Citrus CAPS Marker Database

Locus name: Lp0119

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1400
Comment on PCR:
F-primer: ATACATCAATGGCGAAAACAA
R-primer: CCATGATAGCCGCAACAC

EST info

EST Accession number 1: AU300466
EST Accession number 2: DC893197

sequence-tagged site (STS seq)

STS:
CTCTCTTTCTCCTCCTACTTCACTTGGGTTGCTTCATTTTCCCATCCAACAACAATCCCT
CACCAACAAGAAAGAAACGCAAGGCCTCTCCTCTCTCTCCATCTCCGTACTCCCCGTCTC
GCCTTAAAACTAAACCCCANANGGCTCTCTCATCCTCTTGGTCCTATCTCAAACGTATCT
TCTCTAATTCAAAGACCCTGAAACCCAGCTTGTCCCAGACTAGCTCTACCTCATCAACAT
CAAATATAATTTCCTCCGCGAGGTCATCTCAGCATTCGCTGGTCCCGCCTGATCATCAAA
TTCACTTGTCAGACATANCTCCAAGTGTCCNGGAATCCGACATCTCGGCGGCTGATCACA
ACCCCTTCTTCCCTCTACGTAACGATATCTTCCCATGCACGGCTTGTGGTGAGATCTTTC
AGAANCCCCATCTTCTAGAGCAACACCAATCTATCAAACATGCAGTGTCAGAGCTCATCG
ATGGNGATTCCGGCAAGAATATTGTGAACATAATATTCAAAACCGGCTGGTCTAATAAGG
AGAGGAATCCTGAGATACATAGAATCTTGAAGATCCANAACAGCTCAAAGATTCTATCAA
GATTTGAAGAGTACAGAGAGCTTGTCAAAACNAAAGCAGCGAGAAACGGCGCCGTACGGA
AGCGGGAACGAGAGATGTATTGCTGACGGCAACGAGCTTCTGAAATTTACTGCTCNACTT
TTGTATGTGACCTGGGGCAAGCGG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TCACCAACAAGAAAGAAACGCAAGGCCTCTCCTCTCTCTCCATCTCCGTACTCCCCGTCT
CGCCTTAAAACTAAACCCCACAAGGCTCTCTCATCCTCTTGGTCCTATCTCAAACGTATC
TTCTCTAATTCAAAGACCCTGAAACCCAGCTTGTCCCAGACTAGCTCTACCTCATCAACA
TCAAATATAATTTCCTCCGCGAGGTCATCTCAGCATTCGCTGGTCCCGCCTGATCATCAA
ATTCACTTGTCAGACATACCTCCAAGTGTCCCGGAATCCGACATCTCGGCGGCTGATCAC
AACCCCTTCTTCCCTCTACGTAACGATATCTTCCCATGCACGGCTTGTGGTGAGATCTTT
CAGAA
STS source:
STS Forward / Reverse: Foward read

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: Hae3
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)
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)

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hae3
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: Hae3
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: Msp1
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: Ciclev10028631m
Scaffold: scaffold_8
Start: 24315720
End: 24317671

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00021:mRNA_65.1
Scaffold: C_unshiu_00021
Start: 426040
End: 431920
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 8.544

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/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: SI276
DNA sequence around SNP1:
GGCTCTCTCATCCTCTTGGTCCTATCTCAAACGTATCTTCTCTAATTCAAAG[A/G]CCC
TGAAACCCAGCTTGTCCCAGACTAGCTCTACCTCATCAACATC
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: