Citrus CAPS Marker Database

Locus name: Tf0386

CAPS PCR info

PCR Anneal-Temp (℃) / Method: Td
Main product (bp): 550
Comment on PCR:
F-primer: GACAAGAAAATTACTATACGG
R-primer: GGAATCAACCATGAGTGACA

EST info

EST Accession number 1: CD573987
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
TATCTCATTGATTCAGATAATTATATTAAGACAGCTACAATACAAGTAGTAGTACTTTAG
TAATAAACAGTAGACCTCTAATCTTGAGAGCTATTCTTCGACTCATCGATGGATTTAGAA
TGAAGGAACAATGCCATATCCAGGATCAGTCATCAATGTTGCGGAGAACATTTGATCAAC
TTCAACTTCAGCATCGGTTCTCTTAGCGAACCTGCCCTTGATACGTGGTCTAGTTTCCGC
ATAGGCCTTCCTTGAGGCATACCGGATTGTCTTCTCGAATTTTCTTGTCTTCTTTTTTTC
CCTGTATCTCAAGACTCTGGCCTCCCTGTCCATGGGAGTAAGCTGGGGTGGCATTTGAAT
TGGAGGTCCTGAGAAGAGGTCAATGGTCCCTTTCGGTGGCCTCGAGTGTGAAATCGAT
STS source: Clementine haploid
STS Forward / Reverse: Combined sequence of both reads
STS:
GCGAACCTGCCCTTGATACGTGGTCTAGTTTCCGCATAGGCCTTCCTTGAGGCATACCGG
ATTGTCTTCTCGAATTTTCTTGTCTTCTTTTTTTCCCTGTATCTCAAGACTCTGGCCTCC
CTGTCCATGGGAGTAAGCTGGGGTGGCATTTGAATTGGAGGTCCTGAGAAGAGGTCAATG
GTCCCTTTCGGTGGCCTCG
STS source:
STS Forward / Reverse: Foward read
STS:
GCAAAAGAAATATCTCATTGATTCAGATAATTATATTAAGACAGCTACAATACAAGTAGT
AGTACTTTAGTAATAAACAGTAGACCTCTAATCTTGAGAGCTATTCTTCGACTCATCGAT
GGATTTAGAATGAAGGAACAATGCCATATCCAGGATCAGTCATCAATGTTGCGGAGAACA
TTTGATCAACTTCAACTTCAGCATCGGTTCTCTTAGCGAACCTGCCCCTGATACGTGGTC
TAGTTTCCGCATAGGCC
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:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Msp1
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: Msp1
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
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: Msp1
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: Sty1
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: Ciclev10012022m
Scaffold: scaffold_6
Start: 23593516
End: 23595492

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00098:mRNA_56.1
Scaffold: C_unshiu_00098
Start: 370300
End: 372260
Gene function: COL1 protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 41.367

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: M,T

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

SNP1: SI044
DNA sequence around SNP1:
ATCAGTCATCAATGTTGCGGAGAACATTTGATCAACTTCAACTTCAGCATCGGTTCTCTT
[A/C]GCGAACCTGCCCCTGATACGTGGTCTAGTTTCCGCATAGGCC
SNP2: SI095
DNA sequence around SNP2:
GCGAACCTGCCCTTGATACGTGGTCTAGTTTCCGCATAGGCCTTCCTTGAGGCATACC[T
/G]GATTGTCTTCTCGAATTTTCTTGTCTTCTTTTTTTCCCTGTATCTCAAGACTCTGGC
CTC
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: