Citrus CAPS Marker Database

Locus name: Lp0102

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 60
Main product (bp): 2200
Comment on PCR:
F-primer: GAATCCGGCGTTAGTTGT
R-primer: CATGGTCTATTCGGTATCTCA

EST info

EST Accession number 1: AU300902
EST Accession number 2: DC893163

sequence-tagged site (STS seq)

STS:

CNTTTCTGATGATACTTTGATTTCACAGATACCAGTTATTGACATGCAAAGCTTACTTTC
TGNAGAATCAATGGATTCTGAGCTAGCCAAGCTCGACTTCGCATGCAAAGAATGGGGTTT
TTTCCAGGTATAATGCTTTAGCAAAGTTAGAAAATTGTTTCGCCAGAACATGCTTGTTTG
TGAACAAGAATCGAGAAATATGCAAATTNTCAATCNAATAGGCAAAATTAAAATTCATAT
TTATTTCTTAAACCCACGTATCATTGATGTTAGCAGATCATGGTTTCACTTTTCGGTGTT
GTCNGTGGCTTAGGACTGCAGCTTGTGAAAAGAAGAACTTGTCTCTGGTTTATTTATTAT
TGACTTTCTATACTGCTTTACCTTTCCCCCTCCAGACATGGGTTAATTAGCTATTTCATT
CCTAAATGNCAAACACGCAATATGGTATTAAAAAGACGGGTCTTGAGAAATTTCCCCTCC
TCTGCCTCAATGGCTTTTGGTACCTTATGAGAAATATGCTTCTGTCAAAATTTTAAAAGA
TATACTATCGTAAATTGNGTAAGACCTCTTAGAAAATGTACTCATTTCTGTAGTCAATGT
TGCAAATTNCCCNTNATTTAAAGACAT

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

STS:

TTTCACAGATACCAGTTATTGACATGCAAAGCTTACTTTCTGNAGAATCAATGGATTCTG
AGCTAGCCAAGCTCGACTTCGCATGCAAAGAATGGGGTTTTTTCCAGGTATAATGCTTTA
GCAAAATTAGAAAATTGTTTCGCCAGAACATGCTTGTTTGTGAACAAGAATCGAGAAATA
TGCAAATTGTCAATCAAATAGGCAAAATTAAAATTCATATTTATTTCTTAAACCCACGTA
TCATTGATGTTAGCAGATCATGGTTTCACTTTT

STS source:
STS Forward / Reverse: Foward read

STS:

TTCTTTGAAAATGGAGTGCAAGCAATGAGGATGAATTATTACCCTCCATGTCCTCAGCCC
GAGAAGGTTATGGGCCTGTCGCCGCATTCTGATGCAGCTGCACTTACCATTCTGCNACAA
CTTAATGAAGTGGAGGGTCTCCAGATAAAGAAGGATGGAAAGTGGATTCCTGTTACCCCA
CTCCCGGATGCTTTCATTGTCAACATTGGAGACACATTGGAGGTAATAATTATNATAAAT
TACCTTAACCTGGCATTTTTATGCGCTTGCTTATGTGCTTTAATAANTTTTNCATGGCAG
ATTATAACCAATGGGACATACCGTAGCATTGAGCATCGNGCAGTTGTAAACTCTGTACAG
GAAAGACTTTCCNTTGCCACAGNTTACTCAGTGAGATATGATGGTGAAGTNTATCCTGCC
TCCAGTTTGATCTCTGAAAAAACTCCTCCTTTGTTTAGAAGANTGAGAATTGAAGAATAC
TTTAGGAGCCGGTATGCTCGTGAGCTTAGGGGAAAATCTCAGCTGGATTCCCTGAGAATT
CAACATNGTCAAGGCTAGTATAAGTTTATTTCGGATAACTAAAGAGTTTGGTACAAAAAC
TCTGAAGGNCCTTGCNATTAAGATTGTGTGTGGAACTGAAAATAAGAAATACGTTCTATG
AANACTGTGGTATAACCTG

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

STS:

CCTTCAGAGTTTTTGTACCAAACTCTTTAGTTATCCGAAATAAACTTATACTAGCCTTGA
CAATGTTGAATTCTCAGGGAATCCAGCTGAGATTTTCCCCTAAGCTCACGAGCATACCGG
CTCCTAAAGTATTCTTCAATTCTCAATCTTCTAAACAAAGGAGGAGTTTTTTCAGAGATC
AAACTGGAGGCAGGATA

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

STS:

CAATGGGACATACCGCAGCATTGAGCATCGTGCAGTTGTAAACTCTGTACAGGAAAGACT
TTCCGTTGCCACAGTTTACTCAGTGAGATATGATGGTGAAGTGTATCCTGCCTCCAGTTT
GATCTCTGAAAAAACTCCTCCTTTGTTTAGAAGAGTGAGAATTGAAGAATACTTTAGGAG
CCGGTATGCTCGTGAGCTTAGGGGAAAATCTCAGTTGGATTCCCTGAGAATTCAACATGG
TCAAGGCTAGTATAAGTTTATTTTGGATAACTAAAGAGTTTGGTACAAAAACTCTT

STS source:
STS Forward / Reverse:

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:

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

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Msp1
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)

Resriction enzyme: Pvu2
Rank as CAPS marker: Disagree by Marco analysis
Comment:
Figure legend:

Experiments: CAPS pattern of Citrus collection

Rsetriction enzyme: Hha1
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: PCR_condition: 56C 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: Hha1
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: Msp1
Comment:
Figure legend:

Population name: Kiyomi x Miyagawa-wase
Restriction enzyme: Msp1
Comment:
Figure legend:

Population name: Kiyomi x Okitsu41gou
Restriction enzyme: Msp1
Comment:
Figure legend:

Population name: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
Restriction enzyme: Pvu2
Comment:
Figure legend:

Target on C. clementina (v1.0)

Transcript ID: Ciclev10020840m
Scaffold: scaffold_3
Start: 30648732
End: 30651259

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_00759:mRNA_1.1
Scaffold: C_unshiu_00759
Start: 917
End: 3353
Gene function: Senescence-related gene 1

AGI map info (Shimada et al. 2014)

AGI LG: AGI-05
AGI cM: 42.737

KmMg map info (Omura et al. 2003)

KmMg LG: KmG-05S
KmMg cM: 41.895

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-05
JtTr cM: 28.682

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

Km/O41 LG: NAT-05
Km/O41 cM: 37.917

Rp/Sa map info (Ohta et al. 2011)

Rp/Sa LG: RP-05
Rp/Sa cM: 51.879

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: SI080
DNA sequence around SNP1:

CTTCAGAGTTTTTGTACCAAACTCTTTAGTTATCCGAAATAAACTTATACTAGCCTTGAC
[A/C]ATGTTGAATTCTCAGGGAATCCAGCTGAGATTTTCCCCTAAGCTCACGAGCATAC
CGGCT

SNP2: SI319
DNA sequence around SNP2:

TGAGAATTGAAGAATACTTTAGGAGCCGGTATGCTCGTGAGCTTAGGGGAAAATCTCAG[
T/C]TGGATTCCCTGAGAATTCAACAT

SNP3: SI360
DNA sequence around SNP3:

GCCAAGCTCGACTTCGCATGCAAAGAATGGGGTTTTTTCCAGGTATAATGCTTTAGCAAA
[A/G]TTAGAAAATTGTTTCGCCAGAACATGCTTGTTTGTGAACAAGAATCGAGAAATAT
GCAAA

SNP4: SI378
DNA sequence around SNP4:

GCAGTTGTAAACTCTGTACAGGAAAGACTTTCC[A/G]TTGCCACAGTTTACTCAGTGAG
ATATGATGGTGAAGTGTATCCTGCCTCCAGTTTGATCT