Citrus CAPS Marker Database

Locus name: Al0029

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 1200
Comment on PCR:
F-primer: TGGGGAAAGAAAGACTACAAT
R-primer: AAAACCTAACCCGCAAAT

EST info

EST Accession number 1: C95227
EST Accession number 2: DC892873

sequence-tagged site (STS seq)

STS:
AACAAGAAACAAAAACAAAAGAATGAAAAACAATTATTTTTGTTTTTGTAAAACAGAACA
CGCTCTCCCCAAAAACCAACCACACCCACCCACTCACACACGCACACTCATGACTCGCTC
GCCAAAAGAAACAAAAGCCTAATCAATCCGCAAACCCAATCACCACAAAACGACAATCTA
AAAGCAGCACGCGTGCCCCCACCACCTTTACTACTTTCGCAGATTCCCGCCCTCTCTCTC
TCTCTCTCTATCACCTTTATATGCAACAATGACTTTTTATTTTAATTTATTTTTATTTCT
CTTTTTTGTTTTTTTCAATGAAAAGGGAGGAGGAGGTGGTGATTGTATCCAAGCAAACGG
GCGGAACCCTAACGGAGCTCAGACGACGTCAGCTAACGACAGCTTAACTGTGACGGAACA
CCAAGTGGCTAAGCTGATGGAAGAAGATATGGGGTCAGCCATGCAGTACTTACAAGGCAA
AGGGCTTTGTCTAATGCCCATCTCACTTGCAACTGCTATATCGACTGCCACGTGTCACTC
TAGGAACCCCATCATCAGCACCAGCAACAACAACAATAACAACGGCAATCCCCACCACAA
TCCTTTGCTTCAGTCCAATGGTGAGGGCCCGACCTCACCTAGCATGTCAGTGCTGACTGT
CCAGTCAGCAACTATGGGTAACGGTGGGGCTGATGGCTCCGTCAAAGATGCTGCTNCGTT
TCAAGCCTTGATCACGGCGTNGNCGANTTATGANANGCTCGNCAAGTCTACNAAATAGGC
TCCTAGAGNNGGACTCCCACGCGATTGGGAACTTGGCGATTACACACAAAGCAGAGAGCA
NCAACAACTTTTGTTTTTTT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
AAACAAAGATGAAACCATTTTTTGTTTNTAAACAGACACGTTTTCCCAAAAAACAACACA
CCANCCANTCACACACGCACATTCATGATTGGTCGCCAAAGAAACAAAGCTTATCAATCC
GCAAACCCAATCACCACAAAACGACAATCTANAAGCAGCACGCGTGCCCCCACCACCTTT
ACTACTTTCGCAGATTCCCGCCCTCTCTCTCTCTCTCTCTATCACCTTTATATGCAACAA
TGACTTTTTATTTTAATTTATTTTTATTTCTCTTTTTTGTTTTTTTCAATGAAAAGGGAG
GAGGAGGTGGTGATTGTATCCAAGCAAACGGGCGGAACCCTAACGGAGCTCAGACGACGT
CAGCTAACGACAGCTTAACTGTGACGGAACACCAAGTGGCTAAGCTGATGGAAGAAGATA
TGGGGTCAGCCATGCAGTACTTACAAGGCAAAGGGCTTTGTCTAATGCCCATCTCACTTG
CAACTGCTATATCGACTGCCACGTGTCACTCTAGGAACCCCATCATCAGCACCAGCAACA
ACAACAATAACAACGGCAATCCCCACCACAATCCTTTGCTTCAGTCCAATGGTGAGGGCC
CGACCTCACCTAGCATGTCAGTGCTGACTGTCCAGTCAGCAACTATGGGTAACGGTGGGG
CTGATGGCTCCGTCAAAGATGCTGCTTCCGTTTCCAAGCCTTGATCAACGGCGTCGGCCG
ACTTTATGATGAGGCTCGTCCAAAGTCTACGAAAATAAGGCGTCACTAGATGTTGGGACC
TTCACGACGTCGTATTTGTGTAGACTTTGTGACTGAATCTAACAAACAACAAAAAAGCAA
GAAAGAAGCCAATCCCAAGA
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment: PCR_condition: 58C aneal
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
Rank as CAPS marker: no homozygous cultivar with minor allele
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
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: Hinc2
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: Jutaro unshu x Trovita orange
Restriction enzyme: Hae3
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: Hae3
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: Hae3
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: Hae3
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: Hinc2
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_00305:mRNA_10.1
Scaffold: C_unshiu_00305
Start: 69938
End: 73026
Gene function: Basic helix-loop-helix transcription factor

AGI map info (Shimada et al. 2014)

AGI LG: AGI-01
AGI cM: 37.357

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-01S
JtTr cM: 50

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:
DNA sequence around SNP1:
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: