCACTAATGAATATCACATGTTAACATCTCGAGT
CTCTTTAAATTTATATGAATTTTCTGTAATGCAGTTCAAGCTTTGCAAAGTTAGATCAGT
CCAGTTTGGCCAGAAAGGTATCCCATACATCAACACCTATGATGGGCGTACCATCCGCTA
CCCTGACCCACTCATCAAAGCCAATGATACCATCAAACTTGACTTAGAAGAGAACAAGAT
CACTGACTTCATCAAGTTTGATGTTGGGAATATTGTCATGGTCACTGGGGGTAGAAACAG
AGGTCGAGTTGGAATCATCAAGAACAGGGAAAAGCATAAGGGAAGTTTTGAGACCATCCA
TATTCAAGATGCCCTTGGTCATGAGTTTGCAACTCGNCTAGGCAATGTGTTCACCATCGG
GAAGGGTTCAAAACCATGGGTGTCACTTCCTAAGGGCAAGGGTATTAAGTTGTCCATCAT
TGAGGAAGCTAGGAAGAGACAGGCTGCCCAGGCTGCTGG
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
GCAGCCTGGGCAGCCTGTCTCTTCCTAGCTTCCTCAATGATGGACAACTTAATACCCTTG
CCCTTAGGAAGTGACACCCATGGTTTTGAACCCTTCCCGATGGTGAACACATTGCCTAGA
CGAGTTGCAAACTCATGACCAAGGGCATCTTGAATATGGATGGTCTCAAAACTTCCCTTA
TGCTTTTCCCTGTTCTTGATGATTCCAACTCGACCTCTGTTTCTACCCCCAGTGACCATG
ACAATATTCCCAACATCAAACTTGATGAAGTCAGTGATCTTGTTCTCTTCTAAGTCAAGT
TTGATGGTATCATTGGCTTTGATGAGTGGGTCAGGGTAGCGGATGGTACGCCCATCATAG
GTGTTGATGTATGGGATACCTTTCTGGCCAAACTGGACTGATCTAACTTTGCAAAGCTTG
STS source:
STS Forward / Reverse: Reverse read
STS:
ATGGGTATGT GAACTTCTCT CTTTGCAAGT AACTNGATTT TTTTTCCTTT TTTTG
GAAAT GGTATTCTGT AATCTTGATT TTAGATCTAT TAGTTATATA GGAGTAGCAG
TTTCTTTTCA TTCTTCTGCC CGGCCTATTC TTTGCAGAAT TGTTGGTTTG AGGT
ACTGAG ATTGTTATGT CCTTTTTTTT CTCT
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: Msp1
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: 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
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: Pvu2
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: Msp1
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: Msp1
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: Msp1
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: Msp1
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: Ciclev10012499m
Scaffold: scaffold_6
Start: 16909492
End: 16912088

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00008:mRNA_65.1
Scaffold: C_unshiu_00008
Start: 366943
End: 369504
Gene function: 40S ribosomal protein S4

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 88.433

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 45.755

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-04
Rp/Sa cM: 15.41

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: SI028
DNA sequence around SNP1:
AATCTTGATTTTAGATCTATTAGTTATATAGGAGTAGCAGTTTCTTTTCATTCTTCTGCC
[T/C]GGCCTATTCTTTGCAGAATTGTTGGTTTGAGGTACTGAGATTGTTATGTCCTTTT
TTTTC
SNP2: SI292
DNA sequence around SNP2:
AATCTTGATTTTAGATCTATTAGTTATATAGGAGTAGCAGTTTCTTTTCATTCTTCTGCC
[T/C]GGCCTATTCTTTGCAGAATTGTTGGTTTGAGGTACTGAGATTGTTATGTCCTTTT
TTTT
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: