Citrus CAPS Marker Database

Locus name: Ov0301

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1900
Comment on PCR: Additional band (450 bp)
F-primer: TCCGAATTGCCGTGTTGTA
R-primer: GTATATGACCCGACCCGAATC

EST info

EST Accession number 1: AU186450
EST Accession number 2: DC893861

sequence-tagged site (STS seq)

STS:
GCGGGGTCAAGATCTTCGGGGTCCGATTGACCGACGGCTCAATCCGGAAGAGTGCTAGTA
TGGGCAATCTCAGCCACTACGCCGGTTCGACTTCGGGTCATAATAACAATAACGCGTCAA
ACACTCCTGATTCGCCCGGTGAGACGCCGGATCATCATGCTGACGGGTATGCGTCGGAAG
ATTTCGTTCCCGGGTCATCGTCGAGTCGCGAACGCAAGAAAGGTTGAATTTTTTATTTAT
TCATTTGTTTGTGTTTTCGGTTGTTTACCTGCTACTTTGAAATCTCTGTGTAATTTTAAG
CTTAATTTCGGTGTTTTTCCAGTTGTCTTCANTGTAATTTTGGTGTTAAAATATTCTAGT
ATAATAATAAAATTAGGTCATAGAGTTCGGGCCTGGAGGAGCTNGAAAATTTGATTTCAA
AGGTCATTCACACTCATCTCTGGATAGCTAGCAACTAGCGTGATGGTGGTTTGGAAGTT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CCGACGGCTCAATCCGGAAGAGTGCTAGTATGGGCAATCTCAGCCACTACGCCGGTTCGA
CTTCGGGTCATAATAACAATAACGCGTCAAACACTCCTGATTCGCCCGGTGAGACGCCGG
ATCATCATGCTGACGGGTATGCGTCGGAAGATTTCGTTCCCGGGTCATCGTCGAGTCGCG
AACGCAAGAAAGGTTGAATTTTTTATTTATTCATTTGTTTGTGTTTTCGGTTGTTTACCT
GCTACTTTGAAATCTCTGTGTAATTTTAAGCTTAATTTCGGTGTTTTTCCAGTTGTCTTC
ACTGTAATTTTGGTGTTAAAATATTCTAGTATAATAATAAAATTAGGTCATAGAGTTCGG
GCCTGGAGGAGCT
STS source:
STS Forward / Reverse: Foward read
STS:
GGGCAATCTC AGCCACTACG CCGGTTCGAC TTCGGGTCAT AATAACAATA ACGCG
TCAAA CACTCCTGAT TCGCCCGGTG AGACGCCGGA TCATCATGCT GACGGGTATG
CGTCGGAAGA TTTCGTTCCC GGGTCATCGT CGAGTCGCGA ACGCAAGAAA GGTT
GAATTA TTTATTTATT CATTCGTTTG AGTTTTCGGT TGTTTACCTG CTACTTTGA
A ATCTCTGTG
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: Pvu2
Rank as CAPS marker: no homozygous cultivar with minor allele
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: Jutaro unshu x Trovita orange
Restriction enzyme: Hha1
Comment: PCR_condition: 58C aneal
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: Hha1
Comment: PCR_condition: 58C aneal
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Pvu2
Comment: PCR_condition: 58C aneal
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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10021068m
Scaffold: scaffold_3
Start: 5360113
End: 5362918

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00442:mRNA_18.1
Scaffold: C_unshiu_00442
Start: 163615
End: 166153
Gene function: Transcription factor

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-05S
KmMg cM: 23.526

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 19.932

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-05
Rp/Sa cM: 21.59

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: SI078
DNA sequence around SNP1:
CTACTTTGAAATCTCTGTGTAATTTTAAGCTTAATTTCGGTGTTTTTCCAGTTGTCTTCA
[T/C]TGTAATTTTGGTGTTAAAATATTCTAGTATAATAATAAAATTAGGTCATAGAGTT
CGGGC
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: