Citrus CAPS Marker Database

Locus name: Gn0040

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 600
Comment on PCR:
F-primer: AACTACGAAGACAAATCCGG
R-primer: TCGTTATATGCGGTGGATTTTG

EST info

EST Accession number 1: DC893194
EST Accession number 2: DC893195

sequence-tagged site (STS seq)

STS:
TTCTTCCCTATATTAAAGTACATTCATCCNACTGTACTTGGGAGGTCCCAATAGACAATA
TGTATAATCTCCAGGCACATTCTGGGTGAGGCCCTCAGCACTTTAAACTTTAAGGAGCTC
AAGAACCTTGAGGCAAGACTTGAGAAGGGAATCGGCAGAGTCAGATCCAAGAAGGTATTG
TNTGTGTGTGTGTGTGTGTGGGGCNTCGAGACATAT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GGNATGAACAATCACCAATATAATCGATCGNATATAAATTATGAAAACAACGTATGAATA
TGTATGTGTGTCGCTTGAATTTGATATTTTGGCACAGTTGAATTGCAGGATAGCTGCATC
TACCAGTGAGATATGCAAAAGCCTTTCTGCTACCTTGCATCTATCAGNTTGATGAGAGTA
TGGACGAAC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
GTTCGTCCATACTCTCATCAANCTGATAGATGCAAGGTAGCAGAAAGGCTTTTGCATATC
TCACTGGTAGATGCAGCTATCCTGCAATTCAACTGTGCCAAAATATCAAATTCAAGCGAC
ACACATACATATTCATACGTTGTTTTCATAATTTATATCCGATCGATTATATTGGTGATT
GTTCATNCCNCCC
STS source:
STS Forward / Reverse: Reverse read
STS:
GTTCGTCCATACTCTCATCAANCTGATAGATGCAAGGTAGCAGAAAGGCTTTTGCATATC
TCACTGGTAGATGCAGCTATCCTGCAATTCAACTGTGCCAAAATATCAAATTCAAGCGAC
ACACATACATATTCATACGTTGTTTTCATAATTTATATCCGATCGATTATATTGGTGATT
GTTCATNCCNCCC
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: 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: Ciclev10033176m
Scaffold: scaffold_4
Start: 16232756
End: 16233365

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00086:mRNA_13.2
Scaffold: C_unshiu_00086
Start: 99963
End: 109609
Gene function: AG MADS-box protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 43.542

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-07
KmMg cM: 56.094

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 48.672

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: SI015
DNA sequence around SNP1:
CTGGTAGATGCAGCTATCCTGCAATTCAACTGTGCCAAAATATCAAATTCAAGCGACACA
[A/C]ATACATATTCATACGTTGTTTTCATAATTTATAT
SNP2: SI337
DNA sequence around SNP2:
CTGGTAGATGCAGCTATCCTGCAATTCAACTGTGCCAAAATATCAAATTCAAGCGACACA
[A/C]ATACATATTCATACGTTGTTTTCATAATTTATAT
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: