CH05d04, CH05d04 (genetic_marker) Malus x domestica

Marker Overview
NameCH05d04
Genbank IDN/A
TypeSSR
SpeciesMalus x domestica
Repeat MotifGA
PCR Conditionannealing temp 60 degree
Primer 1CH05d04.forward: CAC GAC GTT GTA AAA CGA CACT TGT GAG CCG TGA GAG GT
Primer 2CH05d04.primer 1: ACTTGTGAGCCGTGAGAGGT
Primer 3CH05d04.primer 2: TCCGAAGGTATGCTTCGATT
Primer 4CH05d04.reverse: TCC GAA GGT ATG CTT CGA TT
Product Length174-214
174–214
Max Length197 bp
PolymorphismP_ CH05d04
Publication[view all]
ContactC. Gessler
Andreas Peil
Miyuki Kunihisa
CommentGenomic DNA was extracted from leaf tissue using Qiagen DNeasy 96 plant kits (QIAGEN GmbH, Hilden Germany). Sixteen SSR primers were selected for amplification based on previously published studies (Table 2; Liebhard et al. 2002; Yamamoto et al. 2002). The M13 primer, 5’ CACGACGTTGTAAAACGA 3’, with fluorescent dye label (6FAM, or VIC, or NED) was covalently bound to the 5’ end for detection on the ABI 3730 was synthetized from Applied Biosystems (Carlsbad, CA). The two unlabeled primers consisted of a specific SSR-targeting forward primer with a 5’ M13 tail and a specific SSR-targeting reverse primer was synthetized from Sangon Biotech (Shanghai, China). Amplification was carried out in two PCR cycles. The first PCR amplification was performed in a 10μl solution of 20 ng genomic DNA, 1×PCR buffer, 0.25 mM dNTP, 0.6 unit Taq DNA polymerase, 2 mM MgCl2, 0.24μM reverse primer, 0.24 μM forward primer with M13 tail. The first PCR amplification was performed under the following conditions: 94℃ (5 min), 35 cycles at 94℃(30 s)/annealing temperature (An.T) (30 s)/72℃ (45 s), and a final extension at 72℃ for 10 min. using the optimal annealing temperature for each locus (Table 2). The second amplification reaction was performed in a 12.1μl solution of 10μl PCR products of the first PCR circle, 0.3μM fluorescent labeled M13 primer, 0.1× supplied PCR buffer, 0.4 unit of Taq DNA polymerase. The conditions of the second PCR amplification were as follows: 94℃ (5 min), 16 cycles at 94℃ (30 s)/53℃(45 s)/72℃ (45 s), and a final extension at 72℃for10 min. The PCR products were cleaned with ethanol, and then denaturated at 94℃ for 5 min. Finally the fluorescent labeled PCR products at each locus were separated using an ABI 3730 DNA Analyzer (Applied Biosystems, Carlsbad, CA).
Publications
YearPublication
2004Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, Weg W.E. van de, Hayashi, T. Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Horticulturae. 2004; 663:51-56.
2009Celton J-M, Tustin DS, Chagne D, Gardiner SE. Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genetics and Genomes. 2009; 5(1):93-107.
2006Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C Patocchi A. Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genetics and Genomes. 2006; 2(4):202-224.
2010Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics. 2010 Oct; 42(10):833-839.
2002Liebhard, R., Gianfranceschi, L., Koller, B., Ryder, C.D., Tarchini, R., Weg, E. van de., Gessler, C. Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.) Mol. breed. 2002. v. 10 (4) p. 217-241.
2014Wöhner TW, Flachowsky H, Richter K, Garcia-Libreros T, Trognitz F, Hanke M, Peil A. QTL mapping of fire blight resistance in Malus ×robusta 5 after inoculation with different strains of Erwinia amylovora. Molecular breeding. 2014; 34(1):217-230.
2012Schouten HJ, van de Weg WE, Carling J, Khan SI, McKay SJ, van Kaauwen MPW, Wittenberg AHJ, Koehorst-van Putten HJJ, Noordijk Y, Gao Z, Rees DJG, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A. Diversity arrays technology (DArT) markers in apple for genetic linkage maps. Molecular breeding 2012 29:645–660
2012Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC genomics. 2012; 13:203.
2014Kunihisa M, Moriya S, Abe K, Okada K, Haji T, Hayashi T, Kim H, Nishitani C, Terakami S, Yamamoto T. Identification of QTLs for fruit quality traits in Japanese apples: QTLs for early ripening are tightly related to preharvest fruit drop. Breeding science. 2014 Sep; 64(3):240-51.
2015Ben Sadok I, Tiecher A, Galvez-Lopez D, Lahaye M, Lasserre-Zuber P, Bruneau M, Hanteville S, Robic R, Cournol R, Laurens F. Apple fruit texture QTLs: year and cold storage effects on sensory and instrumental traits. Tree Genetics & Genomes 2015 11:119
2004Plant Breeding, 123(4):321
2002R. Liebhard, L. Gianfranceschi, B. Koller, C.D. Ryder, R. Tarchini, E. Van De Weg, C. Gessler. Development and characterization of 140 new microsatellites in apple. Molecular Breeding December 2002, 10(4):217-241
Contact
NameDetails
C. Gessler
First name:Cesare
Last name:Gessler
Institution:ETH Zurich
Address:ZTH Zurich Institut f. Integrative Biologie LFW C 15 Universitatstrasse 2 8092 Zurich
Country:Switzerland
Email:cesare.gessler@agrl.ethz.ch
Phone:+41 44 632 38 71
Fax:+41 (0) 632 11 08
Last update:May 2002
Andreas Peil
First name:Andreas
Last name:Peil
Title:Researcher
Institution:Institute for Breeding Research on Fruit
Address:Kulius Kuhn-Institut (JKI), Pillnitzer Platz 3a, 01326
Country:Dresden, Germany
Email:andreas.peil@jki.bund.de
Miyuki Kunihisa
First name:Miyuki
Last name:Kunihisa
Institution:NARO Institute of Fruit Tree Science
Address:2-1 Fujimoto, Tsukuba, Ibaraki 305-8605
Country:Japan
Email:miyuky@affrc.go.jp
Phone:81-29-838-6437
Keywords:fruit drop
Relationships

This genetic_marker is adjacent to the following primer feature(s):

Feature NameUnique NameSpeciesType
primer 1CH05d04.primer 1Malus x domesticaprimer
primer 2CH05d04.primer 2Malus x domesticaprimer
forwardCH05d04.forwardMalus x domesticaprimer
reverseCH05d04.reverseMalus x domesticaprimer


The following marker_locus feature(s) are an instance of this genetic_marker:

Feature NameUnique NameSpeciesType
CH05d04CH05d04Malus x domesticamarker_locus
CH05d04CH05d04-1.8Malus x domesticamarker_locus
CH05d04-1CH05d04-1-63Malus x domesticamarker_locus
CH05d04-2CH05d04-2-52.9Malus x domesticamarker_locus
CH05d04-1CH05d04-1-62.953Malus x domesticamarker_locus
CH05d04-1CH05d04-1-63.349Malus x domesticamarker_locus
CH05d04CH05d04-50.716Malus x domesticamarker_locus
CH05d04CH05d04-70.44Malus x domesticamarker_locus
CH05d04CH05d04-62.97Malus x domesticamarker_locus


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple-DT-F112N/A8CH05d04View
2Apple Integrated map12N/A4.4CH05d04View
3Pear-BH-F1Ba12N/A18.6CH05d04View
4Apple-FD-F1-2006F12N/A10.8CH05d04View
5Apple-FD-F1-2006D12N/A12.6CH05d04View
6Apple-IM-F1-IdaredIda LG 12N/A0CH05d04View
7Apple-IM-F1-IdaredIda LG 13N/A0CH05d04View
8Apple-IM-F1-Mr5Mr5 LG 12N/A5.8CH05d04View
9Pear-PM-F1-PEAR312N/A0CH05d04View
10Apple-2000-2012-F1ch12N/A5CH05d04View
11Apple-MM-F112N/A0.9CH05d04View
12Apple-OA-F1-OrinOR12N/A0CH05d04View
13Apple-OA-F1-AkaneAK12N/A1.4CH05d04View
14Apple-X3259X3263-F112N/A0CH05d04View
15Apple-GDxJ-F1-2012LG12N/A21.5CH05d04View
16Apple-M432-2012LG12N/A0CH05d04View
17Apple-JGD-F1-2014J12N/A6CH05d04View
18Apple-JGD-F1-2014G12N/A9.4CH05d04View
19Apple-RGTxGD-F1-2015RGT_12N/A4.4CH05d04View
20Apple-RGTxGD-F1-2015GD_12N/A3.49CH05d04View
21Apple-RGxPI6-F1LG12N/A3.9CH05d04View
22Apple-DP-F1-2013P12N/A7.1CH05d04View
23Apple-X5210X8402-F1-ConsensusLG12N/A8.7CH05d04View
24Apple-X5210X8402-F1-X5210LG12N/A4.5CH05d04View
25Apple-X5210X8402-F1-X8402LG12N/A0CH05d04View
26Pear-Ba-F1-2013Ba12N/A0CH05d04View
27Apple-JM7xS63-F1S12N/A0CH05d04View
28Pear-BD-F1-2014-geneticLG12N/A122.9CH05d04View
29Pear-Bartlett-F1-2007Ba12N/A0CH05d04View
30Pear-La_France-F1-2007La12N/A5.7CH05d04View
31Apple-FD-Discovery-F1-2003D12N/A12.6CH05d04View
32Apple-JM7xS63-F1J12N/A1.8CH05d04View
33Pear-BD-F1-2015LG12N/A63CH05d04-1View
34Pear-BD-F1-2015LG14N/A52.9CH05d04-2View
35Pear-Bayuehong-F1-2015LG12N/A62.95CH05d04-1View
36Pear-Dangshansuli-F1-2015LG12N/A63.35CH05d04-1View
37Pear-Dangshansuli-F1-2015LG14N/A50.72CH05d04View
38Pear-integrated_consensus_map-IPCG-2017LG14N/A70.44CH05d04View
39Pear-integrated_consensus_map-IPCG-2017LG12N/A62.97CH05d04View