Citrus CAPS Marker Database

Locus name: Gn0051

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 500
Comment on PCR:
F-primer: GCCGCTGAAAACATGGTATAGG
R-primer: AATCAGCCAGAAAAGGTCAGAG

EST info

EST Accession number 1: DC895375
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

CTCTGTGGGCATTCTGGTTGGTTGGTTCTTCAGGTGGTCTTGTTTGTTTTTCTGGGCTTG
ATGGGCTAACTTTCAGAACACTCGTGTGCAATCCGCTTACCCAATCATGGAGGACATTGC
CGAGCATGCATTATAATCAGCAAAGACAGTTGATAATGGTTGTTGACCGGGTGGACCGTT
CATTCAAAGTGATTGCGACTAGTGATATATATGGTGACAAGTCATTGCCCACTGAAGTGT
ATGATTCAAAACTTGACAGATGGGCTGTCCACCAGATAATGCCTGCAGTTAATCTTTGCT
CTTCAAAGATGGCGTATTGTGACTCCCGGTTGTATTTGGAAACTCTTTCGCCACTGGGTT
TGATGATGTACAGGCTAGACACAGGTTACTGGGAACACATCCCGGCGAAGTTCCCCCGTT
CCTTGTTAGACGGGTATTTGGTTGCTGGTACACAGAAGCGTCTGTTTCTTGTTGGAAGGA
TTGGTCTCTATAGTACCCTCCAGAGCATGAGAATTTGGGAATTGGATCATTCAAAGATTA
TGTGGGTGGAGATGAGTAGGATGCCGCCAAANTATTTTCGAGCTTTATTAAGGCTATCAG
CTGAAAGATTTGAGTGCTTTGGACAGGATAATTTAATCTGTTTTACATCNTGGAACCAAG
GGAAGGGCCTTCTTTACGATGTGGATAAGA

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

STS:

AAAGACAGTTGATAATGGTTGTTGACCGGGTGGACCGTTCATTCAAAGTGATTGCGACTA
GTGATATATATGGTGACAAGTCATTGCCCACTGAAGTGTATGATTCAAAACTTGACAGAT
GGGCTGTCCACCAGATAATGCCTGCAGTTAATCTTTGCTCTTCAAAGATGGCGTATTGTG
ACTCCCGGTTGTATTTGGAAACTCTTTCGCCACTGGGTTTGATGATGTACAGGCTAGACA
CAGGTTACTGGGAACACATCCCGGCGAAGTTCCCCCGTTCCTTGTTAGACGGGTATTTGG
TTGCTGGTACACAGAAGCGTCTGTTTCTTGTTGGAAGGATTGGTCTCTATAGTACCCTCC
AGAGCATGAGAATTTGGGAATTGGATCATTCAAAGATTATGTGGGTGGAGATGAGTAGGA
TGCCGCCAAAATATTTTCGAGCTTTATTAAGGCTATCAGCTGAAAGATTTGAGTGCTTTG
GACAGGATAATTTAATCTGTTTTACATCNTGGAACCAAGGGAAGGGCCTTCTTTACGATG
TGGATAAGAAAGCTTGGTCTTGGATTGCTGGATGTGCTCTTCAGTCGTATAATAGCCAGG
TCTGCTTTTATGAGCCAAGATTTGATGCTTCCATCTATTGAGCTGGAAATTTTTAGCTTC
GGGGCTTAACATTTTATTTTCTATTGAGAGGTTTATGAGGGTATAATCTTCACTTTTAAC
CTCCTCTTTACTAATTNCGC

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

STS:

TAAAGAGGAGGTTAAAAGTGAAGATTATACCCTCATAAACCTCTCAATAGAAAATAAAAT
GTTAAGCCCCGAAGCTAAAAATTTCCAGCTCAATAGATGGAAGCATCAAATCTTGGCTCA
TAAAAGCAGACCTGGCTATTATACGACTGAAGAGCACATCCAGCAATCCAAGACCAAGCT
TTCTTATCCACATCGTAAAGAAGGCCCTTCCCTTGGTTCCACGATGTAAAACAGATTAAA
TTATCCTGTCCAAAGCACTCAAATCTTTCAGCTGATAGCCTTAATAAAGCTCGAAAATAC
TTTGGCGGCATCCTACTCATCTCCACCCACATAATCTTTGAATGATCCAATTCCCAAATT
CTCATGCTCTGGAGGGTACTATAGAGACCAATCCTTCCAACAAGAAACAGACGCTTCTGT
GTACCAGCAACCAAATACCCGTCTAACAAGGAACGGGGGAACTTCGCCGG

STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

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

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Target on C. clementina (v1.0)

Transcript ID: Ciclev10011780m
Scaffold: scaffold_6
Start: 24082263
End: 24084635

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00133:mRNA_13.1
Scaffold: C_unshiu_00133
Start: 63870
End: 65165
Gene function: Protein UNUSUAL FLORAL ORGANS

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 39.51

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 0.447

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: SI306
DNA sequence around SNP1:

ATTATCCTGTCCAAAGCACTCAAATCTTTCAGCTGATAGCCTTAATAAAGCTCGAAAATA
[T/C]TTTGGCGGCATCCTACTCATCTCCACCCACATAATCTTTGAATGATCCAATTCCC
AAATT

SNP2: SI366
DNA sequence around SNP2:

GAGGAGGTTAAAAGTGAAGATTATACCCTCATAAACCTCTCAATAGAAAATAAAATGTTA
[A/G]GCCCCGAAGCTAAAAATTTCCAGCTCAATAGATGGAAGCATCAAATCTTGGCTCA
TAAAA

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: