Citrus CAPS Marker Database

Locus name: Tf0376

CAPS PCR info

PCR Anneal-Temp (℃) / Method: Td
Main product (bp): 600
Comment on PCR:
F-primer: TGGATTGCATTTCGAGTCAAG
R-primer: GTGAAAGAAGCAAACCCTC

EST info

EST Accession number 1: DC898619
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
AATGGGTATGCGAGCTGCGCGAACCCAACAAGAAATCACGCATTTGGCTAGGTACTTATC
CTACGCCAGAAATGGCTGCGAGGGCACATGATGTGGCAGCATTAGCCCTGAGAGGGAAAT
CCACGTGCCTGAATTTCGCTGACTCGGCATGGAGGTTGCCGGTGCCGGCTTCGGCGGATG
CTGATGATGTAAGAAAGGCTGCAGCTGAGGCAGCAGAAGCATTCAGGCTGTCCCATGATG
ATGAAGATCAATTTGAAGAAAATGGTTTGTTGCCGGAGAAAAATGTGTTTTACATGGATG
AAGAGGCGGTTTTTGATATGCCGGGACTGCTTGTGAACATG
STS source: Clementine haploid
STS Forward / Reverse: Combined sequence of both reads
STS:
CAGAATGAGAAACAATAACAAATGGGTATGCGAGCTGCGTGAACCCAACAAGAAATCACG
CATTTGGCTAGGTACTTATCCTACGCCAGAAATGGCTGCGAGGGCACATGATGTGGCAGC
ATTAGCCCTGAGAGGGAAATCCACGTGCCTGAATTTCGCTGACTCGGCATGGAGGTTGCC
GGTGCCGGCTTCCGCGGATGCTGATGATGTAAGAAAGGCTGCAGCTGAGGCAGCAGAAGC
ATTCAGGCTGTCCCATGATGATGAAGATCAATTTGAAGAAAATGGTTTGTTGCCGGAGAA
AAATGTGTTTTACATGGATGAAGAGGCGGTTTTTGATATGCCGGGACTGCTTGTGAACAT
G
STS source:
STS Forward / Reverse: Foward read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hha1
Rank as CAPS marker: Available marker
Comment: DNA sample: New CCN
Figure legend: DNA sample: Lane 9 (Mato) not analyzed.
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: Hha1
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: Hae3
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: Hha1
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: Ciclev10022680m
Scaffold: scaffold_3
Start: 8528292
End: 8529236

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00154:mRNA_1.1
Scaffold: C_unshiu_00154
Start: 9832
End: 10761
Gene function: CRT binding factor 3

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 41.853

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: Hb, Cc

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: SI072
DNA sequence around SNP1:
TGAGGCAGCAGAAGCATTCAGGCTGTCCCATGATGATGAAGATCAATTTGAAGAAAATGG
[T/G]TTGTTGCCGGAGAAAAATGTGTTTTACATGGATGAAGAGGCGGTTTTTGATATGC
C
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: