Citrus CAPS Marker Database

Locus name: Ov0109

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 1250
Comment on PCR:
F-primer: AGTGCAAAGTCGCTTCT
R-primer: GTTACTAAACCCAATCAACAG

EST info

EST Accession number 1: AU186389
EST Accession number 2: DC893815

sequence-tagged site (STS seq)

STS:
TCTGGCGAGCACATTGTTGCTGGTGCGGGAGAACTTCACCTTGAGATCTGTTTGAAGGAT
CTGCAGGACGATTTCATGGGAGGTGCTGAAATTATTAAATCTGATCCTGTTGTGTCCTTC
CGTGAAACTGTCCTTGAGAAGTCTTGCCGCACTGTGATGAGTAAGTCTCCCAACAAGCAT
AATCGTCTCTACATGGAAGCCCGACCTCTGGAAGAAGGTCTTGCTGAGGCCATAGATGAT
GGCCGCATTGGTCCAAGGGATGATCCCAAGGCTCGATCTAAGATCTTGTCTGAGGAGTTC
GGCTGGGACAAGGATCTTGCGAAGAAGATTTGGTGTTTTGGTCCTGAGACC
STS source: Clementine haploid
STS Forward / Reverse: Foward read
STS:
GTTTGGCCNAGTCAGATCCTATGGTTGTCTGTACAATTGAGGAGTCTGGCGAGCACATTG
TTGCTGGTGCGGGAGAACTTCACCTTGAGATCTGTTTGAAGGATCTGCAGGACGATTTCA
TGGGAGGTGCTGAAATTATTAAATCTGATCCTGTTGTGTCCTTCCGTGAAACTGTCCTTG
AGAAGTCTTGCCGCACTGTGATGAGTAAGTCTCCCAACAAGCATAATCGTCTCTACATGG
AAGCCCGACCTCTGGAAGAAGGTCTTGCTGAGGCCATAGATGATGGCCGCATTGGTCCAA
GGGATGATCCCAAGGCTCGATCTAAGATCTTGTCTGAGGAGTTCGGCTGGGACAAGGATC
TTGCGAAGAAGATTTGGTGTTTTGGTCCTGAGACCACTGGCCCTAACATGGTCGTTGATA
TGTGTAAGGGAGTTCAATACTTGAATGAAATTAAGGATTCTGTTGTTGCTGGTTTCCAGT
GGGCATCGAAAGAAGGTGCGCTGGCTGAAGAGAACATGAGAGGTATCTGCTTTGAAGTAT
GTGATGTTGTTCTTCACGCTGATGCCATTCACAGAGGTGGTGGTCAAGTCATTCCTACTG
CTAGGAGGGTCATATATGCTTCCCAGCTCACAGCCAAGCCCAGGCTTCTTGAGCCTGTCT
ACATGGTCGAAATACAGGCTCCCGAGCAGGCCCTTGGTGGTATTTACAGTG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CTGGCCCTAACATGTCGTTGATATGTGTAAGGGAGTTCAATACTTGAATGAAATTAAGGA
TTCTGTTGTTGCTGGTTTCCAGTGGGCATCGAAAGAAGGTGCGCTGGCTGAAGAGANCAT
GAGAGGTATCTGCTTTGAAGTATGTGATGTTGTTCTTCACGCTGATGCCATTCACAGAGG
TGGTGGTCAAGTCATTCCTACTGCTAGGAGGGTCATATATGCTTCCCAGCTCACAGCCAA
GCCCAGGCTTCTTGAGCCTGTCTACATGGTCGAAATACAGGCTCCCGAGCAGGCCCTTGG
TGGTATTTACAGTGTTCTCAATCAGAAACGTGGTCACGTGTTCGAGGAAATGCAGAGACC
TGGTACCCCCCTTTACAACATCAAGGCTTACCTTCCCGTCATCGAGTCCTTTGGATTCTC
AGGCACTTTGAGGGCTGCAACGTCAGGACAGGCCTTCCCACAATGTGTGTTTGATCACTG
GGACATGATGTCATCCGATCCACTGGAGCCTGGTACACAGGCTGCACAGCTTGTTGCTGA
TATCAGGAAGAGGAAGGGCTTGAAGGAGCAAATGACACCACTATCTGAGTTTGAGGACAA
GCTGTAAACATTTCGTCTTGACATCAAGGGTGAGATTGCGCAGCTTGTTGCTGATATCAG
GAAGAGGGAGCAAATGACACCGCTATCCGAGTAGAGGACGAGCTGTAAACATTTCATCTT
GACATCAAGGGTGAGATTGCGCAGCA
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
TCTCACCCTTGATGTCAAGATGAAATGTTTACAGCTCGTCCTCTACTCGGATAGCGGTGT
CATTTGCTCCCTCTTCCTGATATCAGCAACAAGCTGCGCAATCTCACCCTTGATGTCAAG
ACGAAATGTTTACAGCTTGTCCTCAAACTCAGATAGTGGTGTCATTTGCTCCTTCAAGCC
CTTCCTCTTCCTGATATCAGCAACAAGCTGTGCAGCCTGTGTACCAGGCTCCAGTGGATC
GGATGACATCATGTCCCAGTGATCAAACACACATTGTGGGAAGGCCTGTCCTGACGTTGC
AGCCCTCAAAGTGCCTGAGAATCCAAAGGACTCGATGACGGGAAGGTAAGCCTTGATGTT
GTAAAGGGGGGTACCAGGTCTCTGCATTTCCTCGAACACGTGACCACGTTTCTGATTGAG
AACACTGTAAATACCACCAAGGGCCTGCTCGGGAGCCTGTATTTCGACCA
STS source:
STS Forward / Reverse: Reverse read
STS:
AGGCACTTTG AGGGCTGCAA CCTCAGGACA GGCCTTCCCA CAATGTGTGT TTGAT
CACTG GGACATGATG TCATCCGATC CACTGGAGCC TGGTACACAG GCTGCACAGC
TTGTTGCTGA TATCAGGAAG AGGAAGGGCT TGAAGGAGCA AATGACACCA CTAT
CTGAGT TTGAGGACAA GCTGTAAACA TTTCGTCTTG ACATCAAGGG TGAGATTGC
G CAGCTTGTTG CTGATATCAG GAAGAGGGAG CAAATGACAC CGCTATCCGA GTA
GAGGACG AGCTGTAAAC ATTTCATCTG
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: Hha1
Rank as CAPS marker: Disagree by Marco analysis
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: Hae3
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: Hha1
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: Hha1
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: Hha1
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: Hha1
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: Msp1
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: Ciclev10004309m
Scaffold: scaffold_9
Start: 30513333
End: 30517676

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00003:mRNA_13.1
Scaffold: C_unshiu_00003
Start: 122283
End: 126575
Gene function: Elongation factor 2

AGI map info (Shimada et al. 2014)

AGI LG: AGI-03
AGI cM: 71.06

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-032
JtTr cM: 13.729

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-03
Rp/Sa cM: 71.532

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: SI172
DNA sequence around SNP1:
GATGTCAAGACGAAATGTTTACAGCTTGTCCTCAAACTCAGATAGTGGTGTCATTTGCTC
[T/C]TTCAAGCCCTTCCTCTTCCTGATATCAGCAACAAGCTGTGCAGCCTGTGTACCAG
GCTCC
SNP2: SI202
DNA sequence around SNP2:
GGAGCCTGGTACACAGGCTGCACAGCTTGTTGCTGATATCAGGAAGAGGAAGGGCTTGAA
[A/G]GAGCAAATGACACCACTATCTGAGTTTGAGGACAAGCTGTAAACATTTCGTCTTG
ACATC
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: