Citrus CAPS Marker Database

Locus name: Ov0404

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1600
Comment on PCR:
F-primer: AGGAAGCGTTAAGCAAAGTTC
R-primer: TAGATCTAGCACCCCAGCAT

EST info

EST Accession number 1: AU186517
EST Accession number 2: DC893937

sequence-tagged site (STS seq)

STS:
TTTTGTTTGTGGAGGCCGAAACAAGCTACGTTCTTGATGATTTGAGTGACTTTGAATCAA
GCTTCGAGCTTCAGAAACTCGTTCCATCGGTTGAATACACAAAAGACATATCTTCTTATC
CATTACTAATAACCCAGGTAGATGACTTAAGACAGAGTCTTTAGTGCTCCTGTGGCACTG
CCCATCCATCATCCAATATTTGCCCTGTGTGTATCAATTTATCTCAATTGATTAAAGTTT
ATATGTGAAAATGAATGAATGAATGAAAAAGGAATAGTACCTCAGAGCACTCAAGATATT
TCTATAATTCATTCTCCTTTTTTCTGCTTAATTATTGACATATTTTGTTTTACTACCAGG
TAACTCATTTCAAGTGTGGAGGAGTTTGCCTTACAGTCGCAATGCACCATACATTAGCTG
ATGCAACTTCAATGATCTACTTCATCAATGCATGGGATGAGGTCACACGTGGTGTCCCTA
TTAGTAATCCGCCATTCATTGATCGAACGTTACTAGGTATTGGGCTCCCAACTTCTCCTA
AATTTCATCA
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read
STS:
GGGATCAAAATGGCAGAATTGAGATCAAATGTAATGGACAGGGTGTTTTGTTTGTGGAGG
CCGAAACAAGCTACGTTCTTGATGATTTGAGTGACTTTGAATCAAGCTTCGAGCTTCAGA
AACTCGTTCCATCGGTTGAATACACAAAAGACATATCTTCTTATCCATTACTAATAACCC
AGGTAGATGACTTAAGACAGAGTCTTTAGTGCTCCTGTGGCACTGCCCATCCATCATCCA
ATATTTGCCCTGTGTGTATCAATTTATCTCAATTGATTAAAGTTTATATGTGAAAATGAA
TGAATGAATGAAAAAGGAATAGTACCTCAGAGCACTCAAGATATTTCTATAATTCATTCT
CCTTTTTTCTGCTTAATTATTGACATATTTTGTTTTACTACCAGGTAACTCATTTCAAGT
GTGGAGGAGTTTGCCTTACAGTCGCAATGCACCATACATTAGCTGATGCAACTTCAATGA
TCTACTTCATCAATGCATGGGATGAGGTCACACGTGGTGTCCCTATTAGTAATCCGCCAT
TCATTGATCGAACGTTACTAGGTATTGGGCTCCCAACTTCTCCTAAATTTCATCACATAG
AATACGACCCACCTCCTTCTATGAATGTCCCTACTCAAAACATAGAACTCCAAGCAAATC
CTAAATCCATTTCCTCTGCTATACTTAATATATCAGTTGATCAAATCNACACACTTAAGG
CAAAATCAAAGCAAGATCATGGAACCCCATTGAGTTTACAGGGTTGAGATCTAGCTGCAC
ATATATGGCGTTGCTTATGTAAGCACGTAGACTTCTATGACNAGTGAGAAATTTATATCC
ATAATGGAC
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CGAATAAGCTCCCATCATTGCTTGGACTTAGAAAAATATGTATCGTCCCATCTATAGGGG
TAAGCGTCCTTACAATCATTGGTCTTCCCCACCCAAAAGTTACATCAGAAACAGGCATAT
GAAACACATTGGAAATATTGAGGTTAGGACACTTAAAAGTGTGTGCTCCTCGTTTTAAAC
CTGTTAGATCAGGCTGTTGGCTTAGGTATGCAAGAGCTGATTTCAAATATTCATCGCCCA
TCCGCATTGTTGCTTCACGAATTCTTTCTGCGGTAGAACTTAACGGTTCTGATATGATAT
CACCAGATAAGCCAATTGTTGTACCAGTAAAAGTTACATTACCAAAATACACAGATGGGA
GTCGCGGATCCAATCTAGACCGTCCATTTATTGGAATATATAATTTACTCACTTGATCAT
TAGAAAGTCTACGTGCTTTACATAAGCAACGCCATATATGTGCAGCTAGTATCTCAAACC
TGGTAAACTCAATTGGGGTTCCATGATCTTGCTTTGATTTTGCCTTAAGTGTGTTGATTT
GATCAACTGATATATTAAGTATAGCAGAGG
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Reverse read
STS:
ATGCAACTTCAATGATTACTCATCAATGCATGGATGAGTCACACGTGTGTCCTATTAGTA
TCCGCCATTCATTGATCGAACGTACTAGGTATTGGGCTCCCAACTTCTCCTAAATTTCAT
CACATAGAATACGACCCACCTCCTTCTATGAATGTCCCTACTCAAANCATAGAACTCCAA
GCAAATCCTAAATCCATTTCCTCTGCTATACTTAATATATCAGTTGATCAAATCAACACA
CTTAAGGCAAAATCAAAGCAAGATCATGGAACCCCAATTGAGTTTACCAGGTTTGAGATA
CTAGCTGCACATATATGGCGTTGCTTATGTAAAGCACGTAGACTTTCTAATGATCAAGTG
AGTAAATTATATATTCCAATAAATGGACGGTCTAGATTGGATCCGCGACTCCCATCTGTG
TATTTTGGTAATGTAACTTTTACTGGTACAACAATTGGCTTATCTGGTGATATCATATCA
GAACCGTTAAGTTCTACCGCAGAAAGAATTCGTGAAGCAACAATGCGGATGGGCGATGAA
TATTTGAAATCAGCTCTTGCATACCTAAGCCAACAGCCTGATCTAACAGGTTTAAAACGA
GGAGCACACACTTTTAAGTGTCCTAACCTCAATATTTCCAATGTGTTTCATATGCCTGTT
TCTGATGTAACTTTTGGGTGGGGAAGACCAATGATTGTAAGGACGCTTACCCCTATAGAT
GGGACGATACATATTTTTCTAAGTCCAAGCAATGATGGGAGCTTATTCGCAGTTGTAAAC
TTGCAAACCCAACACATGC
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): 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: EcoR5
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

Experiments: Segregation pattern

Population name: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: EcoR5
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: EcoR5
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: EcoR5
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: EcoR5
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: Ciclev10002415m
Scaffold: scaffold_5
Start: 29768091
End: 29769281

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00731:mRNA_6.3
Scaffold: C_unshiu_00731
Start: 26598
End: 28767
Gene function: Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-09
KmMg cM: 29.016

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-09S
JtTr cM: 31.495

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: 29.347

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: