Citrus CAPS Marker Database

Locus name: Ov0117

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1000
Comment on PCR:
F-primer: AGCGAGGGGGATAGCAATACA
R-primer: GACTGACATCCCAAACAGCCA

EST info

EST Accession number 1: AU186413
EST Accession number 2: DC893837

sequence-tagged site (STS seq)

STS:
ACTTCCATCAGATAGCATGGGAAGTAATTTCTCAGGAAATCTGCCTGAAAAAACGGCTCA
AAATCCGGATAAGGGAATACCAACTGCGAGTGTTGGTTCTCAACATCAAGGCATCTTTCC
ACCACTTCATAGCCAGAATGTGCAAATTCCAGCATTTCAACCTCCTTCAGCAATGGGTTA
CTACCATCAAAATCCAGTTTCGTGGCCAGCTGCTCCGGCAAATGGATTGATGCCTTTCAC
CCATCCCAATCAGTATCTATATACTGGCCCTCTTGGTTATGGATTAAATGGAAACTCTCG
CTTGTGCATGCAGTATGGAGGAGCACTTCAGCATGTTGCTACTCCCGTTTTTAATCCTAG
CCCGGTGCCGGTTTATCAGTCTATTGCCAAAGCCAACAGCATGGAGAAGCGACCTCACGA
TGGTAAGCCAGGTGCACCGCAAGAAGCATTTAACGATACAAATGCAGAGAGGGCTGCTCT
GGCCCGGTCACATCTAACTGATGCATTGGCTAAAGGAGAAGGTGGACACCAGAATAATGA
TGGCTTTTCCTTGNTTCATTTTGGNGGACCTGTCGGTCTTTCACGGGCTGTAAGTAAATC
CTATGCCTTCAAAGATGAG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TGCATGCACAAGCGAGAGTTTCCATTTAATCCATAACCAAGAGGGCCAGTATATAGATAC
TGATTGGGATGGGTGAAAGGCACCAATCCATTTGCCGGAGCAGCTGGCCACGAAACTGGA
TTTTGATGGTAGTAACCCATTGCTGAAGGAGGTTGAAATGCTGGAATTTGCACATTCTGG
CTATGAAGTGGTGGAAAGATGCTTTGATGTTGAGAACTAACGCTCACAGTTGGTATTCCC
TTATCCGGATTTTGAGCCGTTTTTTCAGGCAGATTTCCTGAGAAATTACTTCCCATGCTA
TCTGATGGAAGTCCAACAAAAGCTCTTCTTCCCAAAGTCTCTCCTCCATCTGTAATCAGT
TTTTTCCCCATTCCAACTTCTTGAAATTCAGAGAAGCCATTTTGAGTGCATGCTGAAGTA
TCTCTTCCT
STS source:
STS Forward / Reverse: Foward read
STS:
AAAACTGATTACAGATGNGGAGAGACTTNGGAAGAGAGCTTTTGTTGACTTCCATCAGAT
AGCATGGGAAGTAATTTCTCAGGAAATCTGCCTGAAAAAACGGCTCAAAATCCGGATAAG
GGAATACCAACTGCGAGTGTTGGTTCTCAACATCAAGGCATCTTTCCACCACTTCATAGC
CAGAATGTGCAAATTCCAGCATTTCAACCTCCTTCAGCAATGGGTTACTACCATCAAAAT
CCAGTTTCGTGGCCAGCTGCTCCGGCAAATGGATTGATGCCTTTCACCCATCCCAATCAG
TATCTATATACTGGCCCTCTTGGTTATGGATTAAATGGAAACTCTCGCTTGTGCATGCAG
TATGGAGGAGCACTTCAGCATGTTGCTACTCCCGTTTTTAATCCTAGCCCGGTGCCGGTT
TATCAGTCTATTGCCAAAGCCAACAGCATGGAGAAGCGACCTCACGATGGTAAGCCAGGT
GCACCGCAAGAAGCATTTAACGATACAAATGCAGAGAGGGCTGCTCTGGCCCGGTCACAT
CTAACTGATGCATTGGCTAAAGGAGAAGGTGGACACCAGAATAATGATGGCTTTTCCTTG
TTTCATTTTGGTGGACCTGTCGGTCTTTCAACGGGCTGTAAAGTAAATCCTATGCCTTCA
AAAGATGAGATTGTTGGGAATTTTTCTTCTCAATTTTCAGCAGATCATGTCGAGAATGAT
CATGCTTGCAATAAGAAAGAGACCACAATTGAACAGTACAACTTGTTTGCTGCAAGTAAT
GGTAACGGCATACGGTGAC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CTTATTGCAAGCATGATCATTCTCGACATGATCTGCTGAAAATTGAGAAGAAAAATTCCC
AACAATCTCATCTTTTGAAGGCATAGGATTTACTTTACAGCCCGTTGAAAGACCGACAGG
TCCACCAAAATGAAACAAGGAAAAGCCATCATTATTCTGGTGTCCACCTTCTCCTTTAGC
CAATGCATCAGTTAGATGTGACCGGGCCAGAGCAGCCCTCTCTGCATTTGTATCGTTAAA
TGCTTCTTGCGGTGCACCTGGCTTACCATCGTGAGGTCGCTTCTCCATGCTGTTGGCTTT
GGCAATAGACTGATAAACCGGCACCGGGCTAGGATT
STS source:
STS Forward / Reverse: Reverse read
STS:
GATTACAGAT GGAGGAGAGA CTTTGGGAAG ANGAGCTTTT GTTGGACTTC CATCA
GATAG CATGGGAAGT AATTTCTCAG GAAATCTGCC TGAAAAAACG GCTCAAAATC
CGGATAAGGG AATACCAACT GCGAGTGTTG GTTCTCAACA TCAAGGCATC TTTC
CACCAC TTCATAGCCA GAATGTGCAA ATTCCAGCAT TTCAACCTCC TTCAGCAAT
G GGTTACTACC ATCAAAATCC AGTTTCGTGG CCAGCTGCTC CGGCAAATGG ATT
GATGCCT TTCACCCATC CCAATCAGTA
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Dra1
Rank as CAPS marker: Available marker
Comment:
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: Dra1
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

Experiments: Segregation pattern

Population name: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Dra1
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: Dra1
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: Dra1
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: Ciclev10010926m
Scaffold: scaffold_6
Start: 19105139
End: 19113780

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00089:mRNA_17.1
Scaffold: C_unshiu_00089
Start: 153791
End: 161685
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 66.455

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-04
Rp/Sa cM: 28.16

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: SI040
DNA sequence around SNP1:
GACCGACAGGTCCACCAAAATGAAACAAGGAAAAGCCATCATTATTCTGGTGTCCACCTT
[T/C]TCCTTTAGCCAATGCATCAGTTAGATGTGACCGGGCC
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: