Citrus CAPS Marker Database

Locus name: Al0515

CAPS PCR info

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

EST info

EST Accession number 1: C95514
EST Accession number 2: DC893061

sequence-tagged site (STS seq)

STS:
CCGGCGACCG GCACGTCACC TCGTGAAAAA TCCTATCGGT GCTTTACCAA TCAAG
AAGTT CCCATCCAGA AACAGCCTCT TCAAAGACTT CTTGTGACTG AACTCCAATG
GGATACCGCC GCGTAANCGG TTGTAACGCA TCGATAGAGA CGACAGCATC GGAT
AATCAG CGAAATTCAC GGGCAAGTAC CCTTGGATCT TGTTGAACCC CAGATCAAC
C GCCACCAGGT CGCTTCTGCC ATCNACTGGC TTCGAGATCN CGACGCGTGT CAA
GGTGTTA TTGGATAGGT TAACTTGCTG
STS source:
STS Forward / Reverse: Foward read
STS:
TCTTTAGACCTTTCTTATAATTCTCTATCCGGGTCTCTCCCAAAAAACACATTTTTGATG
TCGAGTTTGAGAAGACTCGATCTGAGTTACAACAAGCTCACCGGTTCATTACCAAAGCTG
CCGCCAAATCTCTCAGAGCTAGCTCTGAAGAACAATGTTTTATCTGGGGTTATTACAAAG
AACTCCTTTGACGGNTTAACTCAGCTGGAAGTTATCGAACTCAGTGAAAACTCGTTCACC
GGGACACTTGAAGCGTGGTTCTTCCTGTTGCCAGCACTCCAGCAAGTTAACCTATCCAAT
AACACCTTGACACGCGTCGNGATCTCGAAGCCAGTNGATGGCAGAAGCGACCTGGTGGCG
GTTGATCTGGGGTTCAACAAGATCCAAGGGTACTTGCCCGTGAATTTCGCTGATTATCCG
ATGCTGTCGTCTCTNTCGATGCGTTACAACCGNTTACGCGGCGGTATCCCATTGGAGTTC
AGTCACAAGAAGTCTTTGAAGAGGCTGTTTCTGGATGGGAACTTCTTGATTGGTAAAGCA
CCGATAGGATTTTTCACGAGGTGACGTGCCGGTCGCCGG
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
TCCTATCGGTGCTTTACCAATCAAGAAGTTCCCATCCAGAAACAGCCTCTTCAAAGACTT
CTTGTGACTGAACTCCAATGGGATACCGCCGCGTAAACGGTTGTAACGCATCGATAGAGA
CGACAGCATCGGATAATCAGCGAAATTCACGGGCAAGTACCCTTGGATCTTGTTGAACCC
CAGATCAACCGCCACCAGGTCGCTTCTGCCATCTACTGGCTTCGAGATCTCGACGCGTGT
CAAGGTGTTATTGGATAGGTTAACTTGCTGGAGTGCTGGCAACAGGAAGAACCACGCTTC
AAGTGTCCCGGTGAACGAGTTTTCACTGAGTTCGATAACTTCCAGCTGAGTTAATCCGTC
AAAGGAGTTCTTTGTAATAACCCCAGATAAAACATTGTTCTTCAGAGCTAGCTCTGAGAG
ATTTGGCGGCAGCTTTGGTAATGAACCGGTGAGCTTGTTGTAACTCAGATCGAGTCTTCT
CAAACTCGAC
STS source:
STS Forward / Reverse: Reverse read
STS:
ACAAAGAACTCCTTTGACGGATTAACTCAGCTGGAAGTTATCGAACTCAGCGAAAACTCG
TTCACCGGGACACTTGAAGCGTGGTTCTTCCTGTTGCCAGCACTCCAGCAAGTTAACCTA
TCCAATAACACCTTGACACGCGTCGGGATCTCGAAGCCAGTGGATGGCAGAAGCGACCTG
GTGGCGGTTGATCTGGGGTTCAACAAGATCCAAGGGTACTTGCCCGTGAATTTCGCTGAT
TATCCGATGCTGTCGTCTCTGTCGATGCGTTACAACCGATTACGCGGCGGTATCCCATTG
GAGTTCAGTCACAAGAAGTCTTTGAAGAGGCTGTTTCTGGATGGGAAC
STS source:
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): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
Rank as CAPS marker: no homozygous cultivar with minor allele
Comment: PCR_condition: 60C aneal
Figure legend: Restriction enzyme error: Lane3, 34-38 digested by Msp1.
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
Rsetriction enzyme: Hae3
Comment: PCR_condition: 56C aneal
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: PCR_condition: 56C aneal
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: Sty1
Comment: PCR_condition: 56C aneal
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: Hae3
Comment: PCR_condition: 56C 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: Jutaro unshu x Trovita orange
Restriction enzyme: Hae3
Comment: PCR_condition: 56C 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: Hha1
Comment: PCR_condition: 56C 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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10030023m
Scaffold: scaffold_8
Start: 2673135
End: 2674232

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00152:mRNA_38.1
Scaffold: C_unshiu_00152
Start: 273851
End: 275034
Gene function: DNA-damage-repair/toleration protein DRT100

AGI map info (Shimada et al. 2014)

AGI LG: AGI-08
AGI cM: 73.663

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-08
JtTr cM: 14.154

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

Km/O41 LG: NAT-081
Km/O41 cM: 10.596

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: SI178
DNA sequence around SNP1:
TTAACTCAGCTGGAAGTTATCGAACTCAG[T/C]GAAAACTCGTTCACCGGGACACTTGA
AGCGTGGTTCTTCCTGTTGCCAGCACTCCAGCAA
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: