Citrus CAPS Marker Database

Locus name: Bf0028

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 58
Main product (bp): 1800
Comment on PCR:
F-primer: AAAATCTTGTTGAAGGCAAAA
R-primer: CGTTCTCTCCACCCAATC

EST info

EST Accession number 1: DC885165
EST Accession number 2:

sequence-tagged site (STS seq)

STS:
CTTGCTCCATCACTGTCTTGCATAATGAGTTCAACCACTCTCGACCATCATAATAAGCAG
AAATTGCCCTGAAAAATCAATTTCCAAATGAATGCTATACAAAGGAACACAATACTAATG
GAAATACCAGCAAATTTAAAATGCTTGCTCTAGACAAACCTGAAACTGTCATAAGTCATA
CTGGATTGCTTTTGTTTAAAAGGGATCATAAGTGGCTGACCTTCTAGATCCTCATAAATA
TATAATCTACTTGTAGTATGGAATGAAGAAACATGGATGCTGAAATCAACTACATGACTA
CCGCTTAAGAAAAGTAGATTTGCCGACTTACTTGAACAGGAAATAGATTCACTCACCTAT
TAAGAGCATAATCGACTCCAGCAATATCAGCTCCATCAAAACTAAATCCATTTGGTTCAA
GATCTAGGGCTTGTGCTCTCTCTTTATCATGGTCAACATCAAATACAGTGTCATAAAGTC
CTACAGGAGAAATAAATTGGAAATGTTTTGTCAAATACATTATCTTTGCCAAATAGTAAG
STS source:
STS Forward / Reverse: Foward read
STS:
TAACATGTGTAATACCGTAGTCTATGAATATTTCATCCAATGCATCAGTCTAAACTTTCC
TCTTTAGTAGTGGATGTTGATGAGGGGAAGAATCTTTATGATGCCAACATCTTTCAGGGT
TTCATCTAATAAACTAAAACTTATTTTTCTTCTATGTGCGTGTGTCCCAATATCAAGAAT
GTATGATTTTCAATCAAGGAGGAAAGCAGAAACTCCAGTAATGTGAATGCAAGGACAAAA
TGGTGTAGTTTCAGACTCAAAAGTCATGTGCTGACACAGTTGTTGCCGTAGCTTGTTTAG
CATTTTCGCATTTATTCTGAC
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:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hae3
Rank as CAPS marker: Dominant marker
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
Rsetriction enzyme: Msp1
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hae3
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: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: NC
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: Ciclev10014319m
Scaffold: scaffold_2
Start: 35354776
End: 35363026

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00048:mRNA_32.1
Scaffold: C_unshiu_00048
Start: 179733
End: 188796
Gene function: Soluble starch synthase III-1

AGI map info (Shimada et al. 2014)

AGI LG: AGI-06
AGI cM: 17.966

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: K

SNP typing by Illumina GoldenGate assay (Fujii et al. 2013)

SNP1: SI001
DNA sequence around SNP1:
TATCAGCTCCATCAAAACTAAATCCATTTGGTTCAAGATCTAGG[C/G]CTTGTGCTCTC
TCTTTATCATGGTCAACATCAAATACAGTGTCATAAAGTCCTACAGGAG
SNP2:
DNA sequence around SNP2:
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: