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Proposition of a SNP set to replace SSRs for standardized cultivar identification in apple
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Edité par CCSD -
International audience. Apple (Malus domestica Borkh.) is one of the most important fruit crops grown in temperate regions. Ex situ conservation of apple genetic resources mostly relies on grafted trees maintained in orchards, which can be space- and labor-intensive to manage. In order to help collection managers to compare their germplasm with others’ at the national and international levels, Malus UNiQue genotype codes (MUNQ) were proposed for all accessions sharing the same genetic marker profile. These genetic profiles were initially obtained with a standardized set of 16 SSRs. However, SSR marker profiles are time-consuming to produce and require attention to harmonization of genotypic scores across different labs. SNP-based MUNQ assignment is expected to be more streamlined, but just like for SSRs it will be essential that a consistent marker set is used across studies worldwide to enable comparisons among them, without genotyping each unique individual with a larger array. For this reason, we developed a set of 96 SNP markers that can unequivocally distinguish cultivars in apple collections and detect redundancy faster at low cost. To support this approach, we started from genome-wide SNP genotypic data obtained with the apple 20K and/or 480K arrays for 2122 unique individuals, including 2036 with a MUNQ code assigned through SSR markers. A total of 183 SNPs were tested using the KASPar technology in nanofluidic Integrated Fluidic Circuit (IFC) (Standard BioTools Inc.) to finally choose a set of 96 SNP ensuring that each pair of individuals among all 2122 individuals is distinguished by at least 6 SNPs in the absence of missing data. Comparison of MUNQ code assignment for ~800 newly genotyped accessions using the standardized set of 16 SSRs and the new set of 96 SNPs will be presented.
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