Citrus CAPS Marker Database

Locus name: Mf0039

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1500
Comment on PCR:
F-primer: CCAATTCCTCAATATATGCAG
R-primer: CACAAGTATACTGCTGTACCA

EST info

EST Accession number 1: C81786
EST Accession number 2: DC893617

sequence-tagged site (STS seq)

STS:
CAACTCTCTGCCTTTTCATGTGCAAGCTAGCCCTGTCAGTCTTTTGTCTCTGGACTATAG
CAGCAAGTCTACCCACATTTTTATGTCACAAAGGAATGCGCTTGGGTATGTTAGAGACAG
TTATCTACAGGAAGCAGAAATGGAAATGAATTCATTTGTCATGATCCTTTTGATATTAGT
CTACACAGTTGATCTTTCTAGTTAATTTTTACCAAAAATCACATGTGATTTAGCTCTGCN
GATGTCTAGGTTTATGGCCACTAGATATGCATTACCCCTTNTTTTGGCTTCTAAGGATAA
AGGTGTTTTTATTGGTTCCTTTGTTGCTTAACCNTCTCATCTTGTACCTCTTGGATAACT
TATGAAGTATACAGCATGCTTTCTTGTGAGAAAATATTATAATCCCCATTTACTGGGTTT
TCAGTTTATAAACCAATGTAGCAGTTGTAAATAGCTTCTGTTTTGTTAATTATTGAAACC
ATTTCTTTTTNAACATCCAGGTTTTTTGCTGCTTTGCCAATTCGGTGGCCTCTACGCGCT
TTCTTTTGCAAGATGAATTTAACATCCAGACAACTGCCTGTGATAATTGCATCATTGTAC
GGTCACTTACATTATCTATTAACACTATTGCTATAGTTACACATCTTTGNTTATTTGTTA
TATGNGTTTCTTATTTGTATGCAGGGGTTTATGTTTTGCCTCAGCC
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GTCAGTCTTTTGTCTCTGGACTATAGCAGCAAGTCTACCCACATTTTTATGTCACAAAGG
AATGCGCTTGGGTATGTTAGAGACAGTTATCTACAGGAAGCAGAAATGGAAATGAATTCA
TTTGTCATGATCCTTTTGATATTAGTCTACACAGTTGATCTTTCTAGTTAATTTTTACCA
AAAATCACATGTGATTTAGCTCTGCCGATGTCTAGGTTTATGGCCACTAGATATGCATTA
CCCCTTCTTTTGGCTTCTAAGGATAAAGGTGTTTTTATTGGTTCCTTTGTTGCTTAACCC
TCTCATCTTGTACCTCTTGGATAACTTATGAAGTATACAGCATGCTTTCTTGTGAGAAAA
TATTATAATCCCCATTTACTGGGTTTTCAGTTTATAAACCAATGTAGCAGTTGTAAATAG
CTTCTGTTTTGTTAATTATT
STS source:
STS Forward / Reverse: Foward read
STS:
TTCTTTGCAAGATGAATTAACATCCAGACAACTGCCTGTGATAATTGCATCATTGTACGT
CACTTACATTATCTATTANCACTATTGCTATAGTTACACATCTTGGTTATTNGTTATATG
TGTTTCTTATTGGTATGCAGGGGTTTATGTTTTGCCTCAGCCAACTTGCATGCATATTTT
CCTTAGTTGCATGCATCGTGGGAAGTGATGAACTTCAGGAGGCTTCACAGATACTGAATC
TATTGGCTGATTTAGTTTATTGCACGTAAGTGTTTTCCTTCTTTCCACACTGAAAGCTCC
TAGGCAAAATGGCTGCAAAATATCCTACTGATTCTGCTTTATGTTTTGGTTTGCAGGGTC
TGTGCCTGCATGCAGGTATGCAATTNATTCAACCACATGCAAATGAAATTACATTATAAC
GAAATATTTCTTCACAGTTTATTTGAATTGTCTGCAGACACAGCACAAGGTTGAAATGGA
CAAAAGGGATGGTAAATTTGGTCCACAACCAATGGCGGTACCCCCTCATCAACAGATGTC
TCGCATTGATCAGCCATATCCTGCGACGGTTGGATATCCACCTCAACAACAAGCATATGG
TTATCCTCCTCAAGGCTATCCACCACCTCAGGGTCAGGGCTACCCACCACCCCAAGGTCA
AGGCTATCCAGCTGGAGGTTATCCCCCGCCTGCATACAATCAAGGCCATTACCCACCTCC
TACCCATTAAGGCCTAGTTCCGCTGTGGTGCATGTTTGATATTGGTTTGTGAAAATGAAC
TTTTGAGAC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
TCAAACATGCACCACAGCGGAACTAGGCCTTAATGGGTAGGAGGTGGGTAATGGCCTTGA
TTGTATGCAGGCGGGGGATAACCTCCAGCTGGATAGCCTTGACCTTGGGGTGGTGGGTAG
CCCTGACCCTGAGGTGGTGGATAGCCTTGAGGAGGATAACCATATGCTTGTTGTTGAGGT
GGATATCCAACCGTCGCAGGATATGGCTGATCAATGCGAGACATCTGTTGATGAGGGGGT
ACCGCCATTGGTTGTGGACCAAATTTACCATCCCTTTTGTCCATTTCAACCTTGTGCTGT
GTCTGCAGACAATTCAAATAAACTGTGAAGAAATATTTCGTTATAATGTAATTTCATTTG
CATGTGGTTGAATTAATTGCATACCTGCATGCAGGCACAGACCCTGCAAACCAAAACATA
AAGCAGAATCAGTAGGATATTTTGCAGCCATTTTGCCTAGGAGCTTTCAGTGTGGAAAGA
STS source:
STS Forward / Reverse: Reverse read
STS:
GTTATCTACA GGAAGCAGAA ATGGAAATGA ATTCATTTGT CATGATCCTT TTGAT
ATTAG TCTACACAGT TGATCTTTCT AGTTAATTTT TACCAAAAAT CACATGTGAT
TTAGCTCTGC TGATGTCTAG GTTTATGGCC ACTAGATATG CATTACCCCT TATT
TTGGCT TCTAAGGATA AGGTGTTTT TATTGGTTCC TTTGTTGCTT AACCCTCTCA
TCTTGT
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): Miyagawa-wase/Trovita orange
Comment: PCR_condition: 48C aneal
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinf1
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: Hha1
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: Hinf1
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: 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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hinf1
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: Hinf1
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: Hinf1
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: Hinf1
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:
Scaffold:
Start:
End:

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00343:mRNA_25.1
Scaffold: C_unshiu_00343
Start: 221381
End: 224081
Gene function: PLAC8 family protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 5.51

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-05S
KmMg cM: 5.643

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 10.014

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/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: SI016
DNA sequence around SNP1:
TTTTGGCTTCTAAGGATAAAGGTGTTTTTATTGGTTCCTTTGTTGCTTAACC[A/C]TCT
CATCTTGTACCTCTTGGATAACTTATGAAGTATACAGCATGCTTTCTTGTGAGAAAA
SNP2: SI147
DNA sequence around SNP2:
TCAAATAAACTGTGAAGAAATATTTCGTTATAATGTAATTTCATTTGCATGTGGTTGAAT
[T/G]AATTGCATACCTGCATGCAGGCACAGACCCTGCAAACCAAAACATAAAGCAGAAT
CAGTA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: