Citrus CAPS Marker Database

Locus name: Gn0048

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 600
Comment on PCR:
F-primer: ATGGAACAAGTGAAGACCCT
R-primer: ACACTTAGCTTATTTGGAGTCG

EST info

EST Accession number 1: DC895343
EST Accession number 2: DC895344

sequence-tagged site (STS seq)

STS:

GNNANGCCANGATGGAAGACCAAGCAGCTTGAGAAAGACTATGATCTTCTCAAGAGACAA
TATGAAGCAGTCAAAGCCGANCGCGAAGCACTCCAAGCTCAAAATCAGAAGCTTCATGCA
GAGGTTTGTCTTGAATTCCANTGATTTATTTTTGAAATATTACTAGCTTGTTAGTTTGTG
GGGTGCAGAGTGATGAATTATTGTATGTTCTTCTAATAATTATATGCACGTTTTTCCATT
GAATCTGTAGAATAAAGTTGGAAATCATGTCCTTTTTTTAATGGTTTCATAATTTTTGAC
CTTTTCATGTATCATGATTTTCAGAACCTTTTAATAACCAGTGGAGGCTTTTTCATAAAG
CTTTCTTTTCTCCATCATCATTTCTTTAGCTTTTTGATATATTTATTGGGTAACTGTTTA
AAGGTAAATTACGGGTAATCATGGCTAAAACTTTTCTCTTGCATAATTGTCATAGTTTAA
ATTTCTTATATATTTTGTCTATTGGGAAAATTAGAATTATCTCTGGTGACACACACTTTG
AATGGTTAATTTTATGTTGGCAGATAATGGCTCTGAAAAGCAGGGGAGGTGACTGAATCT
ATAAACCTCAATAAGAAACTGAGGGGTCTTGCAGCAATAGAAGTGANACAGTTCTGATAT
CNAGTTGGATATTTCAAGGACACAGCCATTGACAGCCCTATGTCTACCATCCACAAGCAG
AACTGTTCCACAAATCACT

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

STS:

GAGAAAGACTATGATCTTCTCAAGAGACAATATGAAGCAGTCAAAGCCGATCGCGAAGCA
CTCCAAGCTCAAAATCAGAAGCTTCATGCAGAGGTTTGTCTTGAATTCCATTGATTTATT
TTTGAAATATTACTAGCTTGTTAGTTTGTGGGGTGCAGAGTGATGAATTATTGTATGTTC
TTCTAATAATTATATGCACGTTTTTCCATTGAATCTGTAGAATAAAGTTGG

STS source:
STS Forward / Reverse: Foward read

STS:

GAAATCATGTCCTTTTTTTAATGGTTTCATAATTTTTGACCTTTTCATGTATCATGATTT
TCAGAACCTTTTAATAACCAGTGGAGGCTTTTTCATAAAGCTTTCTTTTCTCCATCATCA
TTTCTTTAGCTTTTTGATATATTTATTGGGTAACTGTTTAAAGGTAAATTACGGGTAATC
ATGGCTAAAACTTTTCTCTTGCATAATTGTCATAGTTTAAATTTCTTATATATTTTGTCT
ATTGGGAAAATTAGAATTNTCTCTGGTGACACACACTTTGAATGGTTAATTTTATGTTGG
CAGATAATGGCTCTGAAAAGCAGGGAGGTGACTGAATCTATAAACCTCAATAAAGAAACT
GAGGGGTCTTGCAGCAATAGAAGTGAGAACAGTTCTGATATCAAGTTGGATATTTCAAGG
ACACCAGCCATTGACAGCCCTATGTCTACTCATCCAACAAGCAGAAACTTGTTTCCAACA
AAATCAACATCGTCGGTAAGGCCAACAGTAGCAGCACAACTTTTCCATAACTCATCATCG
TCAAGGCCTGATCTTCAATGCCAGAAGATTGAACAGAATATGCAGGGTACTAAAGATCAA
GAAAGCCTAGCAGC

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

STS:

TGCATATTCTGTTCAATCTTCTGGCATTGAAGATCAGGCCTTGACGATGATGAGTTATGG
AAAAGTTGTGCTGCTACTGTTGGCCTTACCGACGATGTTGATTTTGTTGGAAACAAGTTT
CTGCTTGTTGGATGAGTAGACATAGGGCTGTCAATGGCTGGTGTCCTTGAAATATCCAAC
TTGATATCAGAACTGTTCTCACTTCTATTGCTGCAAGACCCCTCAGTTTCTTTATTGAGG
TTTATAGATTCAGTCACCTCCCTGCTTTTCAGAGCCATTATCTGCCAACATAAAATTAAC
CATTCAAAGTGTGTGTCACCAGAGAAAATTCTAATTTTCCCAATAGACAAAATATATAAG
AAATTTAAACTATGACAATTATGCAAGAGAAAAGTTTTAGCCATGATTACCCGTAATTTA
CCTTTAAACAGTTACCCAAT

STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Pvu2
Rank as CAPS marker: Available marker
Comment: PCR_condition: 54C 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10032275m
Scaffold: scaffold_4
Start: 23695766
End: 23697703

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00001:mRNA_105.2
Scaffold: C_unshiu_00001
Start: 685451
End: 687250
Gene function: Homeobox-leucine zipper protein HAT7

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 74.225

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-07
KmMg cM: 7.964

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 4.2

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: M

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

SNP1: SI289
DNA sequence around SNP1:

GAGAAAGACTATGATCTTCTCAAGAGACAATATGAAGCAGTCAAAGCCGA[T/C]CGCGA
AGCACTCCAAGCTCAAAATCAGAAGCTTCATGCAGAGGTTTGTCTTGAATTCCA

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: