Citrus CAPS Marker Database

Locus name: Al0326

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 600
Comment on PCR:
F-primer: CAGAACAAAGCGATGGAACC
R-primer: CCCAAGTCCTGACCAACACTA

EST info

EST Accession number 1: C95360
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
AGGACCAAGCTGCCTCCGCAAAAGCCGCTATGGAGAAATCTCTCAATTTGAAGTCACCGA
AGCAAATNCATCAGACGCCAGAATTGGAGACTGCCAAGGTGGCTGCTGAGCCCTTTGTGG
GTTCCTCGTCGTCTGCTGCGGCCTCTCAACAGTTGAGTGTTGATCAGCCTGAGCCCCAAG
CCAAGGGGCCTACCAGGTGCTTGAGTTGCAACAAGAAGGTCGGATTGACAGGGTTCAAGT
GTAAGTGCGGGAGTACTTTCTGTGGAATCCATCGGTACCCAGAGAAGCATGATTGTACAT
TTGATTTTAAGGTTACTGGTCGAGATGCTATTGCCAAAGCAAATCCTGTTGTTAAAGCTG
ATAAGCTGGACAGGATCTGAAATCAGAGTCTGGTAATTTGGTTTGCTTTGGTATGGTAAT
TGTCGTCGGTTGGGTTATTGTTGATTTAGCTTAGCTT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
TGCCTCCGCAAAAGCCGCTATGGAGAAATCTCTCAATTTGAAGTCACCGAAGCAAATCCA
TCAGACGCCAGAATTGGAGACTGCCAAGGTGGCTGCTGAGCCCTTTGTGGGTTCCTCGTC
GTCTGCTGCGGCCTCTCAACAGTTGAGTGTTGATCAGCCTGAGCCCCAAGCCAAGGGGCC
TACCAGGTGCTTGAGTTGCAACAAGAAGGTCGGATTGACAGGGTTCAAGTGTAAGTGCGG
GAGTACTTTCTGTGGAATCCATCGGTACCCAGAGAAGCATGATTGTACATTTGATTTTAA
GGTTACTGGTCGA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
GGGGGACCAGCTACACCACATCTGAGCCAAAGCTCTGCGTCAACGGTTGTGGCTTCTTCG
GCACTGCGGCGAATATGGGCTTATGCTCAAAGTGTTACAGGGATTTGCGGGTTAAGGAGG
ACCAAGCTGCCTCCGCAAAAGCCGCTATGGAGAAATCTCTCAATTTGAAGTCACCGAAGC
AAATCCATCAGACGCCAGAATTGGAGACTGCCAAGGTGGCTGCTGAGCCCTTTGTGGGTT
CCTCGTCGTCTGCTGCGGCCTCTCAACAGTTGAGTGTTGATCAGCCTGAGCCCCAAGCCA
AGGGGCCTACCAGGTGCTTGAGTTGCAACAAGAAGGTCGGATTGACAGGGTTCAAGTGTA
AGTGCGGGAGTACTTTCTGTGGAATCCATCGGTACCCAGAGAAGCATGATTGTACATTTG
ATTTTAAGGTTACTGGTCGAGATGCTATTGCCAAAGCAAATCCTGTTGTTAAAGCTGATA
AGCTGGACAGGATCTGAAATCAGAGTCTGGTAATTTGGTTTGCTTTGGTATGGTAATTGT
CGTCGGTTGGGTTATTGTT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
TCTGATTTCAGATCCTGTCCAGCTTATCAGCTTTAACAACAGGATTTGCTTTGGCAATAG
CATCTCGACCAGTAACCTTAAAATCAAATGTACAATCATGCTTCTCTGGGTACCGATGGA
TTCCACAGAAAGTACTCCCGCACTTACACTTGAACCCTGTCAATCCGACCTTCTTGTTGC
AACTCAAGCACCTGGTAGGCCCCTTGGCTTGGGGCTCAGGCTGATCAACACTCAACTGTT
GAGAGGCCGCAGCAGACGACGAGGAACCCACAAAGGGCTCAGCAGCCACCTTGGCAGTCT
CCAATTCTGGCGTCTGATGGATTTGCTTCGGTGACTTCAAATTGAGAGATTTCTCCATAG
CGGCTTTTGCGGAGGCAGCTTGGTCCTCCTTAACCCGCAAATCCCTGTAACACTTTGAGC
ATAAGCCCATATTCGCCGCAGTGCCGAAGAAGCCACAACC
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
TGCCTCCGCA AAAGCCGCTA TGGAGAAATC TCTCAATTTG AAGTCACCGA AGCAA
ATNCA TCAGACGCCA GAATTGGAGA CTGCCAAGGT GGCTGCTGAG CCCTTTGTGG
GTTCCTCGTGGTCTGCTGCG GCCTCTCAAC AGTTGAGTGT TGATCAGCCT GAGCC
CCAAG CCAAGGGGCCTACCAGGTGC TTGAGTTGCA ACAAGAAGGT CGGATTGACA
GGGTTCAAGT
STS source:
STS Forward / Reverse:

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: Nde2
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)

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Population name: Jutaro unshu x Trovita orange
Restriction enzyme: Mbo1
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: Mbo1
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: Nde2
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: Nde2
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: Ciclev10022558m
Scaffold: scaffold_3
Start: 6409311
End: 6411254

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00443:mRNA_7.1
Scaffold: C_unshiu_00443
Start: 62532
End: 64193
Gene function: Zinc finger A20 and AN1 domain-containing stress-associated protein 8

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 42.609

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-05S
KmMg cM: 32.841

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 16.025

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-05
Rp/Sa cM: 27.235

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: K

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI065
DNA sequence around SNP1:
GTCTGCTGCGGCCTCTCAACAGTTGAGTGTTGA[T/G]CAGCCTGAGCCCCAAGCCAAGG
GGCCTACCAGGTGCTTGAGTTGCAACAAGAAGGTCGGA
SNP2: SI344
DNA sequence around SNP2:
TGCCTCCGCAAAAGCCGCTATGGAGAAATCTCTCAATTTGAAGTCACCGAAGCAAAT[A/
C]CATCAGACGCCAGAATTGGAGACTGCCAAGGTGGCTGCTGAGCCCTTTGTGGGTTCCT
CG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: