Citrus CAPS Marker Database

Locus name: Gn0043

CAPS PCR info

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

EST info

EST Accession number 1: DC893225
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

GTTCCGAGGGTGGCCATGGCCATATGTCCGTCAGGATTGAGCCCAACTTTGGGACCAAAG
CTTTCGCCGGGCTCTCCAGAAGCGCTTACACTAGCTCACTGGATCTGCCAGAGCTATAGG
TAAGTTCTGAATCAATCCCCCCACCCCAATTTCATGATAAATATTCAATGAATTAGATGC
ATGTAGTTGNCTTCCATAGTCTGGACAAGGTCAATTTCAGTCGCAAAAGAGAGTTNAAAA
TGTAATATTGAGTTCATAATCTTGATTAGACATGGTCAAGCTATCTTCTGTCACACCATA
ACAAGAAACTTTCAAGTGAAATATCATATAACAGTTCTTACTGATTTGTTTTCAATTGGA
CTATTTTCTATCAAATCCAAACTGATAAGCTGTNANTTGAAACGTGTTCTTGTTGATTTA
ATGAACCAGCTCGATTAGCANTTTTGTGTGAGTTGCTAATATTTCCTTTTTCATCTTTTG
CAGTTATCATTTGGGGGCAGAATTGTTGAGATCTGATTCTGTTGGTGGTGACTCAGTGTT
GAAAAATCTTTGGCNAGCATTCAGATGCTATATTGTGNTGTTCATTAAAGGTACCTTTAC
AGNTTCATCAAAGATAACGATATATCACGTATTAAA

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

STS:

TCAGGATTGAGCCCAACTTTGGGACCAAAGCTTTCGCCGGGCTCTCCAGAAGCGCTTACA
CTAGCTCACTGGATCTGCCAGAGCTATAGGTAAGTTCTGAATCAATCCCCCCACCCCAAT
TTCATGATAAATATTCAATGAATTAGATGCATGTAGTTGGCTTCCATAGTCTGGACAAGG
TCAATTTCAGTCGCAAAAGAGAGTTTAAAATGTAATATTGAGTTCATAATCTTGATTAGA
CATGGTCAAGCTATCTTCTGTCACACCATAACAAGAAACTTTCAAGTGAAATATCATATA
ACAGTTCTTACTGATTTGTTTTCAATTGGACTATTTTCTATCAAATCCAAACTGATAAGC
TG

STS source:
STS Forward / Reverse: Foward read

STS:

TGTAAGTTACCTGTTGCATCAACTTGGCAAAATCAGCACACAATGCCTTGCGCCCAGATT
CATCGAAGATCTTATCCAGTGTGATATCTTGTAGAGCCACTAGAGTTGTCTCCAGCATGT
CAAGGCCAGCTTGGTTTGCAAAGATGAAAACAGGCATTGACTGCAGCATCAACGAAGATG

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

STS:

CTTTCGCCGG GCTCTCCAGA AGCGCTTACA CTAGCTCACT GGATCTGCCA GAGCT
ATAGG TAAGTTCTGA ATCAATCCCC CCACCCCAAT TTCATGATAA ATATTCAATG
AATTAGATGC ATGTAGTTGG CTTCCATAGT CTGGACAAGG TCAATTTCAG TCGC
AAAAGA GAGTTNAAAA TGTAATATTG AGTTCATAAT CTTGATTAGA CATGGTCAA
G CTATCTTCT

STS source:
STS Forward / Reverse:

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: Hinc2
Rank as CAPS marker: Disagree by Marco analysis
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: Ciclev10027790m
Scaffold: scaffold_8
Start: 21953129
End: 21960709

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_02574:mRNA_1.1
Scaffold: C_unshiu_02574
Start:
End: 2470
Gene function: Class III homeodomain leucine zipper protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 30.721

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-08
KmMg cM: 27.458

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: K

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

SNP1: SI323
DNA sequence around SNP1:

AATCAATCCCCCCACCCCAATTTCATGATAAATATTCAATGAATTAGATGCATGTAGTTG
[A/G]CTTCCATAGTCTGGACAAGGTCAATTTCAGTCGCAAAAGAGAGTT

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: