CH04h02, CH04h02 (genetic_marker) Malus x domestica

Marker Overview
NameCH04h02
Genbank IDN/A
TypeSSR
SpeciesMalus x domestica
Repeat MotifGA
PCR Conditionannealing temp 60 degree
Primer 1CH04h02.forward: CAC GAC GTT GTA AAA CGA CGGA AGC TGC ATG ATG AGA CC
Primer 2CH04h02.primer 1: GGAAGCTGCATGATGAGACC
Primer 3CH04h02.primer 2: CTCAAGGATTTCATGCCCAC
Primer 4CH04h02.reverse: CTC AAG GAT TTC ATG CCC AC
Product Length162-262
PolymorphismP_ CH04h02
Publication[view all]
ContactC. Gessler
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.
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.
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
Relationships

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

Feature NameUnique NameSpeciesType
primer 1CH04h02.primer 1Malus x domesticaprimer
primer 2CH04h02.primer 2Malus x domesticaprimer
forwardCH04h02.forwardMalus x domesticaprimer
reverseCH04h02.reverseMalus x domesticaprimer


This genetic_marker is located in the following QTL feature(s):

Feature NameUnique NameSpeciesType
fruit textureqFT.XX-ch11.1-S2Malus x domesticaQTL


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

Feature NameUnique NameSpeciesType
CH04h02CH04h02Malus x domesticamarker_locus
CH04h02CH04h02-132.173Malus x domesticamarker_locus
CH04h02CH04h02-134.853Malus x domesticamarker_locus
CH04h02CH04h02-0.9Malus x domesticamarker_locus
CH04h02CH04h02-74.9Malus x domesticamarker_locus
CH04h02CH04h02-74.962Malus x domesticamarker_locus
CH04h02CH04h02-64.204Malus x domesticamarker_locus
CH04h02CH04h02-37.5Malus x domesticamarker_locus


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple-FD-F1-2006D11N/A0CH04h02View
2Apple-FD-F1-2006F11N/A0CH04h02View
3Pear-BH-F1Ba11N/A11.6CH04h02View
4Pear-BH-F1Ho11N/A0CH04h02View
5Apple-GaxDR-F1LG11N/A0CH04h02View
6Apple Integrated map11N/A0CH04h02View
7Apple-MM-F111N/A0CH04h02View
8Apple-X3259X3263-F111N/A0CH04h02View
9Apple-M432-2012LG11N/A0CH04h02View
10Apple-RGTxGD-F1-2015GD_11N/A0.87CH04h02View
11Apple-M27xM116-2016LG11N/A0CH04h02View
12Apple-X5210X8402-F1-X5210LG11N/A0CH04h02View
13Apple-X5210X8402-F1-X8402LG11N/A0CH04h02View
14Pear-Ba-F1-2013Ba11N/A0CH04h02View
15Apple-GDxBr-F1-2013LG11N/A4.49CH04h02View
16Pear-BD-F1-2014-geneticLG11N/A100.6CH04h02View
17Pear-Bartlett-F1-2007Ba11N/A1.6CH04h02View
18Pear-La_France-F1-2007La11N/A0CH04h02View
19Apple-FD-Discovery-F1-2003D11N/A0CH04h02View
20Pear-M-F1-maleLG11N/A132.17CH04h02View
21Pear-RM-F1-IntegratedLG11N/A134.85CH04h02View
22Apple-JM7xS63-F1J11N/A0.9CH04h02View
23Pear-BD-F1-2015LG11N/A74.9CH04h02View
24Pear-Bayuehong-F1-2015LG11N/A74.96CH04h02View
25Pear-Dangshansuli-F1-2015LG11N/A64.2CH04h02View
26Pear-integrated_consensus_map-IPCG-2017LG11N/A37.5CH04h02View