Citrus CAPS Marker Database

Locus name: Ov0408

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1600
Comment on PCR:
F-primer: TGTATCGACGGTGGAGATTG
R-primer: CACTGACGCTGCTTTAGGTTC

EST info

EST Accession number 1: AU186532
EST Accession number 2: DC893954

sequence-tagged site (STS seq)

STS:

AATCCCCTACCCCAGGAAAAGTCCCCTATTCTTCCCTCGAAACCAAAAAAACCCACGTCA
AAGAAGCTGTCGCTAAGCTCACTGGGTCACCTGACTCGCCAACACTTGCCGGATTTGTTC
TCGACATGTTCTGCATGTGCATGGTTGACGTTGCAGATGAACTTAGGGTTCCTAGTTATG
TCTTCTTCACGTCGAGTGCAGCTTCATTGGGTTCCTTTCTTAACGGCCAAGCTCTTTACG
ACCAAAACAAGCTCACCACTGAGTTGATAGACTCGGGTGCTGATTTGCAAGTTCCGACGC
TTGTGAACTCAATTCCTGCTAGGCTTTTGCCTAGTTCTTTTTTTGATAAAGAGTGGGGCG
AATTTTTATTTGGGCAAGCAAGAAGGTACAGACTTGTTAAGGGCATAATGGTAAACACAT
TTGAAGAGCTAGAACCCTACGCAGTCAAGTCTCTCTACGATGGTAAGATTAAGATTCCGC
CGGTTTATGCCGTGGGGCCCGTTGTGAATA

STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read

STS:

TTTCCTTCCAGATGACAACCAATCCCCTACCCCAGGAAAAGTCCCCTATTCTTCCCTCGA
AACCAAAAAAACCCACGTCAAAGAAGCTGTCGCTAAGCTCACTGGGTCACCTGACTCGCC
AACACTTGCCGGATTTGTTCTCGACATGTTCTGCATGTGCATGGTTGACGTTGCAGATGA
ACTTAGGGTTCCTAGTTATGTCTTCTTCACGTCGAGTGCAGCTTCATTGGGTTCCTTTCT
TAACGGCCAAGCTCTTTACGACCAAAACAAGCTCACCACTGAGTTGATAGACTCGGGTGC
TGATTTGCAAGTTCCGACGCTTGTGAACTCAATTCCTGCTAGGCTTTTGCCTAGTTCTTT
TTTTGATAAAGAGTGGGGCGAATTTTTATTTGGGCAAGCAAGAAGGTACAGACTTGTTAA
GGGCATAATGGTAAACACATTTGAAGAGCTAGAACCCTACGCAGTCAAGTCTCTCTACGA
TGGTAAGATTAAGATTCCGCCGGTTTATGCCGTGGGGCCCGTTGTGAATATCACAGGGGN
ACAATTATGCTTTGGGACCCGGAGGAATTGAGAANAAAGCTGAAGTTATGACGTGGCTGG
ATGATCNACCGGTATCATCAGTCGTGTTCCTGTGCTTCGGGAGCAGGGGATGCTTCNATG
TGGATCAAGCAAGAGAGATCGCGCATGCG

STS source: Okitsu 46
STS Forward / Reverse: Foward read

STS:

GTAAACACATTTGAAGAGCTAGAACCNTACGCAGTCAAGTCTCTCTACGATGGTAAGATT
AAGATTCCCCCCGGTTTATGCCGTGGGGGCCCGTTGTGAATATCACAGGGGACAATTATG
CTTTGGGACCCGGAGGAATTGAGAAGAAAGCTGAAGTTATGACGTGGCTGGATGATCAAC
CGGTATCATCAGTCGTGTTCCTGTGCTTCGGGAGCAGGGGATGCTTCGATGTGGATCAAG
CAAGAGAGATCGCGCATGCGCTAGAACAATGCGGACACCGGTTCTTGTGGTCCCTACGTC
AGGCCCCAACCGAGGATAAGACCGAACTGCCGAGTGATTACGCAGATCTCAAGGGCGTAC
TGCCGGGAGGGTTTTTGGATCGAACGGCTGAGATAGGGAAGGTGATTGGGTGGGCCCCGC
AGGTTGCTGTGCTGAGCCATCCCGCGGTTGGAGGGTTCGTATCGCACTGCGGGTGGAATT
CAACGCTAGAGAGTATTCGGTTTGGCGTTCCGATCGCCACGTGGCCGATGTACGCCGAGC
AACAGGCTAATGCGTTTCAGTTGGTGATAGAGTTGGGACTGGCGGTGGAGATTAAAATGG
ATTATAGGAAGGATATTTTCAATAAAATTCCAACGATGGTTACTGCTGAGGAGATTGAGA
GAGGAATCAAGTGCTTGATGAATCCTGAGAGCGAGATTCGGAAAAGAGTGAAGGAAATGA
GTGAGAAAGCTGGAAGAGCGGTGAGTGGAC

STS source: Okitsu 46
STS Forward / Reverse: Reverse read

STS:

GCTTTCTCACTCATTTCCTTCACTCTTTTCCGAATCTCGCTCTCAGGATTCATCAAGCAC
TTGATTCCTCTCTCAATCTCCTCAGCAGTAACCATCGTTGGAATTTTATTGAAAATATCC
TTCCTATAATCCATTTTAATCTCCACCGCCAGTCCCAACTCTATCACCAACTGAAACGCA
TTAGCCTGTTGCTCGGCGTACATCGGCCACGTGGCGATCGGAACGCCAAACCGAATACTC
TCTAGCGTTGAATTCCACCCGCAGTGCGATACGAACCCTCCAACCGCGGGATGGCTCAGC
ACAGCAACCTGCGGGGCCCACCCAATCACCTTCCCTATCTCAGCCGTTCGATCCAAAAAC
CCTCCCGGCAGTACGCCCTTGAGATCTGCGTAATCACTCGGCAGTTCGGTCTTATCCTCG
GTTGGGGCCTGACGTAGGGACCACAAGAACCGGTGTCCGCATTGTTCTAGCGCATGCGCG
ATCTCTCTTGCTTGATCCACATCGAAGCATCCCCTGCTCC

STS source: Okitsu 46
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: Hinc2
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

Experiments: Segregation pattern

Population name: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Dra1
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: Ciclev10011522m
Scaffold: scaffold_6
Start: 18491789
End: 18493623

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00248:mRNA_30.1
Scaffold: C_unshiu_00248
Start: 247183
End: 248778
Gene function: UDP-glycosyltransferase 71C4

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-04
KmMg cM: 50.902

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-04
Rp/Sa cM: 23.745

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:
DNA sequence around SNP1:

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: