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Last update: May 2021

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Genotyping strategies for genomic selection in layer chickens

Thesis : genotyping strategies for genomic selection in layer chickens
Study of different genotyping strategies of breeders and selection candidates to optimize the accuracy of genomic evaluations and to minimize selection costs.

The main goal of genetic selection is to improve performances of a population by choosing the best breeders of a generation to produce the population of the next generation.
The emergence of molecular markers such as SNP (Single Nucleotide Polymorphisms) in the 2000s enabled the development of biotechnologies which led in 2011 and 2013 to the creation, in poultry production, of high-density SNP chips of 60 000 and 600 000 SNP by Illumina and Affymetrix (Groenen et al., 2011 ; Kranis et al., 2013). Genomic selection was then developed by using this information on DNA polymorphisms, in addition of performance measures, to choose the breeders of the next generation among a set of selection candidates. Concurrently, the development of Next Generation Sequencing (NGS) enables as of now to consider others solutions than SNP chips to do genomic selection.


Develop solution at a lower cost…

Currently, genotyping on high-density SNP chip still remains too expensive for all selection candidates, especially for chickens whose market value of breeders is very low. One of the aims of genomic selection is to develop other solution at a lower cost. A first one is the development of low density SNP chips. To do so, one needs to select a panel of SNP allowing imputation (mathematical prediction) of missing genotypes on the HD chip. Another solution could be the low depth sequencing of selection candidates in order to impute low depth sequences to HD genotyping or high depth sequences.

…the imputation technique

The common point to these two solutions is imputation. This technique enables to deduce missing genotypes of all candidates selection thanks to their genotyping (or low depth sequences) and high density genotyping (or high depth sequences) of a reference population (Dassonneville, 2012). Imputation relies on the rules of Mendelian transmission of the characters and on linkage disequilibrium. Linkage disequilibrium between 2 loci corresponds to a preferential association between alleles carried by the individuals at these 2 loci.

High depth sequencing of breeders to improve the accuracy of genomic evaluations ?

Another lever for optimizing genomic selection in laying hens concerns breeders’ genotyping. These genotypes are obtained with HD chip and permit to obtain a good accuracy of genomic evaluation. It may be worth considering whether high depth sequencing of breeders can improve or not the accuracy of genomic evaluations.
Poultry industries such as Novogen now take the turn of the revolution which genomic selection is. In a very competitive world, selection industries have to implement the best genotyping strategies for their selection schemes in order to produce the best animals and products.


Aims of the thesis

The global aim of the thesis will be, focusing on two laying hens lines selected by Novogen, to study different genotyping strategies of breeders and selection candidates to optimize the accuracy of genomic selection and to minimize selection costs.

  • First of all, a study of the impact of different factors such as SNP density on low density chip, the methodology used to build low density chip, the size and structure of reference and candidate populations, the structure of linkage disequilibrium, and so on… on the effectiveness of imputation will be done.
  • In a second time, based on the observations previously led, a multi-line low density SNP chip for poultry will be designed and its impact on accuracy of genomic evaluation will be studied. Our objectives are to build a chip allowing good results of imputation of the candidate population as well as a good accuracy of genomic evaluations.
  • Finally, in a third time, we will study the interest of using sequences in selection scheme, at the level of breeders with high depth sequences and at the level of candidates with low depth sequences.

Florian Herry is working on this subject of thesis since the 1st november of 2016 for 3 years. He is supervised by Sophie Allais and Pascale Le Roy in the team genetics and genomics.


Florian Herry : florian.herry[at] (PhD Student); Sophie Allais : sophie.allais[at] (Co-supervisor); Pascale Le Roy : pascale.le-roy[at] (Supervisor)



  • Dassonneville, R., 2012. Genomic selection of dairy cows. AgroParisTech, Inra Gabi, Jouy-en-Josas. PhD
  • Groenen, M. A. M., Megens, H. J., Zare, Y., Warren, W. C., Hillier, LD W., Crooijmans, R. P. M. A., Vereijken, A., Okimoto, R., Muir, W. M. et Cheng, H. H., 2011. The development and characterization of a 60K SNP chip for chicken. BMC genomics. Vol. 12, n° 1, pp. 1. [DOI]
  • Kranis, A., Gheyas, A. A, Boschiero, C., Turner, F., Yu, L., Smith, S., Talbot, R., Pirani, A., Brew, F., Kaiser, P., Hocking, P. M., Fife, M., Salmon, N., Fulton, J., Strom, T. M., Haberer, G., Weigend, S., Presinger, R., Gholami, M., Qanbari, S., Simianer, H., Watson, K. A., Woolliams, J. A. and Burt, D. W., 2013. Development of a high density 600K SNP genotyping array for chicken. BMC Genomics. Vol. 14, n° 1, pp. 59. [DOI]