Citrus CAPS Marker Database

Locus name: Tf0088

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 64
Main product (bp): 1000
Comment on PCR: Additional band
F-primer: ACAGAGGCAACAAAGCGACAC
R-primer: GGGCTTGCTCCGTGATG

EST info

EST Accession number 1: CD573726
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

CCCACATGCAAAAAACACCCACAGGTACGTCATCTACCCTTTGCACTTTGCAAGAGGCCG
ATTCTAGCTACTATTTATAATAATTTAATCTCCTTTTGAATCAAATAGCAACATTTAATT
AAATCGATCTAATTTTTTGCCTTTAATTTGAAGATTGCAATAAGCTTCAGTACAGACTAT
AGTCAATTTGATTTCATGCAAATAGC

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: Hind3
Rank as CAPS marker: Disagree by Marco analysis
Comment: DNA sample: New CCN
Figure legend: DNA sample: Lane 9 (Mato), 17 (Encore) and 25 (Mineola) 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: Hind3
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: Kiyomi x Miyagawa-wase
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

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hind3
Comment:
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10001291m
Scaffold: scaffold_5
Start: 41275201
End: 41278829

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00127:mRNA_34.1
Scaffold: C_unshiu_00127
Start: 251592
End: 254627
Gene function: Basic helix-loop-helix DNA-binding superfamily protein, putative isoform 1

AGI map info (Shimada et al. 2014)

AGI LG: AGI-09
AGI cM: 35.763

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

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: SI066
DNA sequence around SNP1:

CCCACATGCAAAAAACACCCACAGGTACGTCATCTACCCTTTGC[A/G]CTTTGCAAGAG
GCCGATTCTAGCTACTATTTATAATAATTTAATCTCCTTTTGAATCAAA

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: