Citrus CAPS Marker Database

Locus name: Mf0095

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 400
Comment on PCR:
F-primer: TTCTATTCGTATGTGGTTGCT
R-primer: TGAAGTGGAAATTCTTTGAGC

EST info

EST Accession number 1: C81912
EST Accession number 2: DC893672

sequence-tagged site (STS seq)

STS:

TAAAGAGATTTCTGAAGGACCAGGGCAATTAGACTCTTTTACAGGAGTTTTCTTGTATTA
GGTGCATGTCAGTTATAGGAACTGCCGTCGTTTGGCTATGAGTTAAGCATTTTTACATGT
GGTTCCATGTTGCATACAATATGGGAGAAGCAGTCAATTGAGGTCATTTTACAGCAATAA
TGCACGATTGAGATGAGTGAACTTCTTAAAACCAAAATTGTAGAGAAAATGAAGGCAATA
GTGAAAACATATTAATATTTCCTTCCTTTTTTCCTTTTTT

STS source: Consensus sequence of 2 cvs, Okitsu 46 and NO 5
STS Forward / Reverse: Foward read

STS:

AAGTTGAAGTCACCTGCTGCTGCCGTGTCATAAAGAGATTTCTGAAGGACCAGGGCAATT
AGACTCTTTTACAGGAGTTTTCTTGTATTAGGTGCATGTCAGTTATAGGAACTGCCGTCG
TTTGGCTATGAGTTAAGCATTTTTACATGTGGTTCCATGTTGCATACAATATGGGAGAAG
CAGTCAATTGAGGTCATTTTACAGCAATAATGCACGATTGAGATGAGTGAACTTCTTAAA
ACCAAAATTGTAGAGAAAATGAAGGCAATAGTGAAAACATATTAATATTTCCTTCCTTTT
TTCCTTTTTTTTTTAAGCTCAAAGAATTTTCCACTTCAAA

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

STS:

AAAAAGGAAGGAAATATTAATATGTTTTCACTATTGCCTTCATTTTCTCTACAATTTTGG
TTTTAAGAAGTTCACTCATCTCAATTGTGCATTATTGCTGTAAAATGACCTCAATTGACT
GCTTCTCCCGGGTGGTAAACAACATGGAACCACATATAAAAATGCTTAACTCATAGCCAG
ACGACGGCAGTTCCTATAACTGACATGCACCTAATACAAGAAAACTCC

STS source:
STS Forward / Reverse: Foward read

STS:

CTGTAAAATGACCTCAATTGACTGCTTCTCCCATATTGTATGCAACATGGAACCACATGT
AAAAATGCTTAACTCATAGCCAAACGACGGCAGTTCCTATAACTGACATGCACCTAATAC
AAGAAAACTCCTGTA

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

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Miyagawa-wase/Trovita orange/Kiyomi
Comment: PCR_condition: 56C aneal
Figure legend:

Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment:
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Rsa1
Rank as CAPS marker: Others
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: Msp1
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

Rsetriction enzyme: Rsa1
Comment: PCR_condition: 60C aneal
Figure legend:

(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: Msp1
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: Kiyomi x Miyagawa-wase
Restriction enzyme: NC
Comment: PCR_condition: 56C aneal
Figure legend:

Population name: Jutaro unshu x Trovita orange
Restriction enzyme: Rsa1
Comment:
Figure legend:

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Rsa1
Comment: PCR_condition: 56C aneal
Figure legend:

Population name: Kiyomi x Okitsu41gou
Restriction enzyme: Rsa1
Comment:
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10005778m
Scaffold: scaffold_9
Start: 21216748
End: 21221111

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00160:mRNA_34.1
Scaffold: C_unshiu_00160
Start: 290257
End: 294371
Gene function: Transmembrane proteins 14C, putative isoform 1

AGI map info (Shimada et al. 2014)

AGI LG:
AGI cM:

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-032
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-031
JtTr cM: 11.958

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-03
Rp/Sa cM: 43.323

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: SI290
DNA sequence around SNP1:

GGTGCATGTCAGTTATAGGAACTGCCGTCGTTTGGCTATGAGTTAAGCATTTTTA[T/C]
ATGTGGTTCCATGTTGCATACAATATGGGAGAAGCAGTCAATTGAGGTCATTTTACAGCA

SNP2:
DNA sequence around SNP2:

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: