Citrus CAPS Marker Database

Locus name: Mf0092

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1800
Comment on PCR:
F-primer: GCTAAAGCCGGTTACACAGGC
R-primer: TGCTCTAGGAAATGGTTCCTC

EST info

EST Accession number 1: C81907
EST Accession number 2: DC893668

sequence-tagged site (STS seq)

STS:
GGAAGAGGCCGAGTTGTCTGTTACATGATAACATTGGCAATGCAAGTATTGGNAGTTGGC
ATGTGCCCCTTATTTGGCTTANCNGNCATGATTTGTTGTCAGATTTGCATAATCATTTGA
AGTTGTAGCCCAATCATCGTCGGTTGGGTGTATGCATTACTCAAGCCANTCCTTTAGGAG
AAATATTCATTAACATGTTGTCTGTTGCTATTACTATAATTCTGTTCTGATCAACTTTCT
CCTTATTTGTCCATGTTTTGTGGTAAAATACTTTTTNTTTTTTTCCCCGGTTTCCTAAAN
TTTTTGGGTTT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
ACGTTGTAAATGAAAATCTGTTCCTTCTCTCTGTTCTGGTGGAAAGGTTAATCAAATTGG
ATCTGTAACTGAGAGCATTGAAGCCGTCAGAATGTCCAAGCAAGCTGGGTGGGGTGTGAT
GGCCAGCCACCGCAGTGGTGAGACTGAAGATACTTTCATTGCCGATCTCTCAGTGGGCTT
GGCCACGGTAAATATGCTCTTTATATAAATGATACCATTGCTCAATTACAAGCAAAGTTT
ATTATAAGACTTTTGTTTCTTATTGTTTTCTTGTTCATGATCAGGGTCAAATTAAGACAG
GAGCACCATGCAGGTCAGAGCGNCTTGCAAAGTATAATCAGGTCAGCATCTTCTTATTTC
ATCTTGAAAGATCATTTGACCTGTCTTCTTTTGCTTTTCCCAAATTTTAACGTTTCAGAA
TTTGTGGGCTTGACTATAATTTAATATGTTCATGTAGCTTCTGAGAATTGAAGAAGAGCT
CGGTGCTGAAGCAGTTTATGCTGGTGCCAAGTTCCGTGCCCCTGTTGAACCCTACTAGAG
TTTGAGATGCTGATCTGGTGTGGTGCTGGATTTGAGCAATGGAGGTTTACTTCAATAAGT
TATGTAAAATGGATTTTTATGGGTTTTAGC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
ATTTTACATAACTTATTGAAGTAAACCTCCATTGCTCAAATCCAGCACCACACCAGATCA
GCATCTCAAACTCTAGTAGGGTTCAACAGGGGCACGGAACTTGGCACCAGCATAAACTGC
TTCAGCACCGAGCTCTTCTTCAATTCTCAGAAGCTACATGAACATATTAAATTATAGTCA
AGCCCACAAATTCTGAAACGTTAAAATTTGGGAAAAGCAAAAGAAGACAGGTCAAATGAT
CTTTCAAGATGAAATAAGAAGATGCTGACCTGATTATACTTTGCAAGACGCTCTGACCTG
CATGGTGCTCCTGTCTTAATTTGACCCTGATCATGAACAAGAAAACAATAAGAAACAAAA
GTCTTATAAT
STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hha1
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hha1
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: Hha1
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: Hha1
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: Hha1
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: Hinf1
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: Hinf1
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: 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10012056m
Scaffold: scaffold_6
Start: 21137783
End: 21142157

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00052:mRNA_27.2
Scaffold: C_unshiu_00052
Start: 168316
End: 172622
Gene function: Phosphopyruvate hydratase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 59.19

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 30.795

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-04
Km/O41 cM: 11.576

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

Rp/Sa LG:
Rp/Sa cM:

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: SI138
DNA sequence around SNP1:
GGTCAAATGATCTTTCAAGATGAAATAAGAAGATGCTGACCTGATTATACTTTGCAAG[A
/G]CGCTCTGACCTGCATGGTGCTCCTGTCTTAATTTGACCCTGATCATGAACAAGAAAA
CAA
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: