Citrus CAPS Marker Database

Locus name: If0206

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 800
Comment on PCR:
F-primer: ACTTCTTGCCTCTTTTCACTG
R-primer: ACCCCATTTGCTTCCA

EST info

EST Accession number 1: DC893495
EST Accession number 2: DC893496

sequence-tagged site (STS seq)

STS:

GGCGCTGGACTTTTCGCCGAGCAGCAAATTTGCTCTATCATGGGCTGTTAATAACTTGCT
TGATAAAGGTGACACTTTGTATATCATCCACATCAACCCCAATTCTCTTGACGAGTCTCG
TAACCTCATGTGGGCTAAATCTGGTTCCCGTAAGTATATTTCTTTTTGCTTATTTTCTGA
CTAATATCAGTTTCTTTGATCTTTGGCCTTTCTTAGCTGGCTACTTATGATTTGATCTGG
GAATTTTGTTTGGTTTTTTTGTTTTTTTTTTGCTA

STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read

STS:

GAATTTGGTTTTTTTTGTTTTTTTTTGCTAGCTCTTATTCCTCTGACTGAGTTCAGAGAG
CCTGAGACTATGGAGAAGTACAATGTTAAAACTGACATTGATGCGCTTGATTTGCTTGAC
ACTGCTTCTAGACAGAAAGAGGTAAATCTTTAACTTTTAGTTTTACTGGCCTTGGACATT
AATTAATTAAATCGTTACTTTGTTATGGTTGGATCGAATGTTTNGAATTGTAATGATGTG
ATTTTGCAGGCGAATATTGTTGCCAAAATTTACTGGGGAGATGCAAGAGAGAGGTTGCTT
GAAGCAATTGAAGATCTGAAGCTGGACTCTCTGGTTATGGGCAGCAGAGGACTTGGTACC
GTTCGAAGGTATGAAATTTTCACTTTTGTCATTTTTGGTTCTTGCTTGTCACCTACGGTG
ATAAAGTGCGACACAGACGCATATTGATGGGTGGTTGGTTGATGAAATGAAATGTAGGAT
AATTTTGGGAAGTGTGAGCAACTATGTGATGACTCATGCACCTTGCCCGGTGACCATCGT
CAAGGATCCAAGCTTCGGCAAGCACTGATCAAATATCACTAGGGCTTTAATTTACAGCCA
ATATCTTATGTTATCCTGAGTGAANTT

STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read

STS:

CTGTAAATTAAAGCCCTAGTGATATTTGATCAGTGCTTGCCGAAGCTTGGATCCTTGACG
ATGGTCACCGGGCAAGGTGCATGAGTCATCACATAGTTGCTCACACTTCCCAAAATTATC
CTACATTTCATTTCATCAACCAACCACCCATCAATATGCGTCTGTGTCGCACTTTATCAC
CGTAGGTGACAAGCAAGAACCAAAAATGACAAAAGTGAAAATTTCATACCTTCGAACGGT
ACCAAGTCCTCTGCTGCCCATAACCAGAGAGTCCAGCTTCAGATCTTCAATTGCTTCAAG
CAACCTCTCTCTTGCATCTCCCCAGTAAATTTTGGCAACAATATTCGCCTGCAAAATCAC
ATCATTACAATTCCAAACATTCGATCCAACCATAACAAAGTAACGATTTAATTAATTAAT
GTCCAAGGCCAGTAAAACTAAAAGTTAAAGATTTACCTCTTTCTGTCTAGAAGCAGTGTC
AAGCAAATCAAGCGCATCAATGTCAGTTTTAACATTGTACTTCTCCATAGTCTCAGGCTC
TCTGAACTCAGTCAGAGGAATAAGAGCTAGC

STS source: Chuukanbohon NO 5
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): A255(Okitsu46gou)/G434(Kankitsu Chuukanbohon Nou5)
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Msp1
Rank as CAPS marker: Dominant 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

Experiments: Segregation pattern

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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10012955m
Scaffold: scaffold_6
Start: 15192652
End: 15194091

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00034:mRNA_78.1
Scaffold: C_unshiu_00034
Start: 662958
End: 664402
Gene function: Universal stress protein A-like protein

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

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: SI208
DNA sequence around SNP1:

GCATCTCCCCAGTAAATTTTGGCAACAATATTCGCCTGCAAAATCACATCATTACAATTC
[T/C]AAACATTCGATCCAACCATAACAAAGTAACGATTTAATTAATTAATGTCCAAGGC
CAGTA

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: