Citrus CAPS Marker Database

Locus name: Vs0005

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 400
Comment on PCR:
F-primer: ATAGGACCCTTCGTGAAA
R-primer: AAATAATAACACAGAGAG

EST info

EST Accession number 1: C21850
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GANAATGGGAGACAAAGACTATTTCCTCAAATTTCCAGGGATTGAGGACTACATAAGAAG
CGGCAAAGCAAAAGACCTTGTGCCCAATTTGGAGATCATACATTTGCCTGAAGGGAGCCA
TTTTGTTCAAGAGCAATCACCAGAAGAAGTGAACCAGCTAATCCTCACCTTTCTCAACAA
ACATGTTTGATTGCCAGCCAAGGCTTTCTTGCTGTATGTCTTAAGGGTTTGCTGGAGATT
ATGCGAGTCCTCTAGAATTATGTCTAGTCTATGTTGCTTGAACAATCGCTCTCTGTGTTA
TTATTTA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TGGGAGACAAAGACTATTTCCTCAAATTTCCAGGGATTGAGGACTACATAAGAAGCGGCA
AAGCAAAAGACCTTGTGCCCAATTTGGAGATCATACATTTGCCTGAAGGGAGCCATTTTG
TTCAAGAGCAATCACCAGAAGAAGTGAACCAGCTAATCCTCACCTTTCTCAACAAACATG
TTTGATTGCCAGCCAAGGCTTTCTTGCTGTATGTCTTAAGGGTTTGCTGGAGATTATGCG
AGTCCTCTAGAATTATGTCTAGTCTATGTTGCTTG
STS source:
STS Forward / Reverse: Foward read
STS:
CTTGGCTGGCAATCAAACATGTTTGTTGAGAAAGGTGAGGATTAGCTGGTTCACTTCTTC
TGGTGATTGCTCTTGAACAAAATGGCTCCCTTCAGGCAAATGTATGATCTCCAAATTGGG
CACAAGGTCTTTTGCTTTGCCGCTTCTTATGTAGTCCTCAATCCCTGGAAATTTGAGGAA
ATAGTCTTTGTCTCCCATTATCAGTAATGCTGGAACTTTAACTGCTGTCACTTCTGGTGT
GCTGAAGTTTTCA
STS source: Okitsu 46
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): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Xba1
Rank as CAPS marker: Others
Comment:
Figure legend: DNA sample: Lane 2'=Ethlog citron, 23'=Duncan GF, Hrd=Hirado buntan, HgNt = Hyuuganatsu
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:
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: NC
Comment:
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: Sty1
Comment:
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: Xba1
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: Jutaro unshu x Trovita orange
Restriction enzyme: Xba1
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: Xba1
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: Kiyomi x Okitsu41gou
Restriction enzyme: Xba1
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: Ciclev10016009m
Scaffold: scaffold_2
Start: 33216839
End: 33219042

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00002:mRNA_211.1
Scaffold: C_unshiu_00002
Start: 1511809
End: 1513915
Gene function: Epoxide hydrolase 2

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 31.521

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-02
KmMg cM: 59.329

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
JtTr cM: 50

Km/O41 map info (Nakano et al. 2003)

Km/O41 LG: NAT-06S
Km/O41 cM: 50

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: SI022
DNA sequence around SNP1:
TTGAACAAAATGGCTCCCTTCAGGCAAATGTATGATCTCCAAATTGGGCACAAGGTCTTT
[T/C]GCTTTGCCGCTTCTTATGTAGTCCTCAATCCCTGGAAATTTGAGGAAATAGTCTT
TGTC
SNP2: SI075
DNA sequence around SNP2:
AGACAAAGACTATTTCCTCAAATTTCCAGGGATTGAGGACTACATAAGAAGCGGCAAAGC
[A/G]AAAGACCTTGTGCCCAATTTGGAGATCATACATTTGCCTGAAGGGAGCCATTTTG
TTCAA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: