Citrus CAPS Marker Database

Locus name: Al0329

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 650
Comment on PCR:
F-primer: ATCTCTCATCGGAATGGAAGC
R-primer: AGATGAATGCAAGGCAAGGA

EST info

EST Accession number 1: DC892963
EST Accession number 2: DC892964

sequence-tagged site (STS seq)

STS:
CTCCTCNACTCCATCATGAAGTGTGATGTGGATATTAGAAAGGATCTGTATGGTAACATT
GNTCTCAGTGGGGGTTCAACTATGTTCCCNGGTATTGCCGACCGTATGAGCAAGGAAATC
ACAGCACTTGCTCCAAGCAGCATGAAGATCAAGGTCGTGGCTCCACCAGAGAGAAAATAC
AGTGTTTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAGGTGAGAAAT
TAATTACCATTCAATTTCTGTTGGCATTCCTGTTTTATTTACACTTCTTCAAAGTCTTGA
CAAAATTCATTGTATCCTTAACAGATGTGGATCTCAAAGGGCGAGTATGATGAGTCTGGT
CCATCCATTGTCCACAGGAAATGCTTCTAAGTTCTTTAAGTGCTTGATGGGTGAGTTCTT
TTTTTCCATTTAGTTGGTTTTTTGTGTCTCGTTTCGCGAACTCAAGTTGGTTGACATGGA
GAAGTGCTAAGGTTGGGGCCATTGAAGGAGGCATATCTCCATATTGATGTTATTATACAA
GCTTCTTACAGCGTTTGAGGGGGGCTTATTTCTGTACTCAACCGTCTTC
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read
STS:
GTGTGATGTGGATATTAGAAAGGATCTGTATGGTAACATTGGTCTCAGTGGGGGTTCAAC
TATGTTCCCCGGTATTGCCGACCGTATGAGCAAGGAAATCACAGCACTTGCTCCAAGCAG
CATGAAGATCAAGGTCGTGGCTCCACCAGAGAGAAAATACAGTGTTTGGATTGGAGGATC
AATCCTTGCATCCCTCAGCACCTTCCAGCAGGTGAGAAATTAATTACCATTCAATTTCTG
TTGGCATTCCTGTTTTATTTACACTTCTTCAAAGTCTTGA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CCAAGCAGCATGAAGATCAAGGTCGTGGCTCCACCAGAGAGAAAATACAGTGTTTGGATT
GGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAGGTGAGAAATTAATTACCATTC
AATTTCTGTTGGCATTCCTGTTTTATTTACACTTCTTCAAAGTCTTGACAAAATTCATTG
TATCCTTAACAGATGTGGATCTCAAAGGGCGAGTATGATGAGTCTGGTCCATCCATTGTC
CACAGGAAATGCTTCTAAGTTCTTTAAGTGCTTGATGGGTGAGTTCTTTTTTTCCATTTA
GTTGGTTTTTTGTGTCTCGTTTCGCGAACTCAAGTTGGTTGACATGGAGAAGTGCTAAGG
TTGGGGCCATTGAAGGAGGCATATCTCCATATTGATGTTATTATACAAGCTTCTTACAGC
GTTTGA
STS source: Chuukanbohon NO 5
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: Msp1
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: 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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
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: 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: Ciclev10025866m
Scaffold: scaffold_7
Start: 17201236
End: 17204282

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00421:mRNA_21.2
Scaffold: C_unshiu_00421
Start: 196945
End: 199790
Gene function: Actin

AGI map info (Shimada et al. 2014)

AGI LG: AGI-02
AGI cM: 25.162

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-02
KmMg cM: 11.218

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-02
JtTr cM: 7.174

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

Km/O41 LG: NAT-02S
Km/O41 cM: 5.552

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG: RP-02
Rp/Sa cM: 8.191

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: SI185
DNA sequence around SNP1:
GTGTGATGTGGATATTAGAAAGGATCTGTATGGTAACATTG[T/G]TCTCAGTGGGGGTT
CAACTATGTTCCC
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: