Citrus CAPS Marker Database

Locus name: If0003

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 62
Main product (bp): 1600
Comment on PCR:
F-primer: GACAATCAATCACCCGTCGTT
R-primer: TTGAGGCAGGGGCTGAAT

EST info

EST Accession number 1: DC893584
EST Accession number 2: DC893585

sequence-tagged site (STS seq)

STS:
ATGGAGCATGCCTATTCAGTACAAGGACTCAATTATGGAATCTACTTTGAATTGTCGGCA
GAATGGTAGTCTCTTTGATGTCTCCCATATGTGTGGGCTGAGCCTCAAAGGGAAGGATTG
CGTCCCTTTCCTTGAGAAGCTTGTGATCGCTGATGTTGCTGGACTTGCCCCAGGAACTGG
GACTCTTACAGTCTTTACAAATGAAAATGGGGGTTCAATTGATGATTCAGTTATTACCAA
GGTGAAGGATGATCACATATACCTTGTTGTGAATGCTGGCTGCAGGGATAAGGATCTTGC
TCACATTGAGGCACATATGAAGAGTTTCACAGCCAAAGGTGGGGATGTCTCG
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read
STS:
CTTTGCCTCAGATGCTGAAAACCTNAAAAAAACTGCCCTTCATGACTTTCATGTGGCTAA
TGGTGGAAAGATGGTTCCATTTGCTGCGATGGAGCATGCCTATTCAGTACAAGGACTCAA
TTATGGAATCTACTTTGAATTGTCGGCAGAATGGTAGTCTCTTTGATGTCTCCCATATGT
GTGGGCTGAGCCTCAAAGGGAAGGATTGCGTCCCTTTCCTTGAGAAGCTTGTGATCGCTG
ATGTTGCTGGACTTGCCCCAGGAACTGGGACTCTTACAGTCTTTACAAATGAAAATGGGG
GTTCAATNGATGATTCAGTTATTACCAAGGTGAAGGATGATCACATATACCTTGTTGTGA
ATGCTGGCTGCAGGGATAAGGATCTTGCTCACATTGAGGCACATATGAAGAGTTTCACAG
CCAAAGGTGGGGATGTCTCGTGGCACATCCATGATGAGAGATCTCTTCTTGCCCTTCAGG
TTACTCAGTGCACTGTTATAGTCTTTTACCTGGCCTTGCTTTTGTTTCACCCCTTGCTTG
AGATGTGATGAATTTAGTTCAGTTTCTCAGAGTTAATATTCTTTATATTTCTAGATANGG
TATCTGTGCTAGGTATGTGTGTATCTGAATTGATTTATCTCTTCANCAATTGTTTATTCC
TATTTGAAGTCTTCATGAATTAGAATAGATCCGCAACAAATAATGGCCGTATGGCAGGCT
CAAAGTTGATGATTANCGTTTCTTCACCG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
TTTTTTGGTACCATATACATTTCAAGTTCTTCTGTCTTTATTATAAGTTGTATGAATAGG
CTGTTCGGGATTTTTAACTACCTTTTTTTGTCTATTACAATTCTCAGGTACACTGGTGAA
GATGGATTTGAAATCTCTGTTCCATCTGAGCGTGCAGTGGATCTTGCCAAAGCAATTCTG
GAGAAATCTGAAGGAAAGGTGAGGTTGACAGGTNCTNCGGTGCTTNGAGGAGCACGTGCT
GCCGACTTGACACGCTAGGCTTAATGGTTTATGAT
STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read
STS:
GGAGCATGCC TATTCAGTAC AAGGACTCA ATTATGGAATC TACTTTGAAT TGTCG
GCAGA ATGGTAGTCT CTTTGATGTC TCCCATATGT GTGGGCTGAG CCTCAAAGGG
AAGGATTGCG TCCCTTTCCT TGAGAAGCTT GTGATTGCTG ATGTTGCTGG ACTT
GCCCCA GGAACTGGGA CTCTTACAGT CTTTACAAAT GAAAATGGGG GTGCAATNG
A TGATTCGGTT ATTACCAAGG TGAAGGATGA TCACATATAC CTTGTTGTGA ATG
CTGGCTG CAGGGATAAG GATCTTGCTC ACATTGAGGC ACATATGAAG AGTTTCAC
AG
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:
Compared cultivars (Left, (Middle), Right): Trovita orange/Kiyomi/Miyagawa-wase
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: EcoR1
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

Experiments: Segregation pattern

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: EcoR1
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: EcoR1
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: EcoR1
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: Nde2
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: Ciclev10015433m
Scaffold: scaffold_2
Start: 35470078
End: 35472862

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00048:mRNA_13.1
Scaffold: C_unshiu_00048
Start: 64652
End: 67377
Gene function: Aminomethyltransferase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 18.136

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-06S
JtTr cM: 67.371

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: SI130
DNA sequence around SNP1:
TATGTGTGGGCTGAGCCTCAAAGGGAAGGATTGCGTCCCTTTCCTTGAGAAGCTTGTGAT
[T/C]GCTGATGTTGCTGGACTTGCCCCAGGAACTGGGACTCTTACAGTCTTTACAAATG
AAAAT
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: