GDR-LIST June 2020

gdr-list@bioinfo.wsu.edu

2 participants
2 discussions

Technology Write For Us — Submit Guest Post at Publishthispost Blog

by shankarpublish＠gmail.com

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3 years, 10 months

Development of apple 50K Axiom array

by Peil, Andreas

Dear colleagues/apple community, The Federal Ministry for Food and Agriculture in Germany asked the Julius Kühn-Institut (JKI), Institute for Breeding Research on Fruit Crops (ZO) to develop a 50K SNP array for the genotyping of the apple germplasm collected in the Deutsche Genbank Obst (German Fruit Gene Bank). A future purpose of the genotypic data will be GWAS. The array will be available to the public. I would therefore like to ask again for your support in the development of a new apple 50k Axiom SNP array, which is in progress with few international partners (Michela Troggio, Helene Muranty, Charles-Eric Durel, Eric van de Weg, Luca Bianco and Nicholas Howard). The new array shall deliver a good and evenly coverage of the apple genome and comparability to both the 20K Illumina SNP array and the 480K Axiom SNP array. The new reference genome HFTH1 will be used to fill in the gaps existing in GDDH13 with SNPs. Therefore, a discovery panel was defined for realignment to HFTH1 by Eric, Nick and Luca. Cultivars were chosen from different clusters gained from principle component analysis done by Nick to ensure high diversity. Eric, Nick and Luca also selected a set of Malus wild species accessions of M. baccata, M. orientalis, M. sieversii, M. sylvestris and M. ×robusta, for realignment to HFTH1 to possibly identify introgressions from these wild species in domesticated apple. WUR in Wageningen has offered capacity for realignment and is in progress. The Axiom array will have space for 46K SNPs in a 6 × 6 µM matrix. The size of the sequences on the array will be 35 nts. We decided to work with haplo blocks. A haplo block will span 125K and will be represented by 8 SNPs with additional blocks for chromosome ends. With an estimated size of 651 Mb of the apple genome, this would require around 41,800 SNPs. The remaining 4,200 SNPS will be contributed towards Malus wild species specific SNPs, for SNPs related to traits (e.g. resistance, quality, self-incompatibility) and possibly to maternal inherited SNPs. We suggest one species specific SNP / Mb. If we calculate 650 Mb for the apple genome this would require a total of 3,250 SNPs that will be needed for wild species. We have 950 SNPs left for trait related and maternal inherited SNPs. I would like to invite you to support and participate in the development of the array by contributing sequences of reliable SNPs linked to traits of interest and/or SNPs inherited maternal and/or your experience. The deadline for contributing SNP sequences is July 1st 2020. If you are willing to promote this project in another way, please contact me as soon as possible. Looking forward to hearing from you 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/> [http://www.jki.bund.de/typo3temp/pics/12b906050c.jpg][http://intranet.jki.b…] [10 Jahre gruen Slogan.jpg] 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.

3 years, 10 months

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GDR-LIST June 2020