Citrus CAPS Marker Database

Locus name: Al0304

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 54
Main product (bp): 450
Comment on PCR:
F-primer: CGCAGATACCAGACACCAG
R-primer: GAGAAACCTCCGCATAATGAT

EST info

EST Accession number 1: C95332
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
CCCCAAAACCAGTATAAAGTGTGGCACATGCCCTTGTGTGACCCATGTGGTCAGCTCCCC
CCTCCACCACCGCCTCCGCCGCCACCACCATCGCCGCCAAAGACTACATACTGTCCTCCG
CAGGTGCAGACACCGCCGCCACCCAGGTTCATCTATGTGACTGGTGAGCCTGGGGAAATT
TACCACACTGATTCTGATGACTGGGGGTTTTACTCGACTGCTCAACCAAATGTGGCTAAA
AATCGGTTGCTTTTGGCTGCATGTGGTGTGTTGGGGCTCTTCATAATTTGGTAAAATTAA
TGTAATATTGTGATCAAACATCTTAGATCTTGACAGTGTCAGTATCCTACATGCTACATA
TACTTGTTAATTTCTCTCTTCATTCGAATTGATCATGTTTTATTTTGATAAGTGGACAAA
ATCATTA
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
CCACCACCATCGCCGCCAAAGACTACATACTGTCCTCCGCAGGTGCAGACACCGCCGCCA
CCCAGGTTCATCTATGTGACTGGTGAGCCTGGGGAAATTTACCACACTGATTCTGATGAC
TGGGGGTTTTACTCGACTGCTCAACCAAATGTGGCTAAAAATTGGTTGCTTTTGGCTGCA
TGTGGTGTGTTGGGGCTCTTCATAATTTGGTAAAATTAATGTAATATTGTGATCAAATAT
CTTAGATCTTGACAGTGTCAGTATCCTACATGCTACATGTACTTGTTAATTTCTCTCTTC
ATTCGAATTGATCATATTTTATTTTGATAAGTGGACAAAATCATT
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GTGTGACCCATGTGGTCAGCTCCCCCCTCCGCCACCACCGCCTCCGCCGCCGCCNCCACC
ACCATCGCCGCCAAAGACTACATACTGTCCTCCGCAGGTGCAGACACCGCCGCCACCCAG
GTTCATCTATGTGACTGGTGAGCCTGGGGAAATTTACCACACTGATTCTGATGACTGGGG
GTTTTACTCGACTGCTCAACCAAATGTGGCTAAAAATCGGTTGCTTTTGGCTGCATGTGG
TGTGTTGGGGCTCTTCATAATTTGGTAAAATTAATGTAATATTGTGATCAAACATCTTAG
ATCTTGACAGTGTCAGTATCCTACATGCTACATATACTTGTTAATTTCTCTCTTCATTCG
AATTGATCATGTTTTATTTTGATAAGTGGACAAAATCATTANGGGGNAGGTTTCTCAA
STS source: Okitsu 46
STS Forward / Reverse:

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: Rsa1
Rank as CAPS marker: Disagree by Marco analysis
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Hinf1
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: Rsa1
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: Rsa1
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: Rsa1
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: Rsa1
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: Ciclev10013536m
Scaffold: scaffold_6
Start: 22616979
End: 22619271

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00038:mRNA_27.1
Scaffold: C_unshiu_00038
Start: 174815
End: 175255
Gene function: Nutrient reservoir, putative

AGI map info (Shimada et al. 2014)

AGI LG: AGI-04
AGI cM: 46.361

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 16.744

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-04
Km/O41 cM:

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

Rp/Sa LG: RP-04
Rp/Sa cM: 54.617

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: SI259
DNA sequence around SNP1:
TACTTGTTAATTTCTCTCTTCATTCGAATTGATCAT[A/G]TTTTATTTTGATAAGTGGA
CAAAATCATTANGGGGNAGGTTTCTCAA
SNP2: SI293
DNA sequence around SNP2:
CACACTGATTCTGATGACTGGGGGTTTTACTCGACTGCTCAACCAAATGTGGCTAAAAAT
[T/C]GGTTGCTTTTGGCTGCATGTGGTGTGTTGGGG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: