Citrus CAPS Marker Database

Locus name: If0211

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 600
Comment on PCR:
F-primer: AAACCGTACAAATACCAGTCT
R-primer: CCAACCTCTTGCATCTG

EST info

EST Accession number 1: DC893574
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
ANGTCTCCTCCGCCACCAACTCCGGTTTACCATTCCCCACCACCTCCAGTTTACCATTCC
CCACCACCACCCAAGAAGCCCTATAAGTACAAGTCTCCCCCACCACCCCCAGTTTACACG
TCCCCACCACATCACCCTTACGTCTATGCATCTCCCCCTCCTCCTNACCACTACTAGAAA
GTGGCCACGAATAGCTCATGCTTTTTTATGGTAAACTCAAAATTATTGAGCTTTAGTTTA
AGCACTGTGTTATATTTTTATATGCAAATTAAGTGAATAAGTGACCACTGACATAGACTG
ATTAACATGTTGTTGCAGGAGAGGCGATTCGCATGCAAATAAAGAAAGCGACAGCTGATT
AAGAGACTTTACCGTGAGAAAAAGAAAAGCGAGTTGCCGCGTTTTAATTATCTTTATCTT
TTTTCCTTTTTGCCCCCCCAAGAGGAATAAANAGTTACATGTAGAAAAGCAAAGTGCTTA
TCATTTTCATGTATGGATCGTTGCTGTGTGTAATTCGCATCTCACGTCTTTTGTAATTGT
CAACCTTTTTGCATGCAGAGGCAAAGAGGTTGGA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
TAAACCGTACAAAAATCCAGTCTCCTCCGCCACCAACTCCAGTTTACCATTCCCCACCAC
CACCAAAGAAACCGTACAAGTATAAGTCTCCTCCGCCACCAACTCCGGTTTACCATTCCC
CACCACCTCCAGTTTACCATTCCCCACCACCACCCAAGAAGCCCTATAAGTACAAGTCTC
CCCCACCACCCCCAGTTTACACGTCCCCACCACATCACCCTTACGTCTATGCATCTCCCC
CTCCTCCTNACCACTACTAGAAAGTGGCCACGAATAGCTCATGCTTTTTTATGGTAAACT
CAAAATTATTGAGCTTTAGTTTAAGCACTGTGTTATATTTTTATATGCAAATTAAGTGAA
TAAGTGACCACAGACATAGTCTGATTAACATGTTGTTGCAGGAGAGGCGATTCGCATGCA
AATAAAGAAAGCGACAGCTGATTAAGAGACTTTACCGTGAGAAAAAGAAAAGCGAGTTGC
CGCGTTTTAATTATCTTTATCTTTTTTCCTTTTTGCCCCCCNAAGAGGAATAAACAGTTA
CATGTAGAAAAGCAAAGTGCTNATCATTTTCANG
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
ATACATGAAAATGATAAGCACTTTGCTTTTCTACATGTAACTGTTTATTCCTCTTCGGGG
GGCAAAAAGGAAAAAAGATAAAGATAATTAAAACGCGGCAACTCGCTTTTCTTTTTCTCA
CGGTAAAGTCTCTTAATCAGCTTTCGCTTTCTTTATTTGCATGCGAATCGCCTCTCCTGC
AACAACATGTTAATCAGACTATGTCAGTGGTCACTTATTCACTTAATTTGCATATAAAAA
TATAACACAGTGCTTAAACTAAAGCTCAATAATTTTGAGTTTACCATAAAAAAGCATGAG
CTATTCGTGGCCACTTTCTAGTAGTGGTAAGGAGGAGGGGGAGATGCATAGACGTAAGGG
TGATGTGGTGGGGACGTGTAAACTGGGGGTGGTGGGGGAGACTTGTACTTATAGGGCTTC
TTGGGTGGTGGTGGGGAATGGTAA
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment: PCR_condition: 56C aneal
Figure legend:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment: PCR_condition: 56C aneal
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Pvu2
Rank as CAPS marker: Available marker
Comment: PCR_condition: 56C 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: Kiyomi x Miyagawa-wase
Restriction enzyme: Pvu2
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: Jutaro unshu x Trovita orange
Restriction enzyme: Pvu2
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: Pvu2
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: Pvu2
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

Target on C. clementina (v1.0)

Transcript ID:
Scaffold:
Start:
End:

Target on C. unshiu (v1.0)

Transcript ID: No
Scaffold:
Start:
End:
Gene function:

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 47.41

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-09
KmMg cM: 60.856

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: SI226
DNA sequence around SNP1:
GATAATTAAAACGCGGCAACTCGCTTTTCTTTTTCTCACGGTAAAGTCTCTTAATCAGCT
[T/G]TCGCTTTCTTTATTTGCATGCGAATCGCCTCTCCTGCAACAACATGTTAATCAGA
CTATG
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: