Citrus CAPS Marker Database

Locus name: Gn0067

CAPS PCR info

PCR Anneal-Temp (℃) / Method: Td
Main product (bp): 550
Comment on PCR:
F-primer: AGACCTTATGGCAGAGTTAAT
R-primer: CGGAATGACACAATGCTC

EST info

EST Accession number 1: AB114652
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
GCAAAAATGCATAACCAATGGTGTTAAGTTTCACCAAGCTAAAGTTATTAAGGTTATTCA
TGAAGAGTCCAAATCTTTGTTGATTTGCAATGATGGTGTGACAATTCAGGCTGCCGTGGT
TCTTGATGCTACGGGGTTCTCTAGGTGTCTTGTCCAGTATGATAAGCCCTATAATCCAGG
TTACCAAGTGGCATATGGAATACTAGCTGAGGTAGAAGAGCACCCGTTTGATTTAGACAA
GATGGTTTTCATGGATTGGAGAGATTCGCATCTGAACAACAATTCGGAGCTCAAAGAGGC
AAATAGCAAAATTCCTACTTTTCTTTATGCCATGCCCTTTTCGTCAAACAGGATATTTCT
TGAAGAGACTTCGCTAGTGGCGCGGCCTGGAGTGCCAATGAAAGATATCCAGGAAAGAAT
GGTGGCTAGA
STS source:
STS Forward / Reverse:

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

Resriction enzyme: Hae3
Rank as CAPS marker: Others
Comment:
Figure legend: DNA sample: Lane 2'=Ethlog citron, 23'=Duncan GF, Hrd=Hirado buntan, HgNt = Hyuuganatsu
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)
Resriction enzyme: Hinf1
Rank as CAPS marker: Others
Comment:
Figure legend: DNA sample: Lane 2'=Ethlog citron, 23'=Duncan GF, Hrd=Hirado buntan, HgNt = Hyuuganatsu
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: Hae3
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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10004730m
Scaffold: scaffold_9
Start: 22728310
End: 22730086

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00295:mRNA_17.1
Scaffold: C_unshiu_00295
Start: 207257
End: 208985
Gene function: Lycopene beta-cyclase

AGI map info (Shimada et al. 2014)

AGI LG: AGI-03
AGI cM: 46.274

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: SI204
DNA sequence around SNP1:
GCAAAAATGCATAACCAATGGTGTTAAGTT[T/C]CACCAAGCTAAAGTTATTAAGGTTA
TTCATGAAGAGTCCAAATCTTTGTTGATTTGCAAT
SNP2: SI349
DNA sequence around SNP2:
CCCTATAATCCAGGTTACCAAGTGGCATATGGAATACTAGCTGAGGTAGAA[C/G]AGCA
CCCGTTTGATTTAGACAAGATGGTTTTCATGGATTGGAGAGATTCGCATCTGAACA
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: