Citrus CAPS Marker Database

Locus name: Al0415

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 2400
Comment on PCR:
F-primer: TCCATCTCCCGAAGCCATTG
R-primer: AATTGCCCTGCCTTTTCCAGA

EST info

EST Accession number 1: C95396
EST Accession number 2: DC892985

sequence-tagged site (STS seq)

STS:
NGTAATTTTTCAAGNCTGCACGTTTATAATATACTGGCTGCTAAATGGTTTTTGATGTAG
CAGGTGCCGCAAGACCTGGGAAAGTTGTCAGTTCAGTGTTGCGTTACAACAATTGTGGAG
CAGCAGCAGCTGCAGAGGCTCTTGATCAGCGGAGAGTGGTTAGGAATCCTGCTGTTTCAA
CTCAATATGCTGCCAGTTCATATCCAAGAAGAAGCTCAGCATGTAAAAACGAGAGGGTGA
ATGATGAATCTGTTGAAGGTTCCAATGGATTGCAGCCAAAGCCTCAGTACATAGCAAGGA
AAGTTGCTGCTGCTCAAGGTGGTTCTGGAAGCAACTGGTATTGATTCATTGCTATGTCGT
TCCTACAGTGGACTCAACCGTCTACACTCCGCTTGATGATGCTAGTTACACAGCATCCAA
GATTGATCTGCTCGCAAGTGGTAAATATCAGACACGGTATGTTTTCCTGGTGCTACATAC
NATCTCAGAGTTTAAAGGATTAGGAGTTTGATATTTTATGTTGGAGAAAGCCCTAAAAGT
TGTAATTTATAGCACTAACTGAAAACGTAGGAGGGGTTAGTTCGGGTTCAACTGTCCACG
ACCCTCTTCC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
CCGAACTAACCCCTCCTACGTTTTCAGTTAGTGCTATAAATTACAACTTTTAGGGCTTTC
TCCAACATAAAATATCAAACTCCTAATCCTTTAAACTCTGAGATGGTATGTAGCACCAGG
AAAACATACCGTGTCTGATATTTACCACTTGCGAGCAGATCAATCTTGGATGATGTGTAA
CTAGCATCATCAAGCGGAGTGTAGACGGTTGAGTCCACTGTAGGAACGACATAGCAATGA
ATCAATACCAGTTGCTTCCAGAACCACCTTGAGCAGCAGCAACTTTCCTTGCTATGTACT
GAGGCTTTGGCTGCAATCCATTGGAACCTTCAACAGATTCATCATTCACCCTCTCGTTTT
TACATGCTGAGCTTCTTCTTGGATATGAACTGGCAGCATATTGAGTTGAAACAGCAGGAT
TCCTAACCACTCTCCGCTGATCAAGAGCCTCTGCAGCTGCTGCTGCTCCACAATTGTTGT
AACGCAACAC
STS source:
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: EcoR1
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: 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: 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: 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: Kiyomi x Okitsu41gou
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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10004660m
Scaffold: scaffold_9
Start: 2732900
End: 2738896

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00040:mRNA_76.1
Scaffold: C_unshiu_00040
Start: 632823
End: 638463
Gene function: Mitogen-activated protein kinase 14

AGI map info (Shimada et al. 2014)

AGI LG: AGI-03
AGI cM: 24.885

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-031
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

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

Km/O41 LG: NAT-03
Km/O41 cM: 41.576

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: SI120
DNA sequence around SNP1:
AACTTTTAGGGCTTTCTCCAACATAAAATATCAAACTCCTAATCCTTTAAACTCTGAGAT
[A/G]GTATGTAGCACCAGGAAAACATACCGTGTCTGATATTTACCACTTG
SNP2: SI310
DNA sequence around SNP2:
TGTGTAACTAGCATCATCAAGCGGAG[A/T]GTAGACGGTTGAGTCCACTGTAGGAAC
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: