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4. Optimization of marker assisted selection

 

Following our results on the advantages of leading recurrent marker assisted selection for the multiparental schemes (Blanc et al., 2006, Theor Appl Genet; Blanc et al., 2008, Euphytica), we developed the OptiMAS software (Valente et al., 2013, Journal of Heredity, available at http://moulon.inra.fr/optimas/) to follow the transmission of favorable alleles in breeding schemes in order to choose the best parents to be crossed to increase the probability of obtaining the molecular ideotype at the targeted QTL.

We also strongly invest in the evaluation of genomic selection, especially for complex traits. This approach is based on the genotyping and phenotyping of a reference sample of individuals for the calibration of a model, which is then applied to predict the value of individuals based only on genotyping data. This avoids QTL detection step, which increases prediction efficiency for highly complex traits.

We showed that his approach was suitable in a multiparental context for a complex trait such as yield (Bardol et al., submitted) and that its efficiency can be significantly increased by optimizing the calibration of the reference population (Rincent et al., 2013, Genetics). A R-code was developed to help choosing the lines to be included in the reference population to increase the reliability of genomic predictions and is available on request.