Citrus CAPS Marker Database

Locus name: Al0417

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 56
Main product (bp): 1800
Comment on PCR:
F-primer: TTCCCATTCTTTTAGGCAATA
R-primer: CGGCCCACAACATAGACT

EST info

EST Accession number 1: C95398
EST Accession number 2: DC892987

sequence-tagged site (STS seq)

STS:

TTCTTTCTTTTACCTCCTAATAGCTTAGATATCTTCTTCTTTTTATTTTCTTTTGTGTGT
GAAAAGTTATAATCTGGGTTCTTCTTGCAAGTTGATATTTTGATTGTTTTTGGTACATAC
GACATTTGAATTTGTATATTTTAGTATTGGTAACGTTTGTACTTTTTGTTTCATGTTCAT
CTCATATGAGGATTGGTGGAAAGGGAATTGTTGTTT

STS source: Chuukanbohon NO 5
STS Forward / Reverse: Foward read

STS:

AACTGGGTTTCAAGGACCCTTGGCTCTTTGTTTTTGCCTTTCACAAGTGTACTGGAAAAA
TTCAGTGGCAGGTTCTAGACCTTACCCACTATTGTTGGCACACTATCCCCGCAATGCCGT
GCAAGGATAAGGTTTGTCCACATGGATTTAGGTGTGTTTCAATCCCTNGTGAGGGTACTT
TGTTTGTGTGTGGAGGTATGGTCTCTGATGTTGATTGTCCTCTTGACTTGGTCTTNAAGT
ATGAAATGCAAAAAAACCGTTGGACAGTCATGAACAAGATGATTACAGCNAGATCATTTT
TTGCTAGTGGGGTGATTGGGGGGATGATATATGTGGCNGGAGGAAGCAGTGCAGACCTTT
TCGAGCTTGACTCAGCTGAGGTTTTNGATCCTGTAAAGGGAAATTGGCGCACCATTGCAA
GCATGGGAACAAACATGGCATCTTATGATGCTGCAGTTCTAGATGGCAAACTTCTTGTGA
CGGAAGGCTGGTTGTGGCCATTTTTTGTCTCTCCGAGAGGTCAGGTCTATGATCCGAGTA
CTGATAATTGGGAAAGCATGGCTGTTGGACTGAGAGAAGGGTGGACTGGTTCAAGTGTTG
TGGTTTATGAGCATTTGTTTGTGGTTTCAGAGCTTGAAAGAATGAAGCTCAAAGTTTATG
ACCCAAGCACTGATTCGTGGGAGACAATAGAGGG

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

STS:

GGGTCATAAACTTTGAGCTTCATTCTTTCAAGCTCTGAAACCACAAACAAATGCTCATAA
ACCACAACACTTGAACCAGTCCACCCTTCTCTCAGTCCAACAGCCATGCTTTCCCAATTA
TCAGTACTCGGATCATAGACCTGACCTCTCGGAGAGACAAAAAATGGCCACAACCAGCCT
TCCGTCACAAGAAGTTTGCCATCTAGAACTGCAGCATCATAAGATGCCATGTTTGTTCCC
ATGCTTGCAATGGTGCGCCAATTTCCCTTTACAGGATCCAAAACCTCAGCTGAGTCAAGC
TCGAAAAGGTCTGCACTGCTTCCTCCAGCCACATATATCATCCCCCCAATCACCCCACTA
GCAAAAAATGATCTAGCTGTAATCATCTTGTTCATGACTGTCCAACGGTTTTTTTGCATT
TCATACTT

STS source: Okitsu 46
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:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
Rank as CAPS marker: Disagree by Marco analysis
Comment: PCR_condition: 60C aneal
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: NC
Comment: PCR_condition: 60C aneal
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: Hae3
Comment: PCR_condition: 60C aneal
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: Hae3
Comment: PCR_condition: 60C aneal
Figure legend:

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Hae3
Comment: PCR_condition: 60C aneal
Figure legend:

Population name: Kiyomi x Okitsu41gou
Restriction enzyme: Hae3
Comment: PCR_condition: 58C aneal
Figure legend:

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: NC
Comment: PCR_condition: 60C aneal
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10015483m
Scaffold: scaffold_2
Start: 35212691
End: 35214865

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00048:mRNA_50.1
Scaffold: C_unshiu_00048
Start: 328418
End: 330513
Gene function: Kelch repeat-containing F-box family protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 20.297

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-06
KmMg cM: 62.256

JtTr map info (Omura et al. 2003)

JtTr LG:
JtTr cM:

Km/O41 map info (Nakano et al. 2003)

Km/O41 LG: NAT-06S
Km/O41 cM: 56.647

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: SI244
DNA sequence around SNP1:

SNP2: SI255
DNA sequence around SNP2:

GCCACATATATCATCCCCCCAATCACCCCACTAGCAAAAAATGATCT[A/G]GCTGTAAT
CATCTTGTTCATGACTGTCCAACGGTTTTTTTGCATTTCATACTT

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: