Citrus CAPS Marker Database

Locus name: Al0636

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1400
Comment on PCR:
F-primer: AAAGATTGGCCACTATTTTGA
R-primer: GGGCGATTGCTTATTTTGT

EST info

EST Accession number 1: C95540
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
TTGCTCCCTCCTTAAGGTCCAACAAGAAAGTCTCCAGTCTAGTAGACAAGGTATTCTCTT
TGCCTCGATCGTTTGCTATAATTCGAGAATCAGTATCTTCATAGTGAATTATCATGTTCA
GTTCTCTGAAATAATTAATGGTTGTATGTAATTTCTATCAGTGGAAAGCAGCCAAAGAGG
AGTTGAATGAGAATGAGGAAGATGAACCTGAAAATGCTTATGAGATTTTAGAGAGGAAGC
GCCAAAGGGAAATAGAGGTTTGTAGAGTGACTGCTTTGGTTACAGATTCCTGTGTGTTTG
ATGCTTTTTTGGTGCCTTACATTTCTTTTTCCTGCAGGAATGGCGTGCTCAGCAAATTGC
CAGTGGAGAAGCCAAAGATAATGCTAATTTTCAGCCCTTGGGTGGTGATTGGTAAGTAAT
CATATATTCTATGTATATTATAAAAGTTCCATATGTTGTGGGCTATCGTGCAATTAGGCC
STS source: Consensus seuqence of 12 cvs.
STS Forward / Reverse: Foward read
STS:
GTTTCATCTTGCTTTATGGATTTGATTTATAACCTGTTATTGGTTTTGCGGCNTTTTGCT
TTTCTCAATAGTTCGAAACAANAATAGCGGACNGTTGCTGTTGCTCCCTCCTTAAGGTCC
AACAAGAAAGTCTCCAGTCTAGTAGACAAGGTATTCTCTTTGCCTCGATCGTTTGCTATA
ATTCGAGAATCAGTATCTTCATAGTGAATTNTCATGTTCAGTTCTCTGAAATAATTAATG
GTTGTATGTAATTTCTATCAGTGGAAAGCAGCCAAAGAGGAGTTGAATGAGAATGAGGAA
GATGAACCTGAAAATGCTTATGAGATTTTAGAGAGGAAGCGCCAAAGGGAAATAGAGGTT
TGTAGAGTGACTGCTTTGGTTACAGATTCCTGTGTGTTTGATGCTTTTTTGGTGCCTTAC
ATTTCTTTTTCCTGCAGGAATGGCGTGCTCAGCAAATTGCCAGTGGAGAAGCCAAAGATA
ATGCTAATTTTCAGCCCTTGGGTGGTGATTGGTAAGTAATCATATATTCTATGTATATTA
TAAAAGTTCCATATGTTGTGGGCTATCGTGCAATTAGGCCAAACACTAATCCAAGTTCAT
GAAATAGATGTCAAGGGTGGTACAAAAAGTTGCAAAGNTTTTTTTTCCATGGNTTTCNAA
GAAATTCTTACAANTGCCATCTNTTGCCATCTCTGTATTT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CTTTTTTTTTCTGTATTTCTTGTCTAAGATTCTGTTCCCCACTTCTGCAGTTGAAATCTT
CTTGTTGCTAATATCTACTTTTTCTCATAGTCAGTTGAACTTATATTTTTGTGTCAATTT
CCTATATGATAGGCGTGAGAAAGTAAAGCGTAGGAGAGCTCAATTAGCCAAGGAAGCTGC
AGANACTCCACCCGAGGCAGAAGCTGACCNAAAACAGGAAAAGCCTGATTTGGTAGATCT
CTCGAAAGATCTCCCATCTGGATGGCAGGTGCAAATTAAGACTTTTTCTCATGATTTATG
ATGGGCGATTGCTTATTTTTGTTGA
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
TGATTTATAACCTGTTATTGGTTTTGCGGCCTTTTGCTTTTCTCAATAGTTCGAAACAAA
AAGCGGACAGTTGCTGTTGCTCCCTCCTTAAGGTCCAACAAGAAAGTCTCCAGTCTAGTA
GACAAGGTATTCTCTTTGCCTCGATCGTTTGCTATAATTCGAGAATCAGTATCTTCATAG
TGAATTTTCATGTTCAGTTCTCTGAAATAATTAATGGTTGTATGTAATTTCTATCAGTGG
AAAGCAGCCAAAGAGGAGTTGAATGAGAATGAGGAAGATGAACCTGAAAATGCTTATGAG
ATTTTAGAGAGGAAGCGCCAAAGGGAAATAGAGGTTTGTAGAGTGACTGCTTTGGTTACA
GATTCCTGTGTGTTTGATGCTTTTTTGGTGCCTTACATTTCTTTTTCCTGCAGGAATGGC
GTGCTCAGCAAATTGCCAGTGGAGAAGCCAAAGATAATGCTAATTTTCAGCCCTTGGGTG
GTGATTGGTAAGTAATCATATATTCTATGTATATTATAAAAGTTCCATATGTTGTGGGCT
ATCG
STS source: Consensus seuqence of 12 cvs.
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:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: EcoR1
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: EcoR1
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: EcoR1
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: EcoR1
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: EcoR1
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: EcoR1
Comment: PCR_condition: 58C aneal
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: EcoR1
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: Nde2
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: Ciclev10007493m
Scaffold: scaffold_1
Start: 23776796
End: 23782088

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00080:mRNA_56.1
Scaffold: C_unshiu_00080
Start: 464290
End: 469444
Gene function: WW domain-containing protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-01
AGI cM: 27.489

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-01
KmMg cM: 25.751

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-01S
JtTr cM: 63.21

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

Km/O41 LG: NAT-01S
Km/O41 cM: 12.652

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG: RP-01
Rp/Sa cM: 48.896

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: K

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

SNP1: SI313
DNA sequence around SNP1:
TGATTTATAACCTGTTATTGGTTTTGCGGC[T/C]TTTTGCTTTTCTCAATAGTTCGAAA
CAAAAAGCGGACAGTTGCTGTTGCTCCCTCCTTAA
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: