Citrus CAPS Marker Database

Locus name: Al0639

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 800
Comment on PCR:
F-primer: TTCTTGGGCACCAGATGTAAA
R-primer: GGGCTGAGATTGTGACGAAA

EST info

EST Accession number 1: C95552
EST Accession number 2: DC893076

sequence-tagged site (STS seq)

STS:
GGTTCCTGAAGGAATAACTTTGCCAGGACGGATGGTTTACTTCTTGTTTGAAAAGCCTTT
GCTTGAATAATCTTCGAGTACTTGTAAGACCATTTTAACTCCGGGTTCCACTTATAACGG
CACTTCTATTATAAGGTCAGGAGCGTTTTACCATCTCAAACCACAAACGAGTGCGTGAAT
CTTTATCATTAAGGCTGGTGATGGCCCCAAAGACTGCAGTTCTCTGAGTAATGGTGAAAG
TAAGAGGGAAGTACAAGCAGATCCGTGAATTACATCTCTCTGAAGTTGTACCAACAATTC
CAAGACAGCCGATCATACAGAGCTGTCCTTCCGAAGATCTCCACATCCCTTCTGCAGAAA
GAGTAAGACCAGAAAGACCTGTTCGACTCGCTGATGTGTATCCATCTTCCCAGGAATGAA
TTAGTCTGAACAAGGCGAAAACTCTTGCAGTTTCGATGTTGTTTTCATCAATTCCTGGAT
CACGTGCAAGTTCTGAACATAAAGTCTGAAGTTGTTAGATCCACCACTGTTGTCCTTGGA
CATTCCGCTGAGAACAAAAGGGCCAAACCTATTTGCATCATCATTTGAGCCAACAGATGT
CNAGCTGTGTACAATATCAAACATCCCATTAGACACCAAACGCCGAAGAGTATTACAGAT
ATTATCATCTTTAAACCNAAAAACTTCCTCATCCACCAGGCTGTCTTGATACGGATATGG
GCTGCAAGCTTTCGCACCAATCTCAGCCC
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TCTCTGAGTAATGGTGAAAGTAAGAGGGAAGTACAAGCAGATCCGTGAATTACATCTCTC
TGAAGTTGTACCAACAATTCCAAGACAGCCGATCATACAGAGCTGTCCTTCCGAAGATCT
CCACATCCCTTCTGCAGAAAGAGTAAGACCAGAAAGACCTGTTCGACTCGCTGATGTGTA
TCCATCTTCCCAGGAATGAATTAGTCTGAACAAGGCGAAAACTCTTGCAGTTTCGATGTT
GTTTTCATCAATTCCTGGATCACGTGCAAGTTCTGAACATAAAGTCTGAAGTTGTTAGAT
CCACCACTGTTGTCCTTGGACATTCCGCTGAGAACAAAAG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TTATAACGGCCTTTTATTATAAGGTCAGGACGTTTTACCATCTCAAACCACAAACGAGTG
CGTGAATCTTTATCATTAAGGCTGGTGATGGCCCCAAAGACTGCAGTTCTCTGAGTAATG
GTGAAAGTAAGAGGGAAGTACAAGCAGATCCGTGAATTACATCTCTCTGAAGTTGTACCA
ACAATTCCAAGACAGCCGATCATACAGAGCTGTCCTTCCGAAGATCTCCACATCCCTTCT
GCAGAAAGAGTAAGACCAGAAAGACCTGTTCGACTCGCTGATGTGTATCCATCTTCCCAG
GAATGAATTAGTCTGAACAAGGCGAAAACTCTTGCAGTTTCGATGTTGTTTTCATCAATT
NCCTGGATCACGTGCAAGTTCTGAACATAAAGTCTGAAGTTGTTAGATNCCGGGCANCNG
GTTTTTCCTTGTGGGCATTTGACGACTTGGTGGAACGAAAAA
STS source: Chuukanbohon NO 5
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:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Pvu2
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: 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: Pvu2
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: Pvu2
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: Pvu2
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: Pvu2
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: Pvu2
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: Ciclev10001091m
Scaffold: scaffold_5
Start: 41703787
End: 41708779

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00009:mRNA_141.1
Scaffold: C_unshiu_00009
Start: 874868
End: 888901
Gene function: IQ calmodulin-binding motif protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-01
AGI cM: 70.494

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-01
KmMg cM: 48.992

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-01S
JtTr cM: 110.675

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

Km/O41 LG: NAT-01S
Km/O41 cM: 94.639

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

Rp/Sa LG: RP-01
Rp/Sa cM: 28.746

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:
DNA sequence around SNP1:
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: