Citrus CAPS Marker Database

Locus name: Ov0425

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1100
Comment on PCR:
F-primer: GCCGGCAACTCCTCAT
R-primer: GAATCTTTTTCTCCCAAACAA

EST info

EST Accession number 1: DC894006
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GGATGGATGTTAGTCTGAATTTGTCAGCCTTTGTTGTTCAAAACTGAGTTATGTTGAATA
ATTTCTAGTTTCTATAAATTGTTCAACTTCACCATTGGCAATATTCTTTCAGATTTGTGA
GCTGATAGGATTTTCCATTTTTCTTGAGTCTTGACAGTGATGCCTTGGTAGTGATGCCTT
GTGCATGAACTTTTATTCCTAGTACCAGTGTGACTGTCTAATTTTTGGGCATGTTGTTGT
TTTCTGTTCAAAGTTCAGTTATTTTTTGCTATTTGAGTAGTGATATCTTGTTTTTGTACA
GTGTTCTTTAACATATTGTTGTTTCTTTTCACCCCAGGAAACACTTTTAAGCAATATGTG
CAAGTGATCGTGGAAATAATATCTNTGAACAGGCCTTTAATAGCCTTGTTAATGCAACTA
GCTAGTTTCTTNAGACATGTTTTTGGAGGCTTCCTTAGATAGCTTTATTGATGCAATTTA
GCTAGTTTCTTAAGACTNTTGTCGAAGGCATCATACATGTTGAATTATGTGATGATATGA
TCTATTCTAGATTCAGATGGAACTACTATTAGAGATTTATTGGATGTGATGCATTGCCCT
TGGTTCCTTTATGCTGAATAATTTCTTGTGTTTGNTTCATGNTATCATCTTATTCATACA
TGCTACTTGTTTCTCTGCAAACAGACCAATTCAAGGCCATAAATGATGAAGGAATGCCTA
TGTATCAGAGGCCATTTATGAGGGGCAAACTGTACATTCATTTCACTGGTGACTTCCTGA
ATCACTGAGCCCAGACAGTGCAGAATGCTGGAGACGTACT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
ATTTCTAGTTTCTATAAATTGTTCAACTTCACCATTGGCAATATTCTTTCAGATTTGTGA
GCTGATAGGATTTTCCATTTTTCTTGAGTCTTGACAGTGATGCCTTGGTAGTGATGCCTT
GTGCATGAACTTTTATTCCTAGTACCAGTGTGACTGTCTAATTTTTGGGCATGTTGTTGT
TTTCTGTTCAAAGTTCAGTTATTTTTTGCTATTTGAGTAGTGATATCTTGTTTTTGTACA
GTGTTCTTTAACATATTGTTGTTTCTTTTCACCCCAGGAAACACTTTTAAGCAATATGTG
CAAGTGATCGTGGAAATAATATCTGTGAACAGGCCTTTAATAGCCTTGTTAATGCAACTA
GCTAGTTTCTTAAGACATGTTTTTGGAGGCTTCCTTAGATAGCTTTATTGATGCAATTTA
GCTAGTTTCTTAAGACTCTTGTCGAAGGCATCATACATGTTGAATTATGTGATGATATGA
TCTATTCTAGATTCAGATGGAACTACTATTAGAGATTTATTGGATGTGATGCATTGCCCT
TGGTTCCTTTATGCTGAATA
STS source:
STS Forward / Reverse: Foward read
STS:
CCTGGTAGTGAGCCTGGGCATGAACTTTTATNCTAGTACCAGTGGACTGTCTAATTTTGG
GCATGTTGTNGTTTCTGTTCAAAGTTCAGTATTTTTTGCTATTNGAGTAGTGATATCTNG
TTTTGTACAGTGTTCTTTAACATATTGTTGTTCTTTTCACCCCAGGAAACACTTTTAAGC
AATATGTGCAAGTGATCGTGGAAATAATATCTNTGAACAGGNCTTTAATAGCCTTGTTAA
TGCAACTAGCTAGTTTCTTTAGACATGTTTTTGGAGGCTTCCTTAGATAGCTTTATTGAT
GCAATTTAGCTAGTTTCTTAAGACTGTTGTCGAAGGCATCATACATGTTGAATTATGTGA
TGATATGATCTATTCTAGATTCAGATGGAACTACTATTAGAGATTTATTGGATGTGATGC
ATTGCCCTTGGTTCCTTTATGCTGAATAATTTCTTGTGTTTGTTTCATGTTATCATCTTA
TTCATACATGCTACTTGTTTCTCTGCAAACAGACCAATTCAAGGCCATAAATGATGAAGG
AATGCCTATGTATCAGAGGCCATTTATGAGGGGCAAACTGTACATTCATTTCANTGTTGA
CTTCCCTGAGTCACTGAGCCCAGACCAGTGCAAGATGCTGGAGACCGTACTACCTCCAAG
GACCTCAGTCCAGCTCACCGATATGGAACTGGATGAGTGTGAAGAAACAACCCTGCATGA
TGTGAACATTGAGGAGGAAATGCGAAGGAAGCAACAAGCAGCTCAGGAGGCATACGATGA
AGATGACGATATGCAAGGTGGTGCCCAGAGAGTGCA
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CTGGGCACCACCTTGCATATCGTCATCTTCATCGTATGCCTCCTGAGCTGCTTGTTGCTT
CCTTCGCATTTCCTCCTCAATGTTCACATCATGCAGGGTTGTTTCTTCACACTCATCCAG
TTCCATATCGGTGAGCTGGACTGAGGTCCTTGGAGGTAGTACGGTCTCCAGCATCTTGCA
CTGGTCTGGGCTCAGTGACTCAGGGAAGTCAACAGTGAAATGAATGTACAGTTTGCCCCT
CATAAATGGCCTCTGATACATAGGCATTCCTTCATCATTTATGGCCTTGAATTGGTCTGT
TTGCAGAGAAACAAGTAGCATGTATGAATAAGATGATAACATGAAACAAACACAAGAAAT
TATTCAGCATAAAGGAACCAAGGGCAATGCATCACATCCAATAAATCTCTAATAGTAGTT
CCATCTGAATCTAGAATAGATCATATCATCACATAATTCAACATGTATGATGCCTTCGAC
STS source:
STS Forward / Reverse: Reverse read
STS:
GTTTTCTGTT CAAAGTTCAG TTATTTTTTG CTATTTGAGT AGTGATATCT TGTTT
TTGTA CAGTGTTCTT TAACATATTG TTGTTTCTTT TCACCCCAGG AAACACTTTT
AAGCAATATG TGCAAGTGAT CGTGGAAATA ATATCTATGA ACAGGCCTTT AATA
GCCTTG TTAATGCAAC TAGCTAGTTT CTTTAGACAT GTTTTTGGAG GCTTCCTTA
G ATAGCTTTAT TGATGCAATT TAGCTAGTTT CTTAAGACTC TTGTCGAAGG CAT
CATACAT GTTGAATTAT GTGATGATAT GATCTATTCT AGATTCAGAT GGAACTAC
TA TTAGAGATTT ATTGGATGTG ATGCATTGCC
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:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinf1
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
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: 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10015385m
Scaffold: scaffold_2
Start: 4021167
End: 4024377

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00992:mRNA_13.1
Scaffold: C_unshiu_00992
Start: 79008
End: 82132
Gene function: DnaJ

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 41.317

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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-07
Rp/Sa cM: 25.534

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: SI051
DNA sequence around SNP1:
CTTTTCACCCCAGGAAACACTTTTAAGCAATATGTGCAAGTGATCGTGGAAATAATATCT
[A/C]TGAACAGGCCTTTAATAGCCTTGTTAATGCAACTAGCTAGTTTCTT
SNP2: SI291
DNA sequence around SNP2:
TGTTTTTGGAGGCTTCCTTAGATAGCTTTATTGATGCAATTTAGCTAGTTTCTTAAGACT
[C/G]TTGTCGAAGGCATCATACATGTTGAATTATGTGATGATATGATCTATTCTAGATT
CAGAT
SNP3: SI351
DNA sequence around SNP3:
TGTTTTTGGAGGCTTCCTTAGATAGCTTTATTGATGCAATTTAGCTAGTTTCTTAAGACT
[C/G]TTGTCGAAGGCATCATACATGTTGAATTATGTGATGATATGATCTATTCTAGATT
CAGAT
SNP4: SI371
DNA sequence around SNP4:
GGTAGTACGGTCTCCAGCATCTTGCACTGGTCTGGGCTCAGTGACTCAGGGAAGTCAACA
[C/G]TGAAATGAATGTACAGTTTGCCCCTCATAAATGGCCTCTGATACATAGGCATTCC
TTCAT