Citrus CAPS Marker Database

Locus name: Vs0002

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1200
Comment on PCR:
F-primer: CTAGATGCTGATGTCAAA
R-primer: TAAAGCTTACAACCGACT

EST info

EST Accession number 1: C21910
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GTCTGGACTAGACCCTAGATTGACTTATGNTTTTGCATCCAAGAAAAATTCTAAAGTGAT
AACGATGAGACCAACTATTAACACCTGCCTTCATGCTACTAGAAAACATTGTAATACCAG
AAATCAGATAACAAAAGGGTGTATAGCTCTATTCATGTGAATTATCATAGATCAGCTGAT
CTTTATCTGCCACTACTGGTCCCCTCCTTCCCAGTCACAATTTCTTTATAAAGAGATGTT
ACCTTCCAATGAGATAAATTTTGCATAACTGCTCTCCCGCACTTGGTATTAACTGGTTTT
TTACACTTGCAGATCCTTGGGCCTGATAGTGGTTGGCAGCCAATTCCACTAACAGATCTT
ATAGCAACTGCTGCTGTGAAGAAAGCATACAAGAAGGCCACACTTGTTGTTCATCCCGAC
AAGTTACAGCAGCGAGGTGCAAGTATACAGCAGAAGTACACATGTGAAAAGGTTTTTGAT
CTTCTAAAGGTGTGTTGTGCAACTTTCTTTCTTTTTTAATTAGCATTTTATAATTTNGTA
TAATTAGTTTCTAAAGGAACTTGGGATCTCATGACATTAATTGGTTTCTAATGATATACT
AGCAAATTGATTGGGTCTTAGCCTGGTGATGATATCTGCTCTATATATTCAATATAGTGN
TATTAAATGAGAAGTATCTTACGTTGAGAGCTCAGTCCCATAATGACGAACTGCATGGGT
TAC
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AAAAATTCTAAAGTGATAACGATGAGACCAACTATTAACACCTGCCTTCATGCTACTAGA
AAACATTGTAATACCAGAAATCAGATAACAAAAGGGTGTATAGCTCTATTCATGTGAATT
ATCATAGATCAGCTGATCTTTATCTGCCACTACTGGTCCCCTCCTTCCCAGTCACAATTT
CTTTATAAAGAGATGTTACCTTCCAATGAGATAAATTTTGCATAACTGCTCTCCCGCACT
TGGTATTAACTGGTTTTTTACACTTGCAGATCCTTGGGCCTGATAGTGGTTGGCAGCCAA
TTCCACTAACAGATCTTATAGCAACTGCTG
STS source:
STS Forward / Reverse: Foward read
STS:
AGCATACAAGAAGGCCACACTTGTTGTTCATCCCGACAAGTTACAGCAGCGAGGTGCAAG
TATACAGCAGAAGTACACATGTGAAAAGGTTTTTGATCTTCTAAAGGTGTGTTGTGCAAC
TTTCTTTCTTTTTTAAATTAGCATTTTATAAATTTNGTATAATTAGTTTCTAAAGGAACT
TGGGATCTCATGACAATTAATTGGTTTCTAAATGATATACTAGCAAATTGATTGGGTCTT
AGCCTGGTGATGATAATACTGCTCTATATAATNCAAATAATAGTGTTTATTAAAATGAGA
AAGTAATCTTAACGGTTGAGAGTCTCAGTCNCCATTAATNTACGATACTGCAATTGGGTT
TTACAACACTCGGTCCGTATCTTATTGGGCCATTACTTTTTCTGTGTTTAGAGGCTCCCT
TCTCTTTCATTCTTGATCATGGTCCCCTGAATCTCATTATTTTGTTGGCTGCAGGANGCG
TGGAACAGATTCAATGCAGAGGAACGATAAACAGGTTTCCTTCAGCCAAGCATTTTCTTA
GGTTAAAGTACGTAATTTATTACCGTATCCTGTAACTAAAAGTAGGAATCGAAGCTTCAC
CAACCATTCTTTTCAGACCC
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
GAGAAGGGAGCCTCTAAACACAGAAAAAGTAATGGCCCAATAAGATACGGACCGAGTGTT
GTAAAACCCAATTGCAGTATCGTAAATTAATGGAGACTGAGACTCTCAACCGTTAAGATT
ACTTTCTCATTTTAATAAACACTATTATTTGNATTATATAGAGCAGTATTATCATCACCA
GGCTAAGACCCAATCAATTTGCTAGTATATCATTTAGAAACCAATTAATTGTCATGAGAT
CCCAAGTTCCTTTAGAAACTAATTATA
STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Miyagawa-wase/Trovita orange
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Shiamese acidless/RP-94
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
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)
Resriction enzyme: Rsa1
Rank as CAPS marker: Disagree by Marco analysis
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: Kiyomi x Miyagawa-wase
Restriction enzyme: Hae3
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: Hae3
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: Hae3
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: 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: Ciclev10000046m
Scaffold: scaffold_5
Start: 41184180
End: 41190033

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00127:mRNA_46.1
Scaffold: C_unshiu_00127
Start: 341430
End: 344325
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 36.685

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-09
KmMg cM: 73.93

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 68.221

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: SI103
DNA sequence around SNP1:
CTCTATTCATGTGAATTATCATAGATCAGCTGATCTTTATCTGCCACTACTGGTCCCCTC
[A/C]TTCCCAGTCACAATTTCTTTATAAAGAGATGTTACCTTCCAATGAGATAAATTTT
GCATA
SNP2: SI115
DNA sequence around SNP2:
CCTTCCAATGAGATAAATTTTGCATAACTGCTCTCCCGCACTTGGTATTAACTGGTTTTT
[A/T]ACACTTGCAGATCCTTGGGCCTGATAGTGGTTGGCAGCCAATTCCACTAACAGAT
CTTAT
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: