Citrus CAPS Marker Database

Locus name: Al0302

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 1600
Comment on PCR:
F-primer: TCGCTTACAACACTCTTTTCC
R-primer: CCCTGAACATGGTGACAAAT

EST info

EST Accession number 1: C95329
EST Accession number 2: DC892942

sequence-tagged site (STS seq)

STS:
GGTTATTATTAATTTCTTTCTTATGCATTTAGGTTATAGGACTAGTTAGTATATTCAAAA
TAACTTGAAATGGTTTATCTCAAAGTTTGTGATCCTTTCTGACAAGTTATGTTTGAGAGA
TGGGCTACATAGGAAAAGCAAATGAAATTGTGCTGATGCGATGTATGATTTGCAGAGTTT
ACACCCAGCTGCAGAGTATCATGGTGCGGCTCGTGCAGTAGGTGGTTGTGCAATCTATGT
TAG
STS source:
STS Forward / Reverse: Combined sequence of both reads
STS:
CCACATCCCC TAACTTTGAG AGAGATTGTG GCGGTTGGAG ATCGGTTGTC ACTGA
GGGAG GAGGTCAGTT CAGAAGATAC TTCACCATCA AAGAGATCTG GCTTCTTCTC
AGACATACGC ACCTCCACAT TCTCGACAGC ACCTCCACTG TTGAACATGT CGAG
CAAGCC TATTGCTGCN AATGAAATGT TTGAAGAGAT CTCCTGCATA
STS source:
STS Forward / Reverse: Combined sequence of both reads
STS:
GGATCTCAACAGGCCATCTGTACATCTCTTCCTCCGGAACCGGGAGTGTCATGGTCATCA
ACCCGGTTGCAGAATCGTAGGTGAAGTCGGTCTGGATGCTGCCCACGGTGCATTTCAGAG
GACGCTGGGAAGAGTAAATGCCAAANCTTCCACATCCCCTAACTTTGAGAGAGATTGTGG
CGGTTGGAGATCGGTTGTCACTGAGGGAGGTGGTCAGTTCAGAAGATACTTCACCATCAA
AGAGATCTGGCTTCTTCTCAGACATATGCACCTCCACATTCTCGACAGCACCTCCACTGT
TGAACATGTCGAGCAAGCCTATTGCTGCGAATGAAATGTTTGAAGAGATCTCCTGCATAA
TGGAAATGGTCATTCAGCAAACCACCATTGTTGAATCATTGGACGAGCTTGAGAAGTTAA
TCCTAAAGAACCTGAAAAAACTCACCTTCAGCGGGCAGAAATGGAATAGCTCGTATTCAA
GAACCTTAAGTGTTACTGGCACTGAAGCACCTTTGGGCAACCGCACAACCTCACCTAATG
TACAAAAGAATTTCCATTCAGCATATTCCAAACCAATGTGTTATTTAGCTTACAACAACA
TGGTAAGAACTAATTTTAAGAATGCATACAAGCCTTTACCCAAAAACCATCAAGATAAGA
AATTTCTTTAATGACATCNATAAGTAATGNTGTGTCGAAGTCACTAAGTTGGGAAGAATG
AAATTCAGAGTAGCAAATACTGATCTATGGGCATAACA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CAGGCCATCTGTACATCTCTTCCTCCGGAACCGGGAGTGTCATGGTCATCAACCCGGTTG
CAGAATCGTAGGTGAAGTCGGTCTGGATGCTGCCCACGGTGCATTTCAGAGGACGCTGGG
AAGAGTAAATGCCAAACCTTCCACATCCCCTAACTTTGAGAGAGATTGTGGCGGTTGGAG
ATCGGTTGTCACTGAGGGAGGAGGTCAGTTCAGAAGATACTTCACCATCAAAGAGATCTG
GCTTCTTCTCAGACATACGCACCTCCACATTCTCGACAGCACCTCCACTGTTGAACATGT
CGAGCAAGCCTATTGCTGCAAATGAAATGTTTGAAGAGATCTCCTGCATAATGGAAATGG
TCATTCAGCAAACCACCATTGTTGAATCATTGGACGAGCTTGAGAAGTTAATCCTAAAGA
ACCTGAAAAAACTCACCTTCAGCGGGCAGAAATGGAATAGCTC
STS source:
STS Forward / Reverse: Foward read
STS:
CATCAGTTACACGAACAGATGCTGTGAGGTACCNGGAGATTCATCATGAATGCGGTTTTC
TTGGTAATCTTGCACCAACCAGCACCTTGACAGTTGAACACACCAACAACACCAGAGCAT
TTGTTCACATTCCATACCTTGAGCAAGCTGCAATATACAATCTTGAGATGAGTCTTTTCT
AAAATCTGCATGTCTACTGGGGAGGAAAATGAAAAATATGACTGTTCTCAACCAAAAAGG
AAGGAAGTAGCAAACCTAGTCCCATCTCGGGCAGGATCAGCAAAGAGACAATCACGTGTA
GGCCTGCCAGGCAGTTGGGCACGAAGAACTGATCCATCAGGAAGTACCAGCTTCCTCAAC
AGGTCGAAATTGTGGTTACCCGGCTTGTCACTGCATTAACAAGAGGAAACAGAGGTTCTT
GTCAGAAGACTGTTACTTCCATCTCTTAATAAGTATGACAGAAGAAGTAATTTAAGCTAA
GCATGGCAATACCTAACATAGATTGCACAACCACCTACTGCACGAGCCGCACCATGATAC
TCTGCAGCTGGGTGTAAACTCTGCAAATCATACATCGCATCAGCACAATTTCATTTGCTT
TTCCTATGTAGCCCATCTCTCAAACATAACTTGTCAGAAAGGATCACAAACTTTGAGATA
AACCATTTCAAGTTATTTTGAATATACTAACTAGTCCTATAACCTAAATGCATAAGAAAG
AAATTAATAATAACC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
AATTTCTTTCTTATGCATTTAGGTTATAGGACTAGTTAGTATATTCAAAATAACTTGAAA
TGGTTTATCTCAAAGTTTGTGATCCTTTCTGACAAATTATGTTTGAGAGATGGGCTACAT
AGGAAAAGCAAATGAAATTGTGCTGATGCAATGTATGATTTGCAGAGTTTACACCCAGCT
GCAGAGTATCATGGTGCGGCTCGTGCAGTAGGTGGATGTGCAATCTATGTTAGGTATTGC
CATGCTTAGCTTAAATTACTTCTTCTGTCATACTTATTAAGAGATGGAAGTAACAGTCTT
CTGACAAGAACCTCTGTTTCCTCTTGTTAATGCAGTGACAAGCCGGGTAACCACAATTTC
GACCTGTTGAGGAAGCTGGTACTTCCTGATGGATCAGTTCTTCGTGCCCAACTGCCTGGC
AGGCCTACACGTGATTGTCTCTTTGCTGATCCTGCCCGAGATGGGACTAGGTTTGCTACT
TCCTTCCTTTTTGGTTGAGAACAGTCATATTTTTCATTTTCCTCCCCAGTAGACATGCAG
ATTTTAGAAA
STS source:
STS Forward / Reverse: Reverse read

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: Hind3
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Hind3
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: Hind3
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: Hind3
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: Hind3
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: Hind3
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: Ciclev10004372m
Scaffold: scaffold_9
Start: 25073693
End: 25080376

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00119:mRNA_33.1
Scaffold: C_unshiu_00119
Start: 346131
End: 352710
Gene function: Putative seed imbibition protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-03
AGI cM: 48.375

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-032
KmMg cM: 18.339

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-033
JtTr cM:

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

Km/O41 LG: NAT-03
Km/O41 cM: 3.773

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG: RP-03
Rp/Sa cM: 36.113

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: M

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI090
DNA sequence around SNP1:
CCATCAAAGAGATCTGGCTTCTTCTCAGACATA[T/C]GCACCTCCACATTCTCGACAGC
ACCTCCACTGTTGAACATGTCGAGCAAGCCTATTGCTG
SNP2: SI311
DNA sequence around SNP2:
TTATGTTTGAGAGATGGGCTACATAGGAAAAGCAAATGAAATTGTGCTGATGC[A/G]AT
GTATGATTTGCAGAGTTTACACCCAGCTGCAGAGTATCATGGTGCGGCTCGTGCAGTA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: