Dear colleagues,
the Julius Kühn-Institut (JKI), Institute for Breeding Research on Fruit Cops (ZO) in Dresden-Pillnitz (Germany) is currently developing a 50 k Axiom® SNP array for apple. JKI is the Federal Research Centre for Cultivated Plants in Germany and belongs to the Federal Ministry of Food and Agriculture. In agreement with the ministry, ZO is responsible for coordinating the activities on preservation of fruit genetic resources. Genotyping as a tool to improve the preservation efficiency (e.g. identification of duplicates, synonyms, homonyms) is therefore one of our tasks. Based on a multi-year discussion with the ministry and the advisory board of our national genebank network we got the order to develop an optimized SNP array useful for genotyping of the German apple collection (DGO) and other applications like GWAS. Making this array useful for the whole apple community is of high priority for us. Therefore, we initiated a discussion with international partners and ThermoFisher (array producer) and TraitGenetics (genotyping service provider) to support the development. Based on this discussion the new array should fulfill the following demands:
§ Results should be (at least to high content) comparable to results obtained with the Illumina 20k SNP array1 and the 480k Axiom® array2.
§ New reliable SNPs linked to specific traits or SNPs should be added to improve the evenly coverage of SNPs on all LGs and to fill existing gaps. The distribution of SNPs will be determined on both the GDDH133 genome sequence as well as the HFTH14 genome sequence.
§ If possible, SNPs markers specific for e.g. Malus sieversii and M. sylvestris should be added to allow the identification of wild species introgressions.
JKI would be happy if you would agree to provide data/SNPs that could be useful for the new array. The array should be produced until the end of 2020 and later on commercially available for the whole apple community via ThermoFisher.
JKI would appreciate your support and input very much.
Do not hesitate to ask for more information. Contact details are:
Julius Kühn-Institut
Institute for Breeding Research on Fruit Crops
Andreas Peil
Pillnitzer Platz 3a
D-01326 Dresden-Pillnitz
Germany
Tel.: +49 (0)3946 478010
Fax: +49 (0)3946 478002
Email: andreas.peil(a)julius-kuehn.de<mailto:andreas.peil@julius-kuehn.de>
If you would like to participate and deliver SNP data and the respective information, please send them to:
andreas.peil(a)julius-kuehn.de<mailto:andreas.peil@julius-kuehn.de>
until 31st of May 2020.
Looking forward to hearing from you
Andreas Peil
1 Bianco, L. et al. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus ×domestica Borkh). PLoS One 9, e110377 (2014).
2 Bianco, L. et al. Development and validation of the Axiom® Apple480K SNP genotyping array. The Plant Journal 86, 62-74 (2016).
3 Daccord, N. et al. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat. Genet. 49, 1099-1106 (2017).
4 Zhang, L. et al. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications 10, 1494, doi:10.1038/s41467-019-09518-x (2019).
Im Auftrag
Dr. Andreas Peil
__________________________________________________
Institut für Züchtungsforschung an Obst
Julius Kühn-Institut
Bundesforschungsinstitut für Kulturpflanzen
Pillnitzer Platz 3a,
01326 Dresden
Tel.: +49 (0) 3946 47 8010
Fax: +49 (0) 3946 47 8002
E-Mail: andreas.peil(a)julius-kuehn.de<mailto:andreas.peil@julius-kuehn.de>
www.julius-kuehn.de<http://www.julius-kuehn.de/>
www.deutsche-genbank-obst.de<http://www.deutsche-genbank-obst.de/>
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Das Julius Kühn-Institut (JKI) vereint unter seinem Dach 17 Fachinstitute.. Das JKI berät als Forschungsinstitut des Bundesministeriums für Ernährung und Landwirtschaft (BMEL) die Politik. Es forscht u. a. in den Bereichen Pflanzenbau, Züchtung, Pflanzen-, Bienen- und Vorratsschutz sowie der Pflanzengesundheit. Hauptsitz ist Quedlinburg. Weitere Standorte sind Braunschweig, Berlin, Kleinmachnow, Dresden, Darmstadt, Dossenheim, Münster, Siebeldingen und Groß Lüsewitz.
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