Citrus CAPS Marker Database

Locus name: Lp0143

CAPS PCR info

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

EST info

EST Accession number 1: AU300576
EST Accession number 2: DC893258

sequence-tagged site (STS seq)

STS:
GTATGCTGGGTCGCTTTCTGCAGGATCTTATGTGCTGAACGCAAACAAAGGAAAGAAGGA
GAGAATTGGTAGACTTTTGGAAATGCATGCCAACAGTAGGGAGGATGTAAAGGTTGCCTT
AGCAGGTGACATCATTGCTCTTGCAGGTCTTAAAGACACCATTACTGGTGAAACACTTTG
TGATGCAGACCATCCAATTCTGCTTGAACGAATGGACTTCCCCGATCCTGTGATTAAGGT
TGCAATTGAGCCCAAGACTAAAGCTGATATTGACAAAATGGCAAATGGCCTGATCAAACT
TGCTCAAGAAGACCCTTCATTCCACTTCTCACGAGANGAAGAGATCAACCAGACAGTGAT
TGAGGGTATGGGAGAATTGCATCTTGAGATTATCGTCGATCGCCTAAAGAGGGAATTTAA
GGTATATATTGGCCCCTCCATACATCTGAGTATCATGTTAATGTTAGGTATTTTTTTACT
TCACTTTATTGGGTTTAAACCTTATTCATGGTACTTTTTTCTTGGAATATATGATTGATN
TTAGTGTATAGGTATATACTTTTACATACAATACTTGTACGCATATCAGTTGTTGTGAAT
ATCAGTATGCACAGTGATATAGTTTTATGTCNGTGAGCAGAAGAGAACTAAAAGATGCAA
TAAAATTGTTTGACTGATGCTATTCTTATTTCCTGCAAATTGCAAAGAAAAATATGTTCT
GGATGCATAGACTTTTTCTTTGTCTTAACTGATGATCTTTGGGGCTAATA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TGTGCTGAACGCAAACAAAGGAAAGAAGGAGAGAATTGGTAGACTTTTGGAAATGCATGC
CAACAGTAGGGAGGATGTAAAGGTTGCCTTAGCAGGTGACATCATTGCTCTTGCAGGTCT
TAAAGACACCATTACTGGTGAAACACTTTGTGATGCAGACCATCCAATTCTGCTTGAACG
AATGGACTTCCCCGATCCTGTGATTAAGGTTGCAATTGAGCCCAAGACTAAAGCTGATAT
TGACAAAATGGCAAATGGCCTGATCAAACTTGCTCAAGAAGACCCTTCATTCCACTTCTC
ACGAGATGAAGAGATCAACCAGACAGTGATTGAGGGTATGGGAGAATTGCATCTTGAGAT
TATCGTCGATCGCCTAAAGAGGGAATTTAAGGTATATATTGGCCCCTCCATACATCTGAG
TATCATGTTAATGTTAGGTATTTTTTTACTTCACTTTATTGGGTTTAAACCTTATTCATG
GTACTTTTTT
STS source:
STS Forward / Reverse: Foward read
STS:
GATTTGAGCCTATGGAGGCAGGAAAGGGGATATGAGTTCAAGAGTGAGATCAAGGGAGGT
GCAGTGCCAAAAGAATATATTCCTGGGGTGATGAAAGGACTAGAAGAATGCATGAGCAAT
GGTGTGCTTGCAGGCTTCCCTGTTGTTGACGTACGTGCTGCACTAGTTGATGGTTCCTAC
CATGATGTTGATTCTAGTGTCTTGGCATTTCAACTTGCGGCCAGGGGAGCTTTCAGGGAG
GGCATGAGAAAGGCTGGCCCTAAAATGCTGGAACCTATAATGAAAGTCGAAGTTGTCACA
CCTGAAGAACACTTGGGAGATGTGATTGGTGATCTCAACTCGAGGAGAGGTCAGATCANC
AGTTTTGGTGACAAACCTGGTGGTTTGAAGGTACATTGAATTTCTTTCTCAGCACTCTGT
CCGGATATACATCCATCTGGTTAATTCCTAAGTGTCTTTGATTCTTGATCTTTCTTTCCT
TAGTTTTTCCCGCTGCAGTCTAAATTTTNGATTCATGGGATATTTTGGTATTATCGCAGG
TGGTTGATGCGCTGGTTGCCACTGGCAGAAATGTTNCAATATGTTAGTGCACTCCCGAGG
GATNACAAAAGGCCGTGCA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
GAGAATTGGT AGACTTTTGG AAATGCATGC CAACAGTAGG GAGGATGTAA AGGTT
GCCTT AGCAGGTGAC ATCATTGCTC TTGCAGGTCT TAAAGACACC ATTACTGGTG
AAACACTTTG TGATGCAGAC CATCCAATTC TGCTTGAACG AATGGACTTC CCCG
ATCCTG TGATTAAGGT TGCAATTGAG CCCAAGACTA AAGCTGATAT TGACAAAAT
G GCAAATGGC
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): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinc2
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: Nde2
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hinc2
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: Mbo1
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: Ciclev10019139m
Scaffold: scaffold_3
Start: 6076949
End: 6080875

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00159:mRNA_40.1
Scaffold: C_unshiu_00159
Start: 339926
End: 343475
Gene function: Translation elongation factor G

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 45.297

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 18.056

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:
DNA sequence around SNP1:
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: