Citrus CAPS Marker Database

Locus name: Ov0005

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 900
Comment on PCR:
F-primer: TCCTATGGATCTCGCTGTGTG
R-primer: GGCTGGCTTCACCTCAGTGT

EST info

EST Accession number 1: AU186258
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

GAGCCGTCCCAAGGCTATGACCGTCTTCTGGTCCTCCTTGGCTCAGAGCATGACTGCTCG
CCCAATGAAGGGAATGCTTACTGGCCCTGTCACCATTCTCAACTGGTCCTTTGTCAGAAA
TGACCAGCCCAGGTATATAAATGAGAACTGGTTCACTATTGGTTAACCTTTTGAAATGGA
AACATTGTTTAACATAAATTGCTGCCAATTTTGCAGACATGAAACCTGCTACCAGATTGC
TTTGGCCATCAAGGACGAAGTCGAGGATCTTGAGAAGGCAGGCATTAACNTTATTCAAAT
TGATGAGGCTGCCTTGAGGGAAGGATTGCCTCTNAGGAAATCTGAGCATGCTTTCTACTT
GGACTGGGCAGTCCACTCCTTCAGAATCACCAACTGNGGNGTCCAGGACACTACCCAGGT
CAGTTNCCCTTTNAATCTCCAATCTCAT

STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read

STS:

GTCCTCCTTGGCTCAGAGCATGACTGCTCGCCCAATGAAGGGAATGCTTACTGGCCCTGT
CACCATTCTCAACTGGTCCTTTGTCAGAAATGACCAGCCCAGGTATATAAATGAGAACTG
GTTCACTATTGGTTAACCTTTTGAAATGGAAACATTGTTTAACATAAATTGCTGCCAATT
TTGCAGACATGAAACCTGCTACCAGATTGCTTTGGCCATCAAGGACGAAGTCGAGGATCT
TGAGAAGGCAGGCATTAACGTTATTCAAATTGATGAGGCTGCCTTGAGGGAAGGATTGCC
TCTTAGGAAATCTGAGCATGCTTTCTACTTGGACTGGGCAGTCCACTCCTTCAGAATCAC
CAACTG

STS source:
STS Forward / Reverse: Foward read

STS:

TGCCAATTTTGCAGACATGAAACCTGCTACCAGATTGCTTTGGCCATCAAGGACGAAGTN
GAGGATCTTGAGAAGGCAGGCATTAACGTTATTCAAATTGATGAGGCTGCCTTGAGGGAA
GGATTGCCTCTNAGGAAATNTGAGCATGCTTTNTACTTGGACTGGGCAGTCCACTCCTTC
AGAATCACCAACTGTGGCATCCAGGACNCTACCCAGGTCAGTTACCCTTTTAATCNCCAA
TCTCATCNCTTTAATTTANCTGNTGATGTTGTATCTCATCNTATTGTTTATTGATTGACA
GATCCACACCCACATGTGCTACTCCAACTTCAACGACATTATCCACTCAATTATCGACAT
GGATGCTGATGTGATCACCATTGAGAACTCTCGTTCTAATGAGAAGCTCCTGTCAGTCTT
CCGTGAGGGAGTCCAGTATGNTGCTGCAATTGGCCCTGGTGTGTGGCTGG

STS source: Okitsu 46
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

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: Hinc2
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hinc2
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: Ciclev10019557m
Scaffold: scaffold_3
Start: 41636616
End: 41641083

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_02126:mRNA_2.1
Scaffold: C_unshiu_02126
Start: 9391
End: 13319
Gene function: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 47.986

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: SI243
DNA sequence around SNP1:

TTATTCAAATTGATGAGGCTGCCTTGAGGGAAGGATTGCCTCT[T/C]AGGAAATCTGAG
CATGCTTTCTACTTGGACTGGGCAGTCCACTCCTTCAGAATCACCAAC

SNP2: SI331
DNA sequence around SNP2:

AATGAGAACTGGTTCACTATTGGTTAACCTTTTGAAATGGAAACATTGTTTAACATAAAT
[T/G]GCTGCCAATTTTGCAGACATGAAACCTGCTACCAGATTGCTTTGGCCATCAAGGA
CGAAG

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: