Citrus CAPS Marker Database

Locus name: If0216

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 1600
Comment on PCR:
F-primer: CTCAGTCCCCATCTTCAGTTC
R-primer: CAATTCCCAAACCAGCACTT

EST info

EST Accession number 1: DC893436
EST Accession number 2: DC893437

sequence-tagged site (STS seq)

STS:
AGCACATGGTTTGGACTGCCTCAACCCTCATCCCGTAATTCAGCTTAATTTTCTCCAATC
ACTTTCTCCTCTCATATTTGTTTTCCCAGAAGCCAAACAGACAAGTTACATACAATACCG
AGAAAAAAAATTACAAAAGAGAGGGAAAATGCCCATTTGGCCAACCCACAATCATGAGCT
TCTTCCCGACATGTCATCTTTGTTAACAATGATGCTCATCACAAACTTAAACAGCTGGAT
GATCTTGTTCGCGGAGGTGTTGGGCTCTGAATATGCAGGCATAGCAACCCTTGCTCCAAC
CTTAGTCTTGGTCTGGGGATTCAGCATCAGAATCGACTCAGCTTCTTCGATCTTTTACTG
GGCACAATACGTAGTAGCTTTATCTCATCTCTGCACACAAAGCAGCGGGCCGGCG
TTCTGCTCTCTTTAAGCATCAATGTGTATTATTTTATTCTCTCGATTTACATACCTTTGC
TGCTCAACTTCTTTCGTGATGCTTTTCGTAGTGCAGATTTGCGTCCCGCACATC
STS source:
STS Forward / Reverse: Foward read
STS:
AATCGTTGTGAAGGTCATAATCAAGCCATCATCAGACAGTCCGTGCTCTCCACGGACGGC
AGCAGCTATAACCTCGTGATAAATCCATAACATTGCAACAACATTTTCCATCAAGAAACG
ATGTGCGGGACGCAAATCTGCACTACGAAAAGCATCACGAAAGAAGTTGAGCAGCAAAGG
TATGTAAATCGAGAGAATAAAATAATACACATTGATGCTTAAAGAGAGCAGAACGCCGGC
CCGCCTGCTTTGTGTGCAGAGATGAGATAAAGCTACTACGTATTGTGCCCAGTAAAAGAT
CGAAGAAGCTGAGTCGATTCTGATGCTGAATCCCCAGACCAAGACTAAGGTTGGAGCAAG
GGTTGCTATGCCTGCATATTCAGAGCCCAACACCTCCGCGAACAAGATCATCCAGCTGTT
TAAGTTTGTGATGAGCATCATTGTTAACAAAGATGACATGTCGGGAAGAAGCTCATGATT
GTGGGTTGGCCAAATGGGCATTTTCCCTCTCTTTTGTAATTTTTTTTCTCGGTATTGTAT
GTAACTTGTCTGTTTGGCTTCTGGGAAAACAAATATGAGAGGAGAAAGTGATTGGAGAAA
ATTAAGCTGAATTACGGGATGAGGGTTGAGGCAGTCCAAACCATGTGCTTCTACTCTGTT
AGTGCATTTACCTATCACATATAACAAATGGAAATTGGC
STS source: Okitsu 46
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): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Sty1
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: NC
Comment: PCR_condition: 56C aneal
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: Sty1
Comment: PCR_condition: 56C aneal
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: NC
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: Sty1
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: Ciclev10015257m
Scaffold: scaffold_2
Start: 12876952
End: 12881843

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_01838:mRNA_2.1
Scaffold: C_unshiu_01838
Start: 23594
End: 31186
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 74.076

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-01
KmMg cM: 26.42

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-01S
JtTr cM: 66.382

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-09
Rp/Sa cM: 29.224

CAPS genotyping (Hybrid cv/Citrus collection)

CAPS genotyping:

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: SI174
DNA sequence around SNP1:
TGTTTTCCCAGAAGCCAAACAGACAAGTTACATACAATACCGAGAAAAAAAATTACAAAA
[A/G]AGAGGGAAAATGCCCATTTGGCCAACCCACAATCATGAGCTTCTTCCCGACATGT
CATCT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: