Citrus CAPS Marker Database

Locus name: Tf0026

CAPS PCR info

PCR Anneal-Temp (℃) / Method: Td
Main product (bp): 2000
Comment on PCR:
F-primer: TGGAGATGAGGTAAGCGAATC
R-primer: CTGACGCAGAGTGCTAGGGT

EST info

EST Accession number 1: DC898171
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GGAGTAAGGTGAATATCCGATGCTCGAACGGCACAAAATTTTCGGTGGATATCGATCTGG
AATCCAGCGTTGAAACATTCAAAGCGGCGTTGGCGGAAAAGTGCGAGGTTCCGCCTCAGC
AACAGCGGTTGATTTATAAAGGTCGGATCTTGAAGGACGATCAAACCCTCAAAAGCTATG
GTACGATACAACTAATAATTCCGTCATTTTTCTAATTTTTAATTTTTTATTAGTTCCGTC
ATTTTTTTTCCTTATTTCGTTTTCTTTTCTGGATTTACTGGAGTTTNTTTTTTTGATTAA
GGGTTAGGTGCCTAATTTGTGGTTGGTTTTATGGTTATGATCTGATTTTGGGGATTTTAA
ACTTTTAACTTTTCGTTGAATTGCTTTAACAACGATTAACCTTGCGGGAAAAATTTACAA
ATGGTCTTAGGTAACCCTAGACTCATGTTTATGGCCCCATTTAGTTTGCGATTGAGGCTT
ACTTGAGTCCGATGAGGATTTTTGGAGTCGCAA-GTCTAGCTTTCGCGTTGACTTCTACA
TTTTTTTTTTTT
STS source:
STS Forward / Reverse: Foward read
STS:
TACTGGTAATAAGTAGATAACAATGTATCATATGAACTTATTAGAGGTGTCATTTTTGGG
AGTATGGTTCTCATCTTGGCTAGCTTTCAAGCACCACTTTCTGTTATGCTTATTATTCTG
CAATGTTTTTGTTGCCTTCTTGCTCCATTGTTTTGGATTTGTGTCAGAATATTCTTGGTA
TAGTTTTCACTGCTATGATATTTTCTGTAGAATCATATTACATACCCTTTAACGGGAGCC
CTCTTTTTAGCATGTGCAACATAGATCTTTATGGTATTCTAAGTTTATTTGATGT
GCTTATTGAATTATTGAAGCTTGGCCAGGTAAAACTTTGTAGAATTAAGGAAGAACTGCT
TGCTGAATGTTGTGGCCACTCCTTTTTTATTTTCATGGTTAGGTTTGGAGGCAGATCACA
CTGTGCACTTGGTTCGTGGTTTTGCACCTGCTGCATCTACAAACAATGCTGCGCCAACCA
ACTCTGGAGGTTCAACTACTACTCCAAACAGCACAAGGCCCGTGAGTACTAATGAAGGTG
ATGCTCTTGGAGGAGCTGGTCTTGGAGCTTCTCTGTTTCCTGGACTTGGCATCAATGGTT
TAGGTGGCAGCGGAGGTGGTTTGTTTGGAGCTGGACTTCCAGAATTTGAACAAGTGCAGC
AACAACTGACCCGGAACCCCAACATTATGAGAGAGATCATGAATATGCCTGTCGTGCAGA
ATCTTATGAATAACCCTGAGATAATGCGAAACTTGATAATGAACAATCCTCAAATGCGTG
AAATTATTGATCGAAACCCTGAGCTAGCACA
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:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Experiments: CAPS pattern of Citrus collection

Rsetriction enzyme: Hinc2
Comment: DNA sample: New CCN
Figure legend:
CV (No.1 Top) 101 Tahiti, 100 Rangpurlime, 102 Limonia, 104 LisbonL, 99 SweetLime, 92 Hirado, 87 MGF, 85 Kinukawa, 84 Hassaku, 83 Yamamikan, 78 Natsudaidai, 58 Rokugatu, Tr Trovita, 50 WNV, 44 Tankan, 42 Iyo,
(No.1 Bottom) 39 HgNt, 36 Ujukitsu, 32 Kawabata, 30 Shunkokan, 70 Yuzu, 54 Henka, 53 Ichang lemon, 37 Kunenbo, Mg Miyagawa, 31 Yatsushiro, 27 Kabuchii, 26 Ponkan, 25 Medet. 22. Dancy, 14 Tachibana, 11 Hirakishu (26' Ohta ponkan)
(No.2 Top) 6 Cleopatra, 4 CQ, 2 Fukuremikan, FD Hiryuu, 124 Largeleaf, 125 Small leaf, 141 CTV-S, 136 Rubidoaux,
(No.2 Bottom) FD, Hassaku, Km, F1, RP94, SA, 02, 04, 05, 06, 07, 08, 09, 10, 11, 13
BDZ BenDi Zao, SO Shuto, BP Banpeiyu
Rsetriction enzyme: Hind3
Comment: DNA sample: New CCN
Figure legend:
CV (No.1 Top) 101 Tahiti, 100 Rangpurlime, 102 Limonia, 104 LisbonL, 99 SweetLime, 92 Hirado, 87 MGF, 85 Kinukawa, 84 Hassaku, 83 Yamamikan, 78 Natsudaidai, 58 Rokugatu, Tr Trovita, 50 WNV, 44 Tankan, 42 Iyo,
(No.1 Bottom) 39 HgNt, 36 Ujukitsu, 32 Kawabata, 30 Shunkokan, 70 Yuzu, 54 Henka, 53 Ichang lemon, 37 Kunenbo, Mg Miyagawa, 31 Yatsushiro, 27 Kabuchii, 26 Ponkan, 25 Medet. 22. Dancy, 14 Tachibana, 11 Hirakishu (26' Ohta ponkan)
(No.2 Top) 6 Cleopatra, 4 CQ, 2 Fukuremikan, FD Hiryuu, 124 Largeleaf, 125 Small leaf, 141 CTV-S, 136 Rubidoaux,
(No.2 Bottom) FD, Hassaku, Km, F1, RP94, SA, 02, 04, 05, 06, 07, 08, 09, 10, 11, 13
BDZ BenDi Zao, SO Shuto, BP Banpeiyu

Experiments: Segregation pattern

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: Ciclev10025369m
Scaffold: scaffold_7
Start: 285299
End: 292550

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00312:mRNA_28.1
Scaffold: C_unshiu_00312
Start: 151229
End: 158232
Gene function: Ubiquilin

AGI map info (Shimada et al. 2014)

AGI LG: AGI-02
AGI cM: 78.531

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: SI111
DNA sequence around SNP1:
ATTTTGGGGATTTTAAACTTTTAACTTTTCGTTGAATTGCTTTAACAACGATTAACCTTG
[T/C]GGGAAAAATTTACAAATGGTCTTAGGTAACCCTAGACTCATGTTTATGGCCCCAT
TTAGT
SNP2: SI288
DNA sequence around SNP2:
TATTAGAGGTGTCATTTTTGGGAGTATGGTTCTCATCTTGGCT[A/G]GCTTTCAAGCAC
CACTTTCTGTTATGCTTATTATTCTGCAAT
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: