Citrus CAPS Marker Database

Locus name: Mf0079

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1100
Comment on PCR:
F-primer: GGTGACTTTGCGGCCAAGGTC
R-primer: GGCAGTGGCTCATCTCAACGA

EST info

EST Accession number 1: C81861
EST Accession number 2: DC893647

sequence-tagged site (STS seq)

STS:
GGCCTGATTGACATTCCAAGGTACGAGNTTGACTCACTCCTATACCTACATCATAAATAA
TTTTAAAAAAAAAATTGCGTGCACAAGTAGGTTTGCAACAGAAATAATGTTCATGTTTTT
TTATAATCCATGAAAAAATATTTGCAACAGAAACAATGTTCATCTCTTTTTATGATCCAT
GAAAACATATCAGAAATTTGTCTCAAATTTATATAATCATATTGCATGCCAAAGACAAAT
GATCTAGACATGGTAATGCTGAAACGGGAAGATATAAAAGCTTCATGACTCACTTCTGTT
TAGCAATTTATGAACAGCACTTCTGCTTGTTGATCAATGTCAAATATCTGAACTGCTATG
CAAGAAGGCTATTTTTGCCGTACTTGATCCTATGATTTGCCAAAGTCTAGCTTTCTTATG
TAAAATATGACAGTGCCTCAGCTGTTTTATCACGTGGGTAACCAGTACNCATACATACAC
ACTGCCTTCNCACTGAGTTCTTTTCTTCCTAATCTCTTAAGCCTCTAAATCTTTCTTGGT
TTAAGTTCTCTTTTTACAATTGTATTGCTAGAGATCATTAAAAGTTTTAGTCATTATGTC
TGGTTAATTATCGACGTTGAAATTTTCTACATGGATTTCAATCACCCTTCTAGATAATTT
GATGTGTATGGTGAATTGCAAGTTCTTGATAAATTTATAATGCTTCTAAGCTGTATTTTC
CTGCATTTTCATGTAGACTGCCAAAGACACCCACCTGGGTTATGAGGACCAGGATGGAGC
AAAAGCTAT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
TGTCATCTCTTTTATGATCCATGAAAACATATCAGAAATTGTCTCAAAATTATATAATCA
TATTGCATGCCAAAGACAAATGATCTAGACATGGTAATGCTGAAACGGAAGATATAAAAG
CTTCATGACTCACTTCTGTTTAGCAATTTATGAACAGCACTTCTGCTTGTTGATCAATGT
CAAATATCTGAACTGCTATGCAAGAAGGCTATTTTTGCCGTACTTGATCCTATGATTTGC
CAAAGTCTAGCTTTCTTATGTAAAATATGACAGTGCCTCAGCTGTTTTATCACGTGGGTA
ACCAGTACGCATANATACACACTGCCTTCNCACTGAGTTCTTTTCTTCCTAATCTCTTAA
GCCTCTAAATCTTTCTTGGTTTAAGTTCTCTTTTTACAATTGTATTGCTAGAGATCATTA
AAAGTTTTAGTCATTATGTCTGGTTAATTATCGACGTTGAAATTTTCTACATGGATTTCA
ATCACCCTTCTAGATAATTTGATGTGTATGGTGAATTGCAAGTTCTTGATAAATTTATAA
TGCTTCTAAGCTGTATTTTCCTGCATTTTCATGTAGACTGCCAAAAGACACCCAACCTGG
GTTATTGAGGACCAAGGATGGAGCCAAAAAGCTAATGGACTTGGGTTTACAATTCATTCC
CATGGATCAAATCATCAAGGACTCTNTCGAGAGTTTGAAGGCCAAGGGATTTATCTCTTG
ANTGAAAGCTGCAACGTGTCAGCAGCTGCTGATGAACCCATCCGCTTTATNCAAGCAGAG
GGCTGAGAGCTATAGTATAATTAGATAATT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
AATTATACTATAGCTCTCAGCCCTCTGCTTGA/ATAAAGCGGATGGGTTCATCAGCAGCT
GCTGACACGTTGCAGCTTTCATTCAAGAGATAAATCCCTTGGCCTTCAAACTCTCGATAG
AGTCCTTGATGATTTGATCCATGGGAATGAATTGTAAACCCAAGTCCATTAGCTTTTTGG
CTCCATCCTTGGTCCTCAATAACCCAGGTTGGGTGTCTTTTGGCAGTCTACATGAAAATG
CAGGAAAATACAGCTTAGAAGCATTATAAATTTATCAAGAACTTGCAATTCACCATACAC
ATCAAATTATCTAGAAGGGTGATTGAAATCCATGTAGAAAATTTCAACGTCGATAATTAA
CCAGACATAATGACTAAAACTTTTAATGATCTCTAGCAATACAATTGTAAAAAGAGAACT
TAAACCAAGAAAGATTTAGAGGCTTAAGAGATTAGGAAGAAAAGAACTCAG
STS source: Consensus seuqence of 12 cvs.
STS Forward / Reverse: Reverse read
STS:
AAGTTCTCTTTTTCCAATTGTATTGCTAGAGATCATTAAAAGTTTTAGTCATTATGTCTG
GTTAATTATCGACGTTGAAATTTTCTACATGGATTTCAATCACCCTTCTAGATAATGTGA
TGTTTATGGTGAATTGCAAGTTCTTGATAAATTTATAATGCTTCTAAGCTGTATTTTCCT
GCATTTACATGTAGACTGCCAAAAGACACCCAACCTGGGTTATTGAGGACCAAGGATGGA
GCCAAAAAGCTAATGGACTTGGGTTTACAATTCATTCCCATGGATCAAATCATCAAGGAC
TCTGTCGAGAGTTTGAAGGCCAAAGGATTTATCTCTTGAATGAAAGCTGCAACGTGTCAG
CAGCTGCTGAT
STS source: Consensus seuqence of 12 cvs.
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:

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)
Resriction enzyme: Pvu2
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: 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: Kiyomi x Miyagawa-wase
Restriction enzyme: Dra1
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: 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: Kiyomi x Miyagawa-wase
Restriction enzyme: NC
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 Miyagawa-wase
Restriction enzyme: Pvu2
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: Pvu2
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: Taq1
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Xba1
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: Ciclev10028839m
Scaffold: scaffold_8
Start: 24721937
End: 24724569

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00984:mRNA_8.1
Scaffold: C_unshiu_00984
Start: 55676
End: 58212
Gene function: Cinnamoyl CoA reductase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 3.409

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-08
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-082
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, 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: SI067
DNA sequence around SNP1:
TCAAGAGATAAATCCCTTGGCCTTCAAACTCTCGA[T/C]AGAGTCCTTGATGATTTGAT
CCATGGGAATGAATTGTAAACCCAAGTCCATTAGCTTTTT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: