Citrus CAPS Marker Database

Locus name: Al0409

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 600
Comment on PCR:
F-primer: CTAATGGAAGGCGATAGAGTG
R-primer: CTTCATGGTTACAGGGGATA

EST info

EST Accession number 1: C95388
EST Accession number 2:

sequence-tagged site (STS seq)

STS:

TGTCACTTTCTAACCTTAAGTGGCATTCTGGATGGACCTCTCAAGGTATTTATTTTCTCT
TTGATTCAGAAACTTGAAACAGACTGCAGACTTCTTTCTTTTCCTTCTCCTTTTATTTAT
TCAATTCTAATTCTCTAGANATGCTTCTGCAGTTGAGATCAATGGTGCTTCCTGATAGAT
ACATTGACCATGGATCACCAGCCGATCAGCTTGAACAATCAGGGCTCTCCTCAAGGCATA
TCTCTGCAACAGTCTTATCTCTCTTAGGGAGGCCAAAAGAAGCCCTTCTGATTTAAGTAA
TCATACAAAATCAAACA

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

STS:

GAAGGGGGGCNGAGTGGCAATTTTGGGCTATGGTTCTNTAGTCCAACAATGTGTGCTAGC
TGCGAACATGCTTAAGAGCCAAGACATTTCCGTGACAGTGGCTGATGCAAGATTTTGCAA
ACCTTTGGATACAGACCTCATTAGACAGTTGGCCAATGAGCATGAAATCCTAATTACTGT
GGAAGAGGGTTCTGTGGGAGGCTTTGGCTCTCATGTATGTCACTTTCTAACCTTAAGTGG
CATTCTGGATGGACCTCTCAAGGTATTTATTTTCTCTTTGATTCAGAAACTTGAAACAGA
CTGCAGACTTCTTTCTTTTCCTTCTCCTTTTATTTATTCAATTCTAATTCTCTAGACATG
CTTCTGCAGTTGAGATCAATGGTGCTTCCTGATAGATACATTGACCATGGATCACCAGCC
GATCAGCTTGAANAATCAGGGCTCTCCTCAAGGCATATCTCTGCAACAGTCTTATCTCTC
TTAGGGAGGCCAAAAGAAGCCCTTCTGATTTAAGTAATCATACAAAATCAAACAGCATCT
TGCCCTTNGGATCCAACTTACAATTCCAAGTTGGGGGTGTTATACACTA

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

STS:

TATAACACCCCCAACTTGGAATTGTAAGTTGGATCCAAAGGGCAAGATGCTGTTTGATTT
TGTATGATTACTTAAATCAGAAGGGCTTCTTTTGGCCTCCCTAAGAGAGATAAGACTGTT
GCAGAGATATGCCTTGAGGAGAGCCCTGATGTTCAAGCTGATCGGCTGGTGATCCATGGT
CAATGTATCTATCAGGAAGCACCATTGATCTCAACTGCAGAAGCATGTCTAGAGAATTAG
AATTGAATAAATAAAAGGAGAAGGAAAAGAAAGAAGTCTGCAGTCTGTTTCAAGTTTCT

STS source:
STS Forward / Reverse: Reverse read

STS:

TTTGATTTTGTATGATTACTTAAATCAGAAGGGCTTCTTTTGGCCTCCCTAAGAGAGATA
AGACTGTTGCAGAGATATGCCTTGAGGAGAGCCCTGATTCTTCAAGCTGATCGGCTGGTG
ATCCATGGTCAATGTATCTATCAGGAAGCACCATTGATCTCAACTGCAGAAGCATGTCTA
GAGAATTAGAATTGAATAAATAAAAGGAGAAGGAAAAGAAAGAAGTCTGCAGTCTG

STS source:
STS Forward / Reverse:

Experiments: Restriction fragment profile

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

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hinf1
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: Hinf1
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: NC
Comment:
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Hinf1
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: Jutaro unshu x Trovita orange
Restriction enzyme: Hinf1
Comment:
Figure legend:

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Hinf1
Comment:
Figure legend:

Population name: Kiyomi x Okitsu41gou
Restriction enzyme: Hinf1
Comment:
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10024949m
Scaffold: scaffold_7
Start: 5042508
End: 5046271

Target on C. unshiu (v1.0)

Transcript ID: No
Scaffold:
Start:
End:
Gene function:

AGI map info (Shimada et al. 2014)

AGI LG: AGI-02
AGI cM: 50.758

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-02
KmMg cM: 44.93

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-02
JtTr cM: 29.462

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

Km/O41 LG: NAT-02S
Km/O41 cM: 90.742

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: SI201
DNA sequence around SNP1:

TTCAAGCTGATCGGCTGGTGATCCATGGTC[A/G]ATGTATCTATCAGGAAGCACCATTG
ATCTCAACTGCAGA

SNP2: SI252
DNA sequence around SNP2:

TTCAAGCTGATCGGCTGGTGATCCATGGTC[A/G]ATGTATCTATCAGGAAGCACCATTG
ATCTCAACTGCAGA

SNP3:
DNA sequence around SNP3:

SNP4:
DNA sequence around SNP4: