Citrus CAPS Marker Database

Locus name: Ov0412

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1200
Comment on PCR:
F-primer: AAAGGAGCTGAGGGGATTGA
R-primer: CCTTCATCAGTTGGCACAAAC

EST info

EST Accession number 1: DC893973
EST Accession number 2: DC893974

sequence-tagged site (STS seq)

STS:
TAGGTGAATGATGCATTGGAGATGCTGAAAATACGCTTCAGTGGAGGAAGGGGAACAANA
TTGATTCCATTTTGGATGAGGATTTGGAGGTAGATTTAAGCTCTGCTGCTTATATGAACG
GCGTCGATCGGGAAGGTCACCCTGTTTGCTACAACATTTATGGGGTGTTTGAGAGTGATG
AGCTTTATCAGAAGACTTTTGGTACTGAGGAGAAGCGTGGCCAGTTCTTGAGATGGAGGC
TGAGGCTGATGGAGCAGGGCATTCAGAAGCTTGATTTCAAGCCTGGTGGCATTTCTTCGT
TGCTTCAGATCAATGATTTGAAGAATGCTCCAGTACTAGCAAAGAAGGAACTGAGGGTTG
CCACAAAACAAGCTGTCGATCTATTGCAGAACAATTACCCTGAATTTGTTGCCAGAAATG
TAAGCAATTCCTTTAATTACTCGTTAATCTTATTTCCCTTTGCTTCTTCTAATTAATCAA
ATTTGATGGGGGTCTTTNGTTTTGATTGATTGCAGATAATTATTAATGCTCCATTTTGGT
ACTATGCTTTGAATGCTCTCATATCACCTTTCTTAACGCAAAGAACTAAGAGCAAATTTG
TTGTTGCTCGCCCGGCCAAGGTCACAGAAANACTTCTGAAGTAAGTATTATCTTTCCTTT
TACCTACGTGNTAATTTCTGAAAATGTGCTGTAGCTAAAG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TACGCTTCAGTGGAGGAAGGGGAACAAGATTGATTCCATTTTGGATGAGGATTTGGAGGT
AGATTTAAGCTCTGCTGCTTATATGAACGGCGTCGATCGGGAAGGTCACCCTGTTTGCTA
CAACATTTATGGGGTGTTTGAGAGTGATGAGCTTTATCAGAAGACTTTTGGTACTGAGGA
GAAGCGTGGCCAGTTCTTGAGATGGAGGCTGAGGCTGATGGAGCAGGGCATTCAGAAGCT
TGATTTCAAGCCTGGTGGCATTTCTTCGTTGCTTCAGATCAATGATTTGAAGAATGCTCC
AGTACTAGCAAAGAAGGAACTGAGGGTTGCCACAAAACAAGCTGTCGATCTATTGCAGAA
CAATTACCCTGAATTTGTTGCCAGAAATGTAAGCAATTCCTTTAATTACTCGTTAATCTT
ATTTCCCTTTGCTTCTTCTAATTAATCAAATTTGATGGGGGTCTTTCGTTTTGATTGATT
GCAGATAATTATTAATGCTCCATTTTGGTACTATGCTTTGAATGCTCTCATATCACCTTT
CTTAACGCAAAGAACTAAGAGCAAATTTGT
STS source:
STS Forward / Reverse: Foward read
STS:
GTGTTGAGAGTGATGAGCTTATCAGAAGACTTTGGTACTGAGAGAAGCGTGCCAGTTCTG
AGATGGAGGCTGAGGCTGATGGAGCAGGNCATTCAGAAGCTTGATTTCAAGCCTGGTGNC
ATTTCTTCGTTGCTTCAGATCAATGATTTGAAGAATGCTCCAGTACTAGCAAAGAAGGAA
CTGAGGGTTGCCACAAAACAAGCTGTCGATCTATTGCAGAACAATTACCCTGAATTTGTT
GCCAGAAATGTAAGCAATTCCTTTAATTACTCGTTAATCTTATTTCCCTTTGCTTCTTCT
AATTAATCAAATTTGATGGGGGTCTTTCGTTTTGATTGATTGCAGATAATTATTAATGCT
CCATTTTGGTACTATGCTTTGAATGCTCTCATATCACCTTTCTTAACGCAAAGAACTAAG
AGCAAATTTGTTGTTGCTCGCCCGGCCAAGGTCACAGAAACACTTCTGAAGTAAGTATTA
TCTTTCCTTTTACCTACGTGTTAATTTCTGAAAATGTGCTGTAGCTAAAAGCTAATTAAA
GGAGATGAATTATTCTTGATTATAGATACATTCCAGCCGAGGAGCTCCCTGTTCAATATG
GTGGCTTCAAGAGGGAGAATGATTTCGAGTTCTCCAAAGAAGGTGGTGCTGTTTCTGAGA
TTACTCTCAAGGCAGGATCAACTGAAACTATTGAGATTCAAGCTCCTGAGGTATTAATTA
ACTTTATGAAACAAATAACAATCATTTGTTTTTTTCTTGTGGGGCAAGTTGTGAAATTAA
TCATACTTGTAATTATTCTGACAGTAAGG
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
GAATAATTACAAGTATGATTAATTTCACAACTTGCCCCACAAGAAAAAAACAAATGATTG
TTATTTGTTTCATAAAGTTAATTAATACCTCAGGAGCTTGAATCTCAATAGTTTCAGTTG
ATCCTGCCTTGAGAGTAATCTCAGAAACAGCACCACCTTCTTTGGAGAACTCGAAATCAT
TCTCCCTCTTGAAGCCACCATATTGAACAGGGAGCTCCTCGGCTGGAATGTATCTATAAT
CAAGAATAATTCATCTCCTTTAATTAGCTTTTAGCTACAGCACATTTTCAGAAATTAACA
CGTAGGTAAAAGGAAAGATAATACTTACTTCAGAAGTGTTTCTGTGACCTTGGCCGGGCG
AGCAACAACAAATTTGCTCTTAGTTCTTTGCGTTAAGAAAGGTGATATGAGAGCATTCAA
AGCATAGTACCAAAATGGAGCATTAATAATTATCTGCAATCAATCAAAACAAAAGACCCC
CATCAAATTTGATTAATTAGAAGAAGCAAAGGGAAATAAGATTAACGAGTAATTAAAGGA
ATTGCTTACATTTCTGGCAACAAATTCAGGGTAATTGTTCTGCAATAGAT
STS source:
STS Forward / Reverse: Reverse read
STS:
ATTGATTCCA TTTTGGATGA GGATTTGGAG GTAGATTTAA GCTCTGCTGC TTATA
TGAAC GGCGTCGATC GGGAAGGTCA CCCTGTTTGC TACAACATTT ATGGGGTGTT
TGAGAGTGAT GAGCTTTATC AGAAGACTTT TGGTACTGAG GAGAAGCGTG GCCA
GTTCTT GAGATGGAGG CTGAGGCTGA TGGAGCAGGG CATTCAGAAG CTTGATTTC
A AGCCTGGTGG CATTTCTTCG TTGCTTCAGA TCAATGATTT GAAGAATGCT CCA
GTANTAG CAAAGAAGGA ACTGAGGGTT
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: PCR_condition: 56C aneal
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Rsa1
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)
Resriction enzyme: Rsa1
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

Experiments: Segregation pattern

Population name: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Rsa1
Comment: PCR_condition: 56C 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: Rsa1
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: Rsa1
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: Rsa1
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: Rsa1
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: Ciclev10015053m
Scaffold: scaffold_2
Start: 31036088
End: 31038222

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00143:mRNA_11.1
Scaffold: C_unshiu_00143
Start: 67475
End: 69537
Gene function: SEC14 cytosolic factor family protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 42.11

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-06
KmMg cM: 39.373

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
JtTr cM: 15.372

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/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: SI050
DNA sequence around SNP1:
TACTCGTTAATCTTATTTCCCTTTGCTTCTTCTAATTAATCAAATTTGATGGGGGTCTTT
[T/C]GTTTTGATTGATTGCAGATAATTATTAATGCTCCATTTTGGTACTATGCTTTGAA
TGCTC
SNP2: SI222
DNA sequence around SNP2:
GAGCATTCAAAGCATAGTACCAAAATGGAGCATTAATAATTATCTGCAATCAATCAAAAC
[A/G]AAAGACCCCCATCAAATTTGATTAATTAGAAGAAGCAAAGGGAAATAAGATTAAC
GAGTA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: