Citrus CAPS Marker Database

Locus name: Al0407

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1600
Comment on PCR:
F-primer: CGCGAAGAAGAAGAAGG
R-primer: ATCCAGTCTGAAGCCAAAATA

EST info

EST Accession number 1: C95386
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
TGACCAATCCATCCCCTTCTTCTTCTTCGCGATTACATTTATTTATTTATTCGATGTATT
TCAGTATCAATGCTGTTGATCCAAAGACCAAGAAAATTTTGCAGCTTCTCCGTTTGAGAC
AGGTAACCACTCAATCCTCCCTTGTGTTATTGCCATTTAATTTGTTATTAGAAATGTATA
TTAGAGGTCTGCAATTTCCTTTTCAAATTGGATAATTATTGGTATAGTCTGATAGTGTTG
GCAAGCTTAGGGCTTAGCTATCAGTTTTGGATATGCCCGTTACCATTGCTGAAATGTTTG
TATCAAAGTAGTAAATTTGGGTGCATTAACTATAATGTTTTATTGGAATGAAAGAGGTTG
GAATGCTTTTTGTTTGCTAGCCATTTGTTTGGTGGTTGAACTCAAATTTAAGTACTTGGT
TGAGCCATAGGTGTTCTTGGTATAGTTCGATGCTAGGAGTGCTGTTCTCCTCTGATTGTT
CTCGNAGTGTAGATGCTGTAAACTATTGGGAGATTCCTCTTTTGA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
ATTTGTTATTAGAAATGTATATTAGAGGTCTGCAATTTCCTTTTCAAATTGGATAATTAT
TGGTATAGTCTGATAGTGTTGGCAAGCTTAGGGCTTAGCTATCAGTTTTGGATATGCCCG
TTACCATTGCTGAAATGTTTGTATCAAAGTAGTAAATTTGGGTGCATTAACTATAATGTT
TTATTGGAATGAAAGAGGTTGGAATGCTTTT
STS source: Consensus seuqence of 12 cvs.
STS Forward / Reverse: Foward read
STS:
TTTTGCTGTTCCTGAATACAGATTTTAATGGTGTCTTTTGAAAGTGAACAAAGCCACACT
CAATATGCTGCACAGAGTTGAGCCCTATGTAACATATGGGTATGCGTTTGATTTGCTGTT
ACTAATCTGGGTATCGTCTAAAAATTTATCATCTGCACAGCTTGTTTTGAAATTTTCTGT
TGATGATTTCAGGTACCCCAATTTAAAGAGTGTCAAAGAACTGATTTACAAGAGGGGTTA
CGGCAAATTAAATAAGCAGAGGATTGCTTTGACCGACAATTCTATCATCGAACAGGTATG
GTCTACTTAACATTTTTTGTGTGAATTCCTGTGTGTTCATAGGATAATTGTGTCTTCATG
CAAGTAAATAAAATTCAGTTTTGTGTCTAACATATTGGTTTATGATAACCACCGACAGGC
TCTTGGGCAGCATGGAATTATCTGCATGGAAGATCTCATCCATGAGATTTTGACTGTTGG
TCCTCACTTCAAGGAGGCAAACAACTTCCTATGGCCCTTCAAGCTCAAGGCACCATTGGG
TGGCCTGAAGAAGAAGAGGAACCACTATGTTGAAGGCGGTGATGCAGGAAACCGTGAAGA
TTACATCAATGAGCTCATCAGAAGGATGAACTAGGCTTCTGCAGAATATCCTACCCCTTT
TGAAGAAGTTTTGATGTGATCAATATCTTAAATTTTGGCTTTTAGTGTTTCCTATTATTC
CCAGCCTTTTCCCNGGA
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:
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: 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: Hind3
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: 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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hind3
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: Hind3
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: Hind3
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:
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: Ciclev10009315m
Scaffold: scaffold_1
Start: 26576059
End: 26578193

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00131:mRNA_17.1
Scaffold: C_unshiu_00131
Start: 121152
End: 123183
Gene function: 60S ribosomal protein L7

AGI map info (Shimada et al. 2014)

AGI LG: AGI-01
AGI cM: 31.24

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-01
KmMg cM: 15.673

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-01S
JtTr cM: 57.666

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-01
Rp/Sa cM: 79.425

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