Citrus CAPS Marker Database

Locus name: Tf0067

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 64
Main product (bp): 2000
Comment on PCR:
F-primer: GCAGCAACAACGGGCACAACT
R-primer: GGAGCGCCTCTTTCTTCGAGT

EST info

EST Accession number 1: CB291001
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GGGGCGGCGGCTCGTCGCCGGGCGTGGGCGGCCTGAAGTTGTTTGGCGTCCGGCTTACGG
ATGGCTCGATAATCAAGAAGAGCGCGAGCATGGGGAACTTATCGGCGCTGCACTACCATA
GCTCCTCGTCGGCAGCCGCTTCGCCGAATCCTGACTCCCCGTTATCGGATCACGTGCGTG
ACCCGAATCACTTGACCGACGGTTACTTGTCGGATGACCCGGCGCACGGGTCTGGTTCAT
CGAATCGGCGTTGCGAGAGAAAGAAAGGTGAGCACTTTTTTCCATTTATTTTTCTGAAAT
GAATGGAATGGCAGTTTCGTAATTTCGGAGGTCCTGTTTGGTTGTTTTGGGTTTCAAATT
TGATTTTTTTGAGGTTTTTGTTTGTTAATGATGATGTTATGTCTTGGTAAATCTTCTTTC
TTTTTTATTTTAAATGTTATGTTTTATTTTTATTTTATACGTTTGAGCTAATTTCTTGGA
ATAAGTTTGATTTTCATTTTGTGAATTAATTGAATTTTGTTGACGAAGATTAATCTTGTT
ATTCAACATATCAGCTACATGTTTTGTATTATTTATTTACTTTTAGAAGAATCGCTCTTA
CTATCTTTGTTGTTATAATTCTCTGCAATCTCTGGTTTATTTCCAAAGTTGCTTACTATT
TTTT
STS source:
STS Forward / Reverse: Foward read
STS:
CTGCCTGCACATGGATGTTAACAAGAGGCAAATTGGTTAGCTTTTGAAAGTTTTCATTGT
CATTCAATGCAATATTTGCTTTCAATTAGGCAACTAGCAACAATTAGTTTATTCAATCTA
GCATCACAAGTTCACAACATCTTTGCCATTTGTTTTGATCAACAGAGCTGTAGTTGACAA
GTACCTCATGAATTTGGTTGATTGCTAATTTCATCAGAAATCGGTTGCTGATCTTGTGGT
TTATGACAAAAAAGGGAGAATATGTTGCTTCATTTTTTTTCCCTTTTCTTTTCTAACTGA
ATTACTTTGTTTATCTAGTTTCACTTCATTGTTATGTAAATTGTGTTTAATGCATGATAC
CTTCACTGTATAACCAGGGCAACAACCCTGTATGTTGAATTACTCTCGATTTATCCATCT
CACTAATTTATAGTTCATGAAGCATGACTAAGATTTTGTATCTGTAGCAATTTGAGATTT
ATTTTATGCAAACCGGCTTTGTCTTACAGGTGTCCCATGGACAGAAGAGGAGCATCGCCT
GTTTCTAATTGGCCTTCAGAAATTAGGGAAGGGAGACTGGCGTGGTATAGCACGAAATTA
TGTCATGTCCAGGACTCCAACCCAGGTGG-CAAGTCATGCACAGAAGTATTTTATCCGG
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: Rsa1
Rank as CAPS marker: Others
Comment: DNA sample: New CCN
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

Rsetriction enzyme: Rsa1
Comment: DNA sample: New CCN
Figure legend:
CV (No.1 Top) 101 Tahiti, 100 Rangpurlime, 102 Limonia, 104 LisbonL, 99 SweetLime, 92 Hirado, 87 MGF, 85 Kinukawa, 84 Hassaku, 83 Yamamikan, 78 Natsudaidai, 58 Rokugatu, Tr Trovita, 50 WNV, 44 Tankan, 42 Iyo,
(No.1 Bottom) 39 HgNt, 36 Ujukitsu, 32 Kawabata, 30 Shunkokan, 70 Yuzu, 54 Henka, 53 Ichang lemon, 37 Kunenbo, Mg Miyagawa, 31 Yatsushiro, 27 Kabuchii, 26 Ponkan, 25 Medet. 22. Dancy, 14 Tachibana, 11 Hirakishu (26' Ohta ponkan)
(No.2 Top) 6 Cleopatra, 4 CQ, 2 Fukuremikan, FD Hiryuu, 124 Largeleaf, 125 Small leaf, 141 CTV-S, 136 Rubidoaux,
(No.2 Bottom) FD, Hassaku, Km, F1, RP94, SA, 02, 04, 05, 06, 07, 08, 09, 10, 11, 13
BDZ BenDi Zao, SO Shuto, BP Banpeiyu

Experiments: Segregation pattern

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: EcoR1
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
Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Rsa1
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: Ciclev10025950m
Scaffold: scaffold_7
Start: 8438702
End: 8442381

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00290:mRNA_9.1
Scaffold: C_unshiu_00290
Start: 74194
End: 77624
Gene function: Transcription factor

AGI map info (Shimada et al. 2014)

AGI LG: AGI-02
AGI cM: 5.104

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:

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: SI033
DNA sequence around SNP1:
GAAATGAATGGAATGGCAGTTTCGTAATTTCGGAGGTCCTGTTTGGTTGTTTTGGGTTTC
[A/C]AATTTGATTTTTTTGAGGTTTTTGTTTGTTAATGATGATGTTATGTCTTGGTAAA
TCTTC
SNP2: SI187
DNA sequence around SNP2:
TTGTTATGTAAATTGTGTTTAATGCATGATACCTTCACTGTATAACCAGGGCAACAACCC
[T/C]GTATGTTGAATTACTCTCGATTTATCCATCTCACTAATTTAT
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: