Citrus CAPS Marker Database

Locus name: Ov0503

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 64
Main product (bp): 1600
Comment on PCR:
F-primer: GCCATTCCGTGCTCTCCT
R-primer: CTGCAAAATTGCCAAAACAGA

EST info

EST Accession number 1: DC894035
EST Accession number 2: DC894036

sequence-tagged site (STS seq)

STS:
TATATATATATGATGACATTGTTTGCTTTTTTTATGCATGCTTTACTCCTTTATAGATAT
ATACATAAATATGAACATTTCCAAATGCATTTGCCTTTTTATGCGGGATTTATATCCCCA
TCCCTCGATGACTTTTTACAGTCATAGTTGTGAGAATGCCTTGGGAATGTTGTTTGCATT
GCATTATTGACCAGCCAAAGAAATGTGAAGAATTGAACTAATTTTTTGTAATGTATAGAG
TGAATAAAATCGAGTACCTAACCTCCTCTTAGGAATGTAGAGAATTGAACTAATTTTTCT
GTAATGTACAGAGTGAATAAAATGAGTACCCATTCCAGTATCCAACCTCATCTTTTGTAC
ATGTTTTCAGTTGAAGTTATTGATGTTTTCTTTGAGATTGAATGGAACTTATTTTTTGAC
TAGATGGGTTAGTCTATGTCACTTGTTAAGGGGAAATTTGGAAATGCTAATGATTTTTTT
ATTTCAAGCTGTCTTTGTCTTTCCTTGATGTTAATGTAGTTATTTATGTTTGCATCTCAG
GTATAATTTGAAGAAGCTTACTTACGAGGAAAGGAAGGCGAAGCTGGTTGAAAGGCTGAA
TGCCCTTAACTCGGCAGTTGATGAGGAGGACGAATGAAAGCATCATAACTAGATATGAAT
TCAAAATATGTGGCAAATCTGCAGTACACATTTGTTGTTGCAGTTGCTAGAACCTAAAAT
GTTTCTTTGCCCAGNTTTTATTTTATTTTATTTTATCACTCGGGG
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
GAGGTAAAAAAATATATATATATATATGATGCCATNGTTGCTTTTTTATGCATGCTTTAC
TCCTTTATAGATATATACATAAATATGAACATTTCCAAATGCATTTGCCTTTTTATGCGG
GATTTATATCCCCATCCCTCGATGACTTTTTACAGTCATAGTTGTGAGAATGCCTTGGGA
ATGTTGTTTGCATTGCATTATTGACCAGCCAAAGAAATGTGAAGAATTGAACTAATTTTT
TGTAATGTATAGAGTGAATAAAATCGAGTACCTAACCTCCTCTTAGGAATGTAGAGAATT
GAACTAATTTTTCTGTAATGTACAGAGTGAATAAAATGAGTACCCATTCCAGTATCCAAC
CTCATCTTTTGTACATGTTTTCAGTTGAAGTTATTGATGTTTTCTTTGAGATTGAATGGA
ACTTATTTTTTGACTAGATGGGTTAGTCTATGTCACTTGTTAAGGGGAAATTTGGAAATG
CTAATGATTTTTTTATTTCAAGCTGTCTTTGTCTTTCCTTGATGTTAATGTAGTTATTTA
TGTTTGCATCTCAGGTATAATTTGAAGAAGCTTACTTACGAGGAAAGGAAGGCGAAGCTG
GTTGAAAGGCTGAATGCCCTTAACTCGGCAGTTGATGAGGAGGACGAATGAAAGCATCAT
AACTAGATATGAATTCAAAATATGTGGCAAATCTGCAGTACACATTTGTTGTTGCAGTTG
CTAGAACCTAAAA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
TTCATATCTAGTTATGATGCTTTCATTCGTCCTCCTCATCAACTGCCGAGTTAAGGGCAT
TCAGCCTTTCAACCAGCTTCGCCTTCCTTTCCTCGTAAGTAAGCTTCTTCAAATTATACC
TGAGATGCAAACATAAATAACTACATTAACATCAAGGAAAGACAAAGACAGCTTGAAATA
AAAAAATCATTAGCATTTCCAAATTTCCCCTTAACAAGTGACATAGACTAACCCATCTAG
TCAAAAAATAAGTTCCATTCAATCTCAAAGAAAACATCAATAACTTCAACTGAAAACATG
TACAAAAGATGAGGTTGGATACTGGAATGGGTACTCATTTTATTCACTCTGTACATTACA
GAAAAATTAGTTCAATTCTCTACATTCCTAAGAGGAGGTTAGGTACTCGATTTTATTCAC
TCTATACATTACAAAAAATTAGTTCAATTCTTCACATTTCTTTGGCTGGTCAATAATGCA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read

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: Hae3
Rank as CAPS marker: Available marker
Comment: PCR_condition: 60C aneal
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: Nde2
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: 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: Jutaro unshu x Trovita orange
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: Kiyomi x Miyagawa-wase
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: Kiyomi x Okitsu41gou
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
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: Ciclev10020582m
Scaffold: scaffold_3
Start: 28382218
End: 28386683

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00585:mRNA_5.1
Scaffold: C_unshiu_00585
Start: 31636
End: 34824
Gene function: 60S ribosomal protein L5

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

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: NAT-05
Km/O41 cM: 19.042

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:
DNA sequence around SNP1:
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: