Citrus CAPS Marker Database

Locus name: Lp0105

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1000
Comment on PCR:
F-primer: ATATGTCTATTGGCAAAGAGC
R-primer: GCATGCACTTGTTGAGAAC

EST info

EST Accession number 1: AU300400
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

GNGTTTGAGCCTGTCCCCGTCACCAATAATATCATTCCACAGGCTGAAGGCTCTTCCTCT
TCTTGTCCCGTGAATGATGATNTTACGGGCNTTGATGAGAAGAAAGTTTTGGAAGGCCTA
AGCGTTTTGCTTGTTGAAGATCAAGCAGTACTACAAAGGATAGGAATCAGAATGCTNAAA
AAGCTTGGAGCTGGTGTTACTCTAGTCAAAGATGGAGAGGCTGCCGTTGAAGCCATGACC
CTCATGATCAATGCAGCTGGGAAAAATCATCAAATTCAAAACCTCCACCATGGATCCAAT
TTGGAAACTCATAATNCCCCTCACTATGACTTAATCCTCATGGACTGCCAAGTACTCATG
AGCACCGACATCTTTCTCTCAATATATGCATACATTCAACTTTTTTTTTCTGAANTTTTT
TATC

STS source: Okitsu 46
STS Forward / Reverse: Foward read

STS:

CTGTCCCCGTCACCAATAATATCATTCCACAGGCTGAAGGCTCTTCCTCTTCTTGTCCCG
TGAATGATGATGTTACGGGCCTTGATGAGAAGAAAGTTTTGGAAGGCCTAAGCGTTTTGC
TTGTTGAAGATCAAGCAGTACTACAAAGGATAGGAATCAGAATGCTAAAAAAGCTTGGAG
CTGGTGTTACTCTAGTCAAAGATGGAGAGGCTGCCGTTGAAGCCATGACCCTCATGATCA
ATGCAGCTGGGAAAAATCATCAAATTCAAAACCTCCACCATGGATCCAATTTGGAAACTC
ATAATTCCCCTCACTATGACTTAATCCTCATGGACTGCCAAGTACTCATGAGCACCGACA
TCTTTCTCTCAATATATGCATACATTCAACTTTTTTTTTC

STS source:
STS Forward / Reverse: Foward read

STS:

CTTTTTTTTTGANAATTTTTTTATCTAATTTTCACTCCTCCATTTAAGTTAGGATTTGTG
GGNCCGTACAGTCATGGTATCTTTTTCTCCTTCTACATTAGGCATATATCACATTAAATT
TTGCTCATTTTATTGCATGAGNAAGCAATTAATTGAATTAATTTCTAAGCAGATGGGCAG
CATGGATGGCTGTAAAGCAACAAGAGTAATCAGGANGCTAGAAGCTGAAGCTGAAACGGG
TCAAAGCATTCCCATAATTGCATTTACAGCTCTGGTAACCGCAGATAATGAACGAGAATG
CTTCAATTCTGGCATGGATACTTTTCTCAACAAGCCAGCGCAGGAACACCTGTTGGCTGC
CGCCATTGTTGAGACTATTGCTCGTAAAAGTCACAAGTTCTCATGTGATGAGCAAGCAGA
AGCTCAA

STS source: Okitsu 46
STS Forward / Reverse: Reverse read

STS:

GCTTGCTCATCACATGAGAACTTGTGACTTTTACGAGCAATAGTCTCAACAATGGCGGCA
GCCAACAGGTGTTCCTGCGCTGGCTTGTTGAGAAAAGTATCCATGCCAGAATTGAAGCAT
TCTCGTTCATTATCTGCGGTTACCAGAGCTGTAAATGCAATTATGGGAATGCTTTGACCC
GTTTCAGCTTCAGCTTCTAGCTTCCTGATTACTCTTGTTGCTTTACAGCCATCCATGCTG
CCCATCTGCTTAGAAATTAATTCAATTAATTGCTTACTCATGCAATAAAATGAGCAAAAT
TTAATGTGATATATGCCTAATGTAGAAGGAGAAAAAGATACCATGACTGTACGG

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): 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

Resriction enzyme: Pvu2
Rank as CAPS marker: no homozygous cultivar with minor allele
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

Rsetriction enzyme: Pvu2
Comment:
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: Pvu2
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: Pvu2
Comment:
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10026412m
Scaffold: scaffold_7
Start: 815904
End: 817239

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00353:mRNA_13.1
Scaffold: C_unshiu_00353
Start: 92033
End: 93437
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-02
AGI cM: 75.939

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: 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: SI113
DNA sequence around SNP1:

CCTAAGCGTTTTGCTTGTTGAAGATCAAGCAGTACTACAAAGGATAGGAATCAGAATGCT
[A/T]AAAAAGCTTGGAGCTGGTGTTACTCTAGTCAAAGATGGAGAGGCTGCCGTTGAAG
CCATG

SNP2: SI163
DNA sequence around SNP2:

GGCAGCCAACAGGTGTTCCTGCGCTGGCTTGTTGAGAAAAGTATCCATGCCAGAATTGAA
[C/G]CATTCTCGTTCATTATCTGCGGTTACCAGAGCTGTAAATGCAATTATGGGAATGC
TTTGA

SNP3: SI254
DNA sequence around SNP3:

TTACTCTAGTCAAAGATGGAGAGGCTGCCGTTGAAGCCATGACCCTCATGATCAATGCAG
[A/C]TGGGAAAAATCATCAAATTCAAAACCTCCACCATGGATCCAATTTGGAAACTCAT
AAT

SNP4:
DNA sequence around SNP4: