Citrus CAPS Marker Database

Locus name: Vs0003

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 950
Comment on PCR:
F-primer: GTACATACTCAAGGCTGG
R-primer: TATTAATACCATCTTCAA

EST info

EST Accession number 1: C21853
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GGTACCGACGGNGGTTCCTGCAAATTTGACAAAAGCAAAATTGCTGCAGCTGTATCTAAT
TTCAGTGTTATTTCCTCTGATGAAGATCAAATGGCTGCAAATTTGGTGAAACATGGCCCT
CTGGCAGGTAATGTAGCTTCGATACAATTACCTCATATTTCGTTTTCNGTTTCTTGGCTT
TTCTCTTCACTGTGAGCTCTCCAAAATAACATTTGGAAAAGTTAGTTAATTAATTAATTT
CTTTTGAGATGTTGGTAATTTTTTTATTAAACGGAATGGATAGAATGATGACAGAATTTG
TGCTGATCTTGCTGTTTGCTTTTGCAGTGGGTATCAATGCCGTTTGGATGCAAACATATA
TTGGAGGAGTTTCATGCCCATACATTTGCGGGAAGTATTTGGATCATGGAGTGCTTATCG
TGGGCTATGGATCCTCAGGTTTCGCCCCGATCCGATTCAAGGAGAAGCCTTACTGGATCA
TAAAGAACTCCTGGGGAGAGAACTGGGGAGAGAATGGATATTATAAGATCTGCATGGGTC
GCAATGTCT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AAAAGCAAAATTGCTGCAGCTGTATCTAATTTCAGTGTTATTTCCTCTGATGAAGATCAA
ATGGCTGCAAATTTGGTGAAACATGGCCCTCTGGCAGGTAATGTAGCTTCGATACAATTA
CCTCATATTTCGTTTTCTGTTTCTTGGCTTTTCTCTTCACTGTGAGCTCTCCAAAATAAC
ATTTGGAAAAGTTAGTTAATTAATTAATTTCTTTTGAGATGTTGGTAATTTTTTTATTAA
ACGGAATGGATAGAATGATGACAGAATTTGTGCTGATCTTGCTGTTTGCTTTTGCAGTGG
GTATCAATGCCGTTTGGATGCAAACATATATTGGAGGAGTTTCATGCCCATACATTTGCG
GGAAGTATTTGGATCATGGAGTGCTTATCGTGGGCTATGGATCCTCAGGTTTCGCCCCGA
TCCGATTCAAGGAGAAGCCTTACTGGATCATAAAGAACTCCTGGGGAGAG
STS source:
STS Forward / Reverse: Foward read
STS:
CGAGAGAAGACTACCCTACACTGGACCGACGGTGGTCCTGCAATTTGACAAAAGCAAAAT
TGCTGCAGCTGTATCTAATTTCAGTGTTATTNCNTCTGATGAAGATCAAATGGCTGCAAA
TTTGGTGAAACATGGCCCTCTGGCAGGTAATGTAGCTTCGATACAATTACCTCATATTTC
GTTTTCNGTTTCTTGGCTTTTCTCTTCACTGTGAGCTCTCCAAAATAACATTTGGAAAAG
TTAGTTAATTAATTAATTTCTTTTGAGATGTTGGTAATTTTTTTATTAAACGGAATGGAT
AGAATGATGACAGAATTTGTGCTGATCTTGCTGTTTGCTTTTGCAGTGGGTATCAATGCC
GTTTGGATGCAAACATATATTGGAGGAGTTTCATGCCCATACATTTGCGGGAAGTATTTG
GATCATGGAGTGCTTATCGTGGGCTATGGATCNTCAGGTTTCGCCCCGATCNGNTTCAAG
GAGAAGCCTTACTGGATCATAAAGAACTCCTGGGGAGAGAACTGGGGAGAGAATGGATAT
TATAAGATCTGCATGGGTCGCAATGTCTGTGGGGTCGACTCCATGGTCTCATCTGTAGCT
GCTNTCCATACAACCTCAAGCTAGACATTATGGAGGTTGTGCTAGGCAAGTGGAGCTTNT
NTACNNAGATATTATAGGATATCCTTTTAAATATCCGTCTGCAATTATAANGATGCCTAC
ATGCNTGGGCTGAGGCATGAACTTTATATGCTCTTGTAATATTTAAGCAT
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
AAGCTCCACTTGCCTAGCACAACCTCCATAATGTCTAGCTTGAGGTTGTATGGATAGCAG
CTACAGATGAGACCATGGAGTCGACCCCACAGACATTGCGACCCATGCAGATCTTATAAT
ATCCATTCTCTCCCCAGTTCTCTCCCCAGGAGTTCTTTATGATCCAGTAAGGCTTCTCCT
TGAA
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): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinf1
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: BamH1
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: Hinf1
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: BamH1
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: 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: 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: Kiyomi x Okitsu41gou
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

Target on C. clementina (v1.0)

Transcript ID:
Scaffold:
Start:
End:

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00009:mRNA_117.1
Scaffold: C_unshiu_00009
Start: 675718
End: 677501
Gene function: Cysteine proteinase RD19a

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 35.312

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-09
KmMg cM: 72.447

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-09
Km/O41 cM: 93.467

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: SI077
DNA sequence around SNP1:
AAGCTCCACTTGCCTAGCACAACCTCCATAATGTCTAGCTTGAGGTTGTATGGA[T/C]A
GCAGCTACAGATGAGACCATGGAGTCGACCCCACAGACATTGCGACCCATGCAGATCTT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: