Citrus CAPS Marker Database

Locus name: Tf0045

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 64
Main product (bp): 1000
Comment on PCR:
F-primer: GCCGCCGACGATGATAAGC
R-primer: CAGAAACCAAAGCCGCAACAA

EST info

EST Accession number 1: DC899852
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
CGTTGCCGCCTCCAGCCGTGGTGGTGATGGGTCTGCGGGCGAACTGCTCGGTGCTTGATT
TAAAGTCGAGGTTTGAGATCTACGGCGCCATCTCCCGCATCCGCATCGATCGCAATCGTC
TCGGATACATTACCTACCGGACAAAAGATTCTGCTGAAGCTGCCATTGCTGCTGCCCTTG
ATGCCTCCTTCGGCATCACAGTTGATTCACAAAAGGTATAAATAAATTCATGTTGTTTGG
TAAAATTGATTATTATTATTATTATTATTTTTTGGTTGGAGTCAAATTTTGATGCTTTTC
ATTTTTACGTTTGGTTATAGTGACTGAATTGGACTCAATTCAAGTTGATTTTCTGGTTCA
ATTGATTGCAGGAATTTCTAATTTTTTTTTTCCATGAGTTATCTTAGTTTCAAATTAGCA
AAATAAATAAAGAAAGCTTTTCAATTCAACCCTTTGCCTTTTCATACATGGCTTGAAGCG
TGACCTTTGCTTACGAATTTGACCTCGGCTCTTCCAAGTGCTGATATCTTCTTAATTCAG
TATTCTAAAGCTCTTGCGAGCGCTTAGACCATTCGAGTTCTTCTTCTCTTTGGTACCGTT
TGGTTTTAAAATTACAATCAGATACCGACATTGGTGTTCTTGTTGCAGGTCCAGGTTTTA
TGGGCAACAGATCCTCTAGCCCAATGGAAGGAAGCAGTGAAGAGTGGTGCCAATAAGGAC
ATTGGTTCATCTTCTAAGCTTTTGCGTGCTGAGGTGCCTCTCAGCAGACATGGAAGAGGC
ATTAAGCTTGCGTCAGCTATTGTTAACCCCAAAACTAGCGGTGACGGTTCTTCAGCTTTA
GAGGTGCCTTTCAGAGGCAGAGAGATCGTCGCTTATGATGACATCCTGTAACTTCAGAAC
TGATATTTGTGAGGACTTATCCTCCTTTGTAATATTAGATTTGAGTTTAGTTTTAGTTAG
AGTAGGTGGGTATGAAGTATGTGTAGCTAAATGTTGGAAGGGCGGTAGAGTGGAAT
STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

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

Experiments: CAPS pattern of hybrid cultivar

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: EcoR5
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: Hind3
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: Ciclev10032837m
Scaffold: scaffold_4
Start: 23496020
End: 23497466

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00001:mRNA_74.1
Scaffold: C_unshiu_00001
Start: 490607
End: 491890
Gene function: Homeobox transcription factor

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 74.573

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:

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: SI303
DNA sequence around SNP1:
TCTAGCCCAATGGAAGGAAGCAGTGAAGAGTGGTGCCAATAAGGACATTGGTTCATCTTC
[T/C]AAGCTTTTGCGTGCTGAGGTGCCTCTCAGCAGACATGGAAGAGGCATTAAGCTTG
C
SNP2: SI321
DNA sequence around SNP2:
AAAATAAATAAAGAAAGCTTTTCAATTCAACCCTTTGCCTTTTCATACATGGCTTGAAGC
[T/G]TGACCTTTGCTTACGAATTTGACCTCGGCTCTTCCAAGTGCTGATATCTTCTTAA
TTCAG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: