Citrus CAPS Marker Database

Locus name: If0205

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 400
Comment on PCR:
F-primer: CCCATGGACTTCACTCAT
R-primer: AATTCATGTACGAAAACAAAC

EST info

EST Accession number 1: DC893468
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
TCAAAATTCTAAAGCAAATTCCGTAAGCATGATATCCCACTCCCAAACTTCAATGTTTCC
AAAATTTCCTTCGTTTCTCATTGTTCTCGTACCTTTCTTCTTGTGTTTTCAAACTTCCGA
AAGCCTAAAGTTCTTGGCTAGGGGCTCTTCTCTATCTATTGATGACAAATCAGACGTGTT
AACTTCCCCAGACAAAACATTCAC
STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read
STS:
TCTTCTCTGAAAACTTGAACATCAACAGGCTTCCACCATATCAAAATTCTAAAGCAAATT
CCGTAAGCATGATATCCCACTCCCAAACTTCAATGTTTCCAAATTTTCCTTCGTTTCTCA
TTGTTCTCGTACCTTTCTTCTTGTGTTTTCAAACTTCCGAAAGCCTAAAGTTCTTGGCTA
GGGGCTCTTCTCTATCTNTTGATGACAAATCAGACGTGTTAACTTCCCCAGACAAAACAT
TCACNTGTGGATTTTATAG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GTCTTCTCTG AAAACTTGAA CATCAACAGG CTTCCACCAT ATCAAAATTC TAAAG
CAAAT TCCGTAAGCA TGATATCCCA CTCCCAAACT TCAATGTTTC CAAATTTTCC
TTCGTTTCTC ATTGTTCTCG TACCTTTCTT CTTGTGTTTT CAAACTTCCG AAAG
CCTAAA GTTCTTGGCT AGGGGCTCTT CTCTATCTNT TGATGACAAA TCAGACGTG
T TAACT
STS source:
STS Forward / Reverse: Foward read
STS:
ACACGTGAATGTTTTGTCTGGGGAAGTTAACACGTCTGATTTGTCATCAANAGATAGAGA
AGAGNCCCTAGCCAAGAACTTTNGGCTTTCTGAAGTTTGAAAACACAAGAAGAAAGGTAC
GAGAACAATGAGAAACGAAGGAAAATTTGGAAACATTGAAGT
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): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
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

Experiments: Segregation pattern

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: 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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
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

Target on C. clementina (v1.0)

Transcript ID:
Scaffold:
Start:
End:

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00046:mRNA_66.1
Scaffold: C_unshiu_00046
Start: 551244
End: 556744
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 86.28

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 52.96

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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: SI256
DNA sequence around SNP1:
AAAGTTCTTGGCTAGGGGCTCTTCTCTATCT[A/G]TTGATGACAAATCAGACGTGTTAA
CTTCCCCAGACAAAACATTCAC
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: