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Développement d’une puce de génotypage haute densité 600K pour le canard commun et le canard de Barbarie

Abstract : Genomic selection is widely used for genetic improvement of many plant and animal species. This evaluation method could potentially increase genetic gain in ducks for traits that cannot be measured on selection candidates (lethal, expressed in one sex only, or measured on hybrid duck for purebred selection). Implementation of genomic selection depends on the availability of genotyping tools, such as SNP chips, but so far none were developed neither for common duck (Anas platyrhynchos) nor Muscovy duck (Cairina moschata). This paper describes the assembly of the Muscovy duck genome (the common duck genome is already available), and the design of a 600K Thermo Fisher SNP chip. The common duck genome was used as reference for the assembly of the Muscovy genome: 3702 scaffolds were produced, with a N50 of 2.4 Mb. SNP were identified from sequence data: several Muscovy and common ducks populations (Rouen duck, Mallard duck, Pekin duck), were collected, and 50 samples were pooled independently for each population. After raw quality controls, 8.4 million SNPs and 12.2 million SNP were identified for Muscovy and common ducks respectively. Filters based on Minor Allele Frequence and genome coverage were used, and finally 343 950 SNP were kept for the common duck, and 331 241 SNP for the Muscovy duck.
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https://hal.inrae.fr/hal-02738413
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Submitted on : Tuesday, June 2, 2020 - 8:51:05 PM
Last modification on : Friday, November 5, 2021 - 2:38:11 PM

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  • HAL Id : hal-02738413, version 1
  • PRODINRA : 466824

Citation

Noémie Thébault, Juliette Riquet, Christian Diot, Sophie Brard-Fudulea, Daniel Guemene, et al.. Développement d’une puce de génotypage haute densité 600K pour le canard commun et le canard de Barbarie. 13.Journées de la recherche avicole et des palmipèdes à foie gras, Mar 2019, Tours, France. ⟨hal-02738413⟩

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