Citrus CAPS Marker Database

Locus name: Al0217

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 52
Main product (bp): 1800
Comment on PCR:
F-primer: GCTCGTTTTTCCCCTTTT
R-primer: CTTCGGACATGAATAATCAGA

EST info

EST Accession number 1: C95269
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
AGTATCTATGCACCCTGTATTTTTGCTATATGTTTCTAAGTGAAAGGGATACCTTTCCAA
AATAGTTATGAGGAGAAAAAGAGCCAAAACATTCAGTTTGAGTGTTGTATGTATGCACAT
CATATCATTCCACGAAAAGAAAATGCGTTGATACTTTTCCCACGACTCCTGAGAACATTT
TAATGAAGGTTCTGAAGATGTTTCTTCTGATGATCTGAGTTTTCAGCGTTATTTATATCA
AAGAGTGAAATATTACATCTTTTTTTCAGAGTTTGCTCAGGCTGAAAGAGCCAGCTGTGT
TACTGAGATGCCGCAAAGATGACCATCATTTGGTGGAGTJUL
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CTTCAACAGTATCTATGCACCCTGTATTTTTGCTATATGTTTCTAAGTGAAAGGGATACC
TTTCCAAAATAGTTATGAGGAGAAAAAGAGCCAAAACATTCAGTTTGAGTGTTGTATGTA
TGCACATCATATCATTCCACGAAAAGAAAATGCGTTGATACTTTTCCCACGACTCCTGAG
AACATTTTAATGAAGGTTCTGAAGATGTTTCTTCTGATGATCTGAGTTTTCAGCGTTATT
TATATCAAAGAGTGAAATATTACATCTTTTTTTCAGAGTTTGCTCAGGCTGAAAGAGCCA
GCTGTGTTACTGAGATGCCGCAAAGATGACCATCATTTGGTGGAGTCTGTTTTGGAGTCA
GCAAAAGAGGAATATGCACAGAAATTGCAGGTTCACCCACCAGAGATAATTGTGGATCAT
CACATCTATCTTCCGCCTGGCCCTGGCCATCATAATGCCCATGGTCCATCCTGGTAAATT
TTTTCAGCTGAGCTAGCCCGCATTGCTTAAGTGTTGTACATACTGCAGCATTTTCAACCT
TTTAAAAAAAAGCAGTTTATCTACCAATTCATCCACCTATAACTTTTAAGGGGGCTCCGG
TGAATATAATATACTGGGTCAGAACTGTTGCCATAATGCTACCATTGGTCAGTAGAATGC
TTGTGGTGNTTCTCAATTTTTCGAGNTAGTTTTTTTCATCTGNTAATTGTGAAACTAGAA
TAATGCCTAATTGGGGTGCTATCTTTATCNTCTTAA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GGTTTCCATTTTCGAGTAGTTTTTTCATCTGTAATNGGAAACTAGAAAATGCCTAATGGG
TTGCTAATCTTTTATCTTCTTAAATGTTTTCTCTTCATGAGAAAATGGTGATGGAATAGC
TTGCTTATAATAATGNTGGTTTGCTTGAGCAGCTCAGGAGGTGTCGTGGTGGCTTCTCGA
GATGGGAAGATAGTATGTGAGAATACCCTTGATGCACGGTTGGATGTTGTGTTCCGTAAA
AAACTTCCTGAGGTATTCCATTTTTAAAATTTATCATTATTATTGTTTTTGCCTGTTTCT
TTAGCAGTAATCTAACATATCTTGGTGGTATAAATGTTTTATTCTCCTCCATTCCTAATG
TGATCATATTGAAGAATAAATAAGACACGGACAGATAAATTAACTTATTGTTTCACTATT
TAGAAAATAACAATCTTGATGCTGATTCCTTATTTATTCGCATCATCAGGCTTGTCAGCA
ATTGATAATTTTGGTATAATTGAAAACTAGGAATACGATTCAAACTTTATAGTCATCAAT
TAATTTGCCATTGGCTTCTGCATCTGTTGTTGATTTTATAGTGTTAACTAGTAAACAATC
AAATGCTTTTGGAGAAGGCCACTAATATGGTGTTTTTGTGATTATAATTTGGTTTAATTT
TCACAATGTCTTTATTTTTTTTGGTTTTGGGGGGGGACCACAGATTATTTATTTATTTTA
GTACTTGAATAACCTATCGATGATGATGTTCATGTAAGATTGTTTTAATTTGTCAAGTGT
ATTCATTTTTGCTTCTTCTACTGCAGATCCGGAAGCACGCTCGTCAGTC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CACTTGACAAATTAAAACAATCTTACATGAACATCATCATCGATAGGTTATTCAAGTACT
AAAATAAATAAATAATCTGTGGTCCCCCCCCAAAACCAAAAAAAATAAAGACATTTTGAA
AATTAAACCAAATTATAATCACAAAAACACCATATTAGTGGCCTTCTCCAAAAGCATTTG
ATTGTTTACTAGTTAACACTATAAAATCAACAACAGATGCAGAAGCCAATGGCAAATTAA
TTGATGACTATAAAGTTTGAATCGTATTCCTAGTTTTCAATTATACCAAAATTATCAATT
GCTGACAAGCCTGATGATGCGAATAAATAAGGAATCAGCATCAAGATTGTTATTTTCTAA
ATAGTGAAACAATAAGTTAATTTATCTGTCCGTGTCTTATTTATTCTTCAATATGATCAC
ATTAGGAATGGAGGAGAATAAAACATTTATACCACCAAGATATGTTAGAT
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: Hinf1
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)

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: PCR_condition: 62C 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: Ciclev10022061m
Scaffold: scaffold_3
Start: 1203357
End: 1206483

Target on C. unshiu (v1.0)

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

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-05S
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 25.182

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: SI350
DNA sequence around SNP1:
GTACTAAAATAAATAAATAATCTGTGGTCCCCCCCCAAAACCAAAAAAAATAAAGACATT
[T/G]TGAAAATTAAACCAAATTATAATCACAAAAACACCATATTAGTGGCCTTCTCCAA
AAGCA
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: