Citrus CAPS Marker Database

Locus name: Ov0513

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 750
Comment on PCR:
F-primer: TGGTTTACATCTGCGAGTG
R-primer: AAATAAAGTGACAAGGCAAAA

EST info

EST Accession number 1: AU186200
EST Accession number 2: DC894061

sequence-tagged site (STS seq)

STS:
CGTTTTGTGAACCGCGTAGTTGCCTCTATGTTCAACACGGTTTCAAACAAGAAGATTGCC
GTTCTGGGATTTGCCTTCAAGAAGGATACCGGTGACACCAGAGAGACCCCAGCCATTGAT
GTCTGCAAGGGGCTTTTGGGAGACAAAGCTCGGTTGAGCATATACGACCCACAGGTCACC
GAGGACCAGATCCAGAGGGACCTTACAATGAACAAGTTTGACTGGGACCATCCTCTTCAC
CTCCAGCCAATGAGTCCCACCACGGTGAAGCAAGTGAGCGTGGTCTGGGATGCCTATGAA
GCAACAAAAGATGCCCATGGTGTCTGCATCTTGACCGAGTGGGATGAGTTCAAGACTCTT
GACTATCAGAGGATATATGACAACATGCAGAAACCAGCATTCGTGTTTGATGGCAGGAAT
GTTGTTGATGCCAACAAGTTGAGGGAGATTGGTTTCATCGTGTACTCCATT
STS source: Consensus seuqence of 12 cvs.
STS Forward / Reverse: Combined sequence of both reads
STS:
CGTCATTAAGATCAATGATTACCAGAAAAGCCGTTTTGTGAACCGCGTAGTTGCCTCTAT
GTTCAACACGGTTTCAAACAAGAAGATTGCCGTTCTGGGATTTGCCTTCAAGAAGGATAC
CGGTGACACCAGAGAGACCCCAGCCATTGATGTCTGCAAGGGGCTTTTGGGAGACAAAGC
TCGGTTGAGCATATACGACCCACAGGTCACCGAGGACCAGATCCAGAGGGACCTTACAAT
GAACAAGTTTGACTGGGACCATCCTCTTCACCTCCAGCCAATGAGTCCCACCATGGTGAA
GCAAGTGAGCGTGGTCTGGGATGCCTATGAAGCAACAAAAGATGCCCATGGTGTCTGCAT
CTTGACCGAGTGGGATGAGTTCAAGACTCTTGACTATCAGAGGATATATGACAACATGCA
GAAACCAGCATTCGTGTTTGATGGCAGGAATGTTGTTGATGCCAACAAGTTGAGGGAGAT
TGGTTTCATCGTGTACTCCATTGGTAAGCCACTCGATCCATGGTTGAAGGACATGCCGGC
TGTTGCATAAAAGAGACGCCAATGGGCATGCTCGTGTCATCGGGCATCAGATTATAGATG
ATGAAGAAGTCAGTTCAATTCTTTACTATATTTTGATGA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CGCGTAGTTGCCTCTATGTTCAACACGGTTTCAAACAAGAAGATTGCCGTTCTGGGATTT
GCCTTCAAGAAGGATACCGGTGACACCAGAGAGACCCCAGCCATTGATGTCTGCAAGGGG
CTTTTGGGAGACAAAGCTCGGTTGAGCATATACGACCCACAGGTCACCGAGGACCAGATC
CAGAGGGACCTTACAATGAACAAGTTTGACTGGGACCATCCTCTTCACCTCCAGCCAATG
AGTCCCACCATGGTGAAGCAAGTGAGCGTGGTCTGGGATGCCTATGAAGCAACAAAAGAT
GCCCATGGTGTCTGCATCTTGACCGAGTGGGATGAGTTCAAGACTCTTGACTATCAGAGG
ATATATGACAACATGCAGAAACCAGCATTCGTGTTTGATGGCAGGAATGTTGTTGATGCC
AACAAGTTGAGGGAGATTGGTTTCATCGTGTACTCCATTGGTAAGCCACTCGATCCATGG
TTGAAGGACA
STS source:
STS Forward / Reverse: Foward read
STS:
CGGTGACACC AGAGAGACCC CAGCCATTGA TGTCTGCAAG GGGCTTTTGG GAGAC
AAAGC TCGGTTGAGC ATATACGACC CACAGGTCAC CGAGGACCAG ATCCAGAGGG
ACCTTACAAT GAACAAGTTT GACTGGGACC ATCCTCTTCA CCTCCAGCCA ATGA
GTCCCA CCATGGTGAA GCAAGTGAGC GTGGTCTGGG ATGCCTATGA AGCAACAAA
A GATGCCCATG GTGTCTGCAT CTTGACCGAG TGGGATGAGT TCAAGACTCT TGA
CTATCAG AGGATATATG ACAACATGCA
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase/Poncirus
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Msp1
Rank as CAPS marker: Others
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: Msp1
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: 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
Population name: Jutaro unshu x Trovita orange
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
Population name: Kiyomi x Miyagawa-wase
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
Population name: Kiyomi x Okitsu41gou
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: Ciclev10011622m
Scaffold: scaffold_6
Start: 25349417
End: 25351949

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00009:mRNA_59.1
Scaffold: C_unshiu_00009
Start: 325807
End: 333424
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 38.903

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 5.11

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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-04
Rp/Sa cM: 60.491

CAPS genotyping (Hybrid cv/Citrus collection)

CAPS genotyping:

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: