Citrus CAPS Marker Database

Locus name: Al0524

CAPS PCR info

PCR Anneal-Temp (℃) / Method: 55
Main product (bp): 1800
Comment on PCR:
F-primer: GAACTTCCGTCCAGATAGTGT
R-primer: CCTTGGCCATTTTCATTG

EST info

EST Accession number 1: C95551
EST Accession number 2: DC893075

sequence-tagged site (STS seq)

STS:
TGGTTATAGCTGTGAAGAGGCTTAATCAAGAGAGTCTGCAGGGTCATCTGGAATGGTTGG
TGAGCATCACACTTCTACCCCCTTGCAATGCAATTTTAGTTTTCTTAGGACCTTACTTCA
GTGTTTGGACTTTACATTTCCCTTGTTGTTGAGTGATGTTCCCTCTTCCTATTGATAGTA
GTAACTAATTTCTTAGCTCCACTTGTTCTACAGACAGAAATCAAACACCTGGGACAATTG
TATCATCCTAATCTTGTAAAATTGATCGGCTATTGCTTAGAGGATGACCACCGGCTTTTG
GTGTATGAATTTATGCCCAAGGGCAGCTTGGAAAATCATCTATTTAGAAGTGAGTCTATT
AAGATCACCTATGTTTAGTAATGTAGTCTTTTAATTCAACTTTTCATTGTCTATGAACTA
ACXTGTCTCTCTTCTAATTGAATCATTA
STS source:
STS Forward / Reverse: Foward read
STS:
CCAATCCTTACTTTTTTCCTTTTTTGAAGGACATCTAACCGCGAAAAGCGATGTGTACAG
TTTTGGGGTTGTTCTCCTCGAAATGTTAAGCGGTAGACGAGTAATTGACAAGAACAGACC
ATCTAGAGAACATAATTTAATTGAATGGGCCAAACCTTACCTTCAAAGCAAACGCAGAAT
TTTTCAAGTTATGGATGCTCGTATTGAAGGCCAGTACTCACTTGGTGCAGCACTAAAAAC
AGCTGTACTAGCAATCAAATGCCTATCAAATGAACCAAAGTTCAGGCCTACCATGGATGA
G
STS source:
STS Forward / Reverse: Reverse read

Experiments: Restriction fragment profile

Compared cultivars (Left, (Middle), Right): Miyagawa-wase/Trovita orange/Kiyomi
Comment: PCR_condition: 60C aneal
Figure legend:
Compared cultivars (Left, (Middle), Right): Frying dragon/Hyuuganatsu
Comment: PCR_condition: 56C aneal
Figure legend:

Experiments: CAPS pattern of hybrid cultivar

Resriction enzyme: Hha1
Rank as CAPS marker: Available marker
Comment: PCR_condition: 56C aneal
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: EcoR1
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: NC
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

Experiments: Segregation pattern

Population name: Kankitsu Chuukanbohon Nou8gou x Siamese Acidless
Restriction enzyme: EcoR1
Comment: PCR_condition: 56C aneal
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: A255 (Okitsu46gou) x G434 (Kankitsu Chuukanbohon Nou5gou)
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: 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: Kiyomi x Okitsu41gou
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

Target on C. clementina (v1.0)

Transcript ID: Ciclev10031723m
Scaffold: scaffold_4
Start: 115362
End: 118025

Target on C. unshiu (v1.0)

Transcript ID: C_unshiu_02038:mRNA_4.1
Scaffold: C_unshiu_02038
Start: 34256
End: 38775
Gene function: Hypothetical protein

AGI map info (Shimada et al. 2014)

AGI LG: AGI-07
AGI cM: 5.972

KmMg map info (Omura et al. 2003)

KmMg LG:
KmMg cM:

JtTr map info (Omura et al. 2003)

JtTr LG: JtR-07
JtTr cM: 76.06

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-07
Rp/Sa cM: 74.381

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: M

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

SNP1: SI043
DNA sequence around SNP1:
TTGTATCATCCTAATCTTGTAAAATTGATCGGCTATTGCTTAGAGGATGACCACCGGCTT
[T/C]TGGTGTATGAATTTATGCCCAAGGGCAGCTT
SNP2: SI341
DNA sequence around SNP2:
TTTTCCTTTTTTGAAGGACATCTAAC[T/C]GCGAAAAGCGATGTGTACAGTTTTGGGGT
TGTTCTCCTCGAAATGTTAAG
SNP3:
DNA sequence around SNP3:
SNP4:
DNA sequence around SNP4: