Citrus CAPS Marker Database

Locus name: Al0413

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1100
Comment on PCR:
F-primer: ATACCATTCCGGTCCTGAAAG
R-primer: GCTCCACTTGCTCCAAACA

EST info

EST Accession number 1: C95392
EST Accession number 2: DC892983

sequence-tagged site (STS seq)

STS:
CGTGCCTTCAAAGACAAGTTCAAGGACACTTCTTGGTGACACCATTGTGGTAAATACTCA
CATAACTTGTTAATACTTTTCAATTTAGATTGTTAAAGTAGAAGGCTGGTTGATGAATGC
TAAATTATTTGTTACATATAGGAAATCCAAGTGGGAATGGGTCCAGCTGGTGAGCTGCGT
TACCCTTCGTATCCAGAGCAGAATGGGACATGGAAATTCCCAGGAATTGGAGCTTTCCAG
TGTTATGATAAGGTATTTGCTAATTTTTTTTTTCTTGNGTTGTTTTGAGTCTGGTAAATT
TGCGGNGGGATTTGTAGCGNGTGGTTCTCATATTGG
STS source: Okitsu 46
STS Forward / Reverse: Foward read
STS:
GTTTGGAGTTCTGGTAAATTTGCGGTGGGATTNGTAGCGTGTGGTTCTCATATTGGTGTT
TGATGTCTTGATGCAGTATATGCTCAGTAGCTTAAAAGCAGCAGCTGAATCTGCTGGTAA
GCCAGAATGGGGCAGCACAGGCCCTACTGATGCTGGACATTACAACAACTGGCCAGAAGA
TACACAGTTTTTCCGAAAAGAAAATGGTGGTTGGTGTAGCCCTTATGGTGAATTTTTCCT
AAGCTGGTATTCGCAGATGCTCTTAGATCACGGAGAGAGAATTCTCTCATCTGCCAAGGC
AATTTTCGATGCTACAGGTGTTAAGATCTCGGTTAAGGTTGCAGGAATCCACTGGCACTA
TGGGTCTAGGTCCCATGCCCCTGAGCTCACAGCTGGATATTACAATACACGATTCCGTGA
TGGTTACCTCCCTATTGCCCAGATGCTAGCACGACATGGTGCCATATTCAACTTTACTTG
CATAGAGATGCGTGATCATGAACAACCACAAGATGCCCTTTGTGCACCTGAGAAGCTAGT
CAAGCAAGTGGCTTCAGCAACTCAGAAAGCACACGTTCCACTGGCTGGGGAAAATGCGTT
GCCACGTTATGATGAATACGCTCACGAGCAGATCTTGCGAGCAGCATCACTTGATGTAGA
CAAACAGATGTGTGCATTCACGTACTTGAGGATGAATCCACATTTATTCCAACCCGATAA
TTGGAGACAGTTTGTGGC
STS source: Okitsu 46
STS Forward / Reverse: Reverse read
STS:
AATAAATGTGGATTCATCCTCAAGTACGTGAATGCACACATCTGTTTGTCTACATCAAGT
GATGCTGCTCGCAAGATCTGCTCGTGAGCGTATTCATCATAACGTGGCAACGCATTTTCC
CCAGCCAGTGGAACGTGTGCTTTCTGAGTTGCTGAAGCCACTTGCTTGACTAGCTTCTCA
GGTGCACAAAGGGCATCTTGTGGTTGTTCATGATCACGCATCTCTATGCAAGTAAAGTTG
AATATGGCACCATGTCGTGCTAGCATCTGGGCAATAGGGAGGTAACCATCACGGAATCGT
GTATTGTAATATCCAGCTGTGAGCTCAGGGGCATGGGACCTAGACCCATAGTGCCAGTGG
ATTCCTGCAACCTTAACCGAGATCTTAACACCTGTAGCATCGAAAATTGCCTTGGCAGAT
GAGAGAATTCTCTCTCCGTGATCTAAGAGCATCTGCGAATACCAGCTTAG
STS source:
STS Forward / Reverse: Reverse read
STS:
AATTTTCGAT GCTACAGGTG TTAAGATCTC GGTTAAGATT GCAGGAATCC ACTGG
CACTA TGGGTCTAGG TCCCATGCCC CTGAGCTCAC AGCTGGATAT TACAATACAC
GATTCCGTGA TGGTTACCTC CCTATTGCCC AGATGCTAGC ACGACATGGT GCCA
TATTCA ACTTTACTTG CATAGAGATG CGTGATCATG AACAACCACA AGATGCCCT
T TGTGCACCT
STS source:
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: Msp1
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: 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
Population name: Jutaro unshu x Trovita orange
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
Population name: Kiyomi x Miyagawa-wase
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: Ciclev10004620m
Scaffold: scaffold_9
Start: 7579900
End: 7583093

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00063:mRNA_61.1
Scaffold: C_unshiu_00063
Start: 483279
End: 486427
Gene function: Chloroplast beta-amylase 3

AGI map info (Shimada et al. 2014)

AGI LG: AGI-03
AGI cM: 46.197

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-032
KmMg cM: 19.57

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-031
JtTr cM: 10.395

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-03
Rp/Sa cM: 33.559

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: K

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI275
DNA sequence around SNP1:
TGGATATTACAATACACGATTCCGTGATGGTTACCTCCCTATTGCCCAGATGCTAGCACG
[A/G]CATGGTGCCATATTCAACTTTACTTGCATAGAGATGCGTGATCATGAACAACCAC
AAGAT
SNP2: SI299
DNA sequence around SNP2:
ATCTTGTGGTTGTTCATGATCACGCATCTCTATGCAAGTAAAGTTGAATATGGCACCATG
[T/C]CGTGCTAGCATCTGGGCAATAGGGAGGTAACCATCACGGAATCGTGTATTGTAAT
ATCCA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: