Citrus CAPS Marker Database

Locus name: Mf0096

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1200
Comment on PCR:
F-primer: GGAGTATCACCCCCACATGCT
R-primer: AAGTGCACAATGCTCCTTCTC

EST info

EST Accession number 1: C81915
EST Accession number 2: DC893673

sequence-tagged site (STS seq)

STS:
CTCACTTCATGTATCCAAGGTCAGGGATCCAGTTGTTCTTTTATTGCTGATGGATTAATT
TATTGCACAAACAGAAAGTGAGGAGATTTTATTTAGGTGCCATGCACGACTGTAAGGTGT
TTAGGCCCCATCTTTGAGTATGAGAAAGTAATGGAACTACCAGCTACTGGTGGTCCCTTT
AAAATGCCTTCNTTGATTTAAACATATAATGTACATAGGATGTTCCCCACAAGAAAAGTG
CAGGCCATGAGAGCTGACTATTACTCACTGTAATGACATTATTATATTTATTTATTACTC
AACTTTGAAAGTAATTCAATGATGTCTTCCCTTAAGAACTTTCATGTGTGTAAGTATGAC
GTAATTGTCTATCAGCTAAATTGACTGTGTTGTTGAGAAATTACCCCATTGAATGTTCTA
GGATCTCATTGACCTCTGACTCTGGGTTTTACATTGACAGTGGAGTTGACCAGTTTAAGC
AGCAATTTGCCCGCCTTGAGGAGCAATATGGTAAAAGAGAAAGACATATTCCACTCCGAA
GAAAGTATACCTCCTTGCCTAGGTATGGGTGATGCCAAAATTCTGAGCAGTTATTAGGTC
ATTATCATTTTTGTTTAATTAGTTGCTGCCATTTTCTTCTCCACAGGGAAAGAATCAGTA
CATCTGAAGATGAGGCTACAGATCAAACAGATTCTTTGAAGAAACGTACAGCTTCTGTCA
CTCGTGCTACTCTCCAGAGCCCTCCAGTTTGCCCAGGTTTGCTGAAT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
AGTTGTTCTTTTATTGCTGATGGATTAATTTATTGCACAAACAGAAAGTGAGGAGATTTT
ATTTAGGTGCCATGCACGACTGTAAGGTGTTTAGGCCCCATCTTTGAGTATGAGAAAGTA
ATGGAACTACCAGCTACTGGTGGTCCCTTTAAAATGCCTTCATTGATTTAAACATATAAT
GTACATAGGATGTTCCCCACAAGAAAAGTGCAGGCCATGAGAGCTGACTATTACTCACTG
TAATGACATTATTATATTTATTTATTACTCAACTTTGAAAGTAATTCAATGATGTCTTCC
CTTAAGAACTTTCATGTGTGTAAGTATGACGTAATTGTCTATCAGCTAAATTGACTGTGT
TGTTGAGAAATTACCCCATTGAATGTTCTAGGATCTCATTGACCTCTGACTCTGGGTTTT
STS source:
STS Forward / Reverse: Foward read
STS:
CTGGGGTTACTTTCCAGAGCCCTCCNAATTTNNCCCAGGTTTGCTGAATTCCAGTCTGCT
CGGGGAAACTCTTTAACCATGCAGCATGGTTCTAGCAGTCAAAAGTGTGGTGTCCTCTTG
AGGAGTGATAGCATGAGTGCTTCAAAATGTGTGGGTGTCAACGGAAAATATTGCGACTGA
AAAGTGCGTTTTAGGGACAGATAGAAGAGTACCAGACGAGTCATTATCACCCAAAGTCGT
AGGCAATTCTTTTACAATGTCTTATGTCAACATAGATTACATAAAAATTTATATTATTTA
TTGGATCCAAACAAATTCAGAGTAGTCCATAAAGTTCNG
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
TGGATCCAATAAATAATATAAATTTTTATGTAATCTATGTTGACATAAGACATTGTAAAA
GAATTGCCTACGACTTTGGGTGATAATGACTCGTCTGGTACTCTTCTATCTGTCCCTAAA
ACGCACTTTTCAGTCGCAATATTTTCCGTTGACACCCACACATTTTGAAGCACTCATGCT
ATCACTCCTCAAGAGGACACCACACTTTTGACTGCTAGAACCATGCTGCATGGTTAAAGA
GTTTCCCCGAGCAGACTGGAATTCAGCAAACCTG
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: Rsa1
Rank as CAPS marker: 3 or more alleleic model
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: 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)

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: Kiyomi x Miyagawa-wase
Restriction enzyme: NC
Comment: PCR_condition: 56C aneal
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
Population name: Jutaro unshu x Trovita orange
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
Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Rsa1
Comment: PCR_condition: 56C aneal
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: 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: Ciclev10018252m
Scaffold: scaffold_2
Start: 27774863
End: 27778271

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00745:mRNA_6.1
Scaffold: C_unshiu_00745
Start: 48150
End: 62370
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 60.007

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-06
KmMg cM: 22.141

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
JtTr cM: 5.708

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

Km/O41 LG: NAT-06S
Km/O41 cM: 10.082

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: SI249
DNA sequence around SNP1:
CTTTGAGTATGAGAAAGTAATGGAACTACCAGCTACTGGTGGTCCCTTTAAAATGCCTTC
[A/G]TTGATTTAAACATATAATGTACATAGGATGTTCCCCACAAGAAAAGTGCAGGCCA
TGAGA
SNP2: SI333
DNA sequence around SNP2:
ACATTGTAAAAGAATTGCCTACGACTTTGGGTGATAATGACTCGTCTGGTACTCTTCTAT
[T/C]TGTCCCTAAAACGCACTTTTCAGTCGCAATATTTTCCGTTGACACCCACACATTT
TGAAG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: