Citrus CAPS Marker Database

Locus name: Al0633

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1400
Comment on PCR:
F-primer: CCAGGGCACAAGGAAAAGAT
R-primer: GGTCATACCCCCATCAACAAA

EST info

EST Accession number 1: C95520
EST Accession number 2: DC893065

sequence-tagged site (STS seq)

STS:
NCCTCGACGAGCTTTTGAGAGTGGAAACAGAAAGCAGAGGTCATTACCAGATTACAGTGG
GCGTGGTTGGCATGAGTCAAGGAAGCAAGTCATGAATGAGTTTGGAGGCTTGAAGAGATC
ATACTACATGGATCCACAACCATTGAACCATTTCGAGTGGCACCTTTATGAGTATGAGAT
CAATAAGTGTGATGCTTGCGCCTTGTATAGATTAGAACTGAAGCTTGTTGATGGGAAAAA
GAGTGCCAAGGGGAAATTAGCAAATGATTCAGTTGCTGATCTACAGAAGCAGATGGGAAG
GCTCACTGCTGAGTTTCCCTCAGATAACAAGCGCTTAGTTAAAGGAAGGGCCAAAGTTAA
TGCGAAGGCTGGTGTCGGTGGAAATATTTACCCTGCTTCAAATGTTGTTGCATCGACTAA
TGAGAAGTTCGATTATGGGACCAACCGGGCAGTTTGATTATTTGATTGAAAATTTAAGTG
AGTATTACCTGGACGTAAT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GCAGTCATGATGAGTTNGAGGCTGAAGAGATCATACTACATGGATCCACANCCATGAACC
ATTTCGAGTGGCCCTTTATGAGTATGAGATCAATAAGTGTGATGCTTGCGCCTTGTATAG
ATTAGAACTGAAGCTTGTTGATGGGAAAAAGAGTGCCAAGGGGAAATTAGCAAATGATTC
AGTTGCTGATCTACAGAAGCAGATGGGAAGGCTCACTGCTGAGTTTCCCTCAGATAACAA
GCGCTTAGTTAAAGGAAGGGCCAAAGTTAATGCGAAGGCTGGTGTCGGTGGAAATATTTA
CCCTGCTTCAAATGTTGTTGCATCGACTAATGAGAAGTTCGATTATGGACCAACCGGGCA
GTTTGATTATTTGATTGAAAATTTAAGTGAGTATTACCTGACGTAATCAAAGAAGCTTCA
ATGAATATGCTGCAATTTGTTAGTACTTAGATCAGCTGAAGCATATCACCATAGTAATGG
TGGGGGTTATGTGTTTTCACTTGTTTCGTCTATAGTTTCTGGTAGTCAATAACATGAGGC
CAAGCTCTCTCTTTGGCCGCAGGGTTGTCAATAGTTTCCATTCACAGATAGAGCCGCATT
AGGCTGTCCTGGATGCTGGAGTATATACTAACTTATGGTTCTCAGGTATGGAAAATGGCT
GTTTTTCCTCAGCCCATTTTTATAACGGATAAGAATTCGAGATACGTGGTGAACACTCCA
AACCAATCAGTGTCACCAGAATTGGATAGGGTGGATGCAGACTGTTGCAATATATTTTAC
TGACATTTTTATGATTTCAAATACT
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CTCTTTGATCTTTCAGTTCTCGAGGGTGAAACAATTAGGGAGTGGCTCTTTTTTGATAAG
CCTCGACGAGCTTTTGAGAGTGGAAACAGAAAGCAGAGGTCATTACCAGATTACAGTGGG
CGTGGTTGGCATGAGTCAAGGAAGCAAGTCATGAATGAGTTTGGAGGCTTGAAGAGATCA
TACTACATGGATCCACAACCATTGAACCATTTCGAGTGGCACCTTTATGAGTATGAGATC
AATAAGTGTGATGCTTGCGCCTTGTATAGATTAGAACTGAAGCTTGTTGATGGGAAAAAG
AGTGCCAAGGGGAAATTAGCAAATGATTCAGTTGCTGATCTACAGAAGCAGATGGGAAGG
CTCACTGC
STS source: Consensus seuqence of 12 cvs.
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: 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)
Resriction enzyme: Msp1
Rank as CAPS marker: Others
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: 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

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
Population name: Kiyomi x Okitsu41gou
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: Ciclev10015092m
Scaffold: scaffold_2
Start: 33837403
End: 33842156

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00002:mRNA_126.1
Scaffold: C_unshiu_00002
Start: 901824
End: 911260
Gene function: Vascular plant one zinc finger protein isoform 1

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-06
KmMg cM: 55.857

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
JtTr cM: 59.645

Km/O41 map info (Nakano et al. 2003)

Km/O41 LG: NAT-06S
Km/O41 cM: 51.106

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

Rp/Sa LG: RP-06.2
Rp/Sa cM: 27.837

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: SI123
DNA sequence around SNP1:
CTTGAAGAGATCATACTACATGGATCCACAACCATTGAACCATTTCGAGTGGCACCTTTA
[T/C]GAGTATGAGATCAATAAGTGTGATGCTTGCGCCTTGTATAGATTAGAACTGAAGC
TTGTT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: