Citrus CAPS Marker Database

Locus name: Tf0087

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 64
Main product (bp): 1200
Comment on PCR: PCR unstable
F-primer: TCCATGTTGCCATTGTAGAGG
R-primer: CTCTGTTGAGGCACCGAAAC

EST info

EST Accession number 1: CD573723
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

TTTCGTTAATTTTTTACATAGCAATGTCTATGTGCAAAGTAAGGGTTCTTTGTTCACAAA
CTCCAGACCTCCAAAATAGAAGGGAACAATCTTTGTTGTCTGAGGCTAGCTGTTTCTTGA
CAATGCTTTTAGTGGCTTTGCATTCCTCATTCATCTTTTGTTAATTATTTCCCAATGATG
CCAGCAGCTAACAGTATTGCAAGATTCACTTTATTTAATTTGTTAGCTCAAAAATTATTT
TGATAAATTTCCCATTTAGATAAATAGATCCTGATTGCATTTTTCATTGTTTCTGTATGG
TTTTCATCCCATTCATGGATGTAGGTAACCACAAGCAACACTGATGGAAGTTTTAAGTTT
CTTGAAACTGCAAAGGATTTGCCTACTATTAGTAAGTTCCGAAACTACACTTATATCTTC
AGGTTGTATTTATACCTTTGTCTTTGGGGGCTCTATATTTTAGCTTGTTAAAAGTTTCTT
ATTAAATTTTCAAGTTTATTTTTTCCGTTATCAACATCAACACTTGCGTGGTGTTAGAAA
CATATTAATGATTGCTTTCACTGAACATGTTGCACACTTCTAATGCAGTACGTACTTTCT
TCTATTGCAGTAACTTCAAATATTCATTGCTTGAGCACCATGATGAAGTGCATAGCGGTG
AGATTTATTCTAATCTCCATGCACTGCTCAATGTTCATTTAATTAGTTTATTGTGAAATG
CACGTGTGAACGGACTTGATTTATTTCACAGATCATGGTTATGAATCAATTATTTGACAA
TAATTTTCAGCTAGGTGCAGTTGAATTCCTCCGGAAACCACTTTCAGAGGATAAACTCAG
GAACTTATGGCAGCATGTGGTTCATAAGGTACATTTCAGTTCTGCTTATTGTTGCAATTT
ACTGTGAAACAAATGGTAATGCTGTGAGAGAACAGGTCTAATATTTTAATTCCTGTGCAG
GCATTCAATGCTGGGGGAAGCGCCCTCTCTGATTCAATAAAGCCTGTGAAAGAATCCGTG
GTTTCCATGCTGCATCTTAAATTGGAAAATGGAGAATCCAAGAACGAGAAGTCGGAG

STS source:
STS Forward / Reverse: Foward read

STS:

TACGTACTTTCTTCTATTGCAGTAACTTCAAATATTCTTTGCTTGAGCACCATGATGAAG
TGCATAGCGGTGAGATTTATTCTAATCTCCATGCACTGCTCAATGTTCATTTAATTAGTT
TATTGTGAAATGCACGTGTGAACGGACTTGATTTATTTCACAGATCATGGTTATGAATCA
ATTATTTGACAATAATTTTCAGCTAGGTGCAGTTGAATTCCTCCGGAAACCACTTTCAGA
GGA

STS source:
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

Experiments: CAPS pattern of Citrus collection

Experiments: Segregation pattern

Target on C. clementina (v1.0)

Transcript ID: Ciclev10031120m
Scaffold: scaffold_4
Start: 11412331
End: 11417624

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00019:mRNA_18.1
Scaffold: C_unshiu_00019
Start: 190344
End: 195992
Gene function: Two-component response regulator-like APRR2

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 35.897

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: SI166
DNA sequence around SNP1:

CATGTTGCACACTTCTAATGCAGTACGTACTTTCTTCTATTGCAGTAACTTCAAATATTC
[A/T]TTGCTTGAGCACCATGATGAAGTGCATAGCGGTGAGATTTATTCTAATCTCCATG
CACTG

SNP2: SI271
DNA sequence around SNP2:

TTTCGTTAATTTTTTACATAGCAATGTCTATGTGCAAAGTAAGGGT[T/G]CTTTGTTCA
CAAACTCCAGACCTCCAAAATAGAAGGGAACAATCTTTGTTGTCTGAGGCT

SNP3: SI287
DNA sequence around SNP3:

CCTCATTCATCTTTTGTTAATTATTTCCCAATGATGCCAGCAGCTAACAG[T/C]ATTGC
AAGATTCACTTTATTTAATTTGTTAGCTCAAAAATTATTTTGATAAATTTC

SNP4:
DNA sequence around SNP4: