Citrus CAPS Marker Database

Locus name: Mf0010

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 400
Comment on PCR:
F-primer: AATGTTATCATCAATGGCAC
R-primer: ATACCAGCCTTGGCTTCTCC

EST info

EST Accession number 1: C81689
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
TGTCAAACCCACCAAAACCACCATTCTTCACCAAAATAGAACCAAACCCATTTCAAGAAA
CCAAAGGCTCGTTGCTTTAGCAACCCCAGAATCACTCACAGCTGAAGAAGCAACAACAAC
ATCCACAGAGACCATCCCAGCAACCCCAGTAGAAACTAAGGTCCAAACCAAATCTCTCTC
TCCCTCTCTACATATGTGTGTTTATGTGTACTGTTTC
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read
STS:
GCTCCTCATTCCCTTCCCAAAAACTCACTGTCAAACCCACCAAAACCACCATTCTTCACC
AAAATAGAACCAAACCCATTTCAAGAAACCAAAGGCTCGTTGCTTTAGCAACCCCAGAAT
CACTCACAGCTGAAGAAGCAACAACAACATCCACAGAGACCATCCCAGCAACCCCAGTAG
AAACTAAGGTCCAAACCAAATCTCTCTCTCCCTCTCTACATATGTGTGTTTATGTGTACT
GTTTCTATGTGTACTGTTTCACTTAATAAAAGTTGTGTGTTTTCTTTTTCTTTTCTTCTG
GGCAGAAGGCGGGGGTGTCAGTGAAGCAATTGGAGAAGCCAGGGCTGGTAT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TTTGGTTTGGACCTTAGTTTCTACTGGGGTTGCTGGGATGGTCTCTGTGGATGTTGTTGT
TGCTTCTTCAGCTGTGAGTGAAACTGGGGTTGCTAAAGCAACGAGCCTTTGGTTTCTTGA
AATGGGTTTGGTTCTATTTTGGTGAAGAATGGTGGTTTTGGTGGGTTTGACAGTGAGTTT
TTGGGAAGGGAATGAGGAGCGTGTGGTGAAT
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
AAACCACCAT TCTTCACCAA AATAGAACCA AACCCATTTC AAGAAACCAA AGGCT
CGTTG CTTTAGCAAC CCCAGAATCA CTCACAGCTG AAGAAGCAAC AACAACATCC
ACAGAGACCA TCCCAACAAC CCCAGTAGAA ACTAAGGTCC AAACCAAATC TCTC
TCTCCC TCTCTACATA TGTGTGTTTA TGTGTACTGT TTC
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Miyagawa-wase/Trovita orange
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: 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: Pvu2
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)
Resriction enzyme: NC
Rank as CAPS marker: Others
Comment: PCR_condition: 52C aneal
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: 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: 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: 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
Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Pvu2
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: Pvu2
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: Ciclev10032902m
Scaffold: scaffold_4
Start: 19467669
End: 19468803

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00099:mRNA_4.1
Scaffold: C_unshiu_00099
Start: 12446
End: 13357
Gene function: 30S ribosomal protein 3, chloroplastic

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 55.503

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-07
KmMg cM: 42.271

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 35.215

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

Km/O41 LG: NAT-07
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: SI048
DNA sequence around SNP1:
AAGCAACAACAACATCCACAGAGACCATCCCAACAACCCCAGTAGAAACTAAGGTCCAAA
[T/C]CAAATCTCTCTCTCCCTCTCTACATATGTGTGTTTATGTGTACTGTTTC
SNP2: SI149
DNA sequence around SNP2:
GCAACCCCAGAATCACTCACAGCTGAAGAAGCAACAACAACATCCACAGAGACCATCCCA
[A/G]CAACCCCAGTAGAAACTAAGGTCCAAA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: