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Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program


Key message

We review and propose easily implemented and affordable indicators to assess the genetic diversity and the potential of a breeding population and propose solutions for its long-term management.


Successful plant breeding programs rely on balanced efforts between short-term goals to develop competitive cultivars and long-term goals to improve and maintain diversity in the genetic pool. Indicators of the sustainability of response to selection in breeding pools are of key importance in this context. We reviewed and proposed sets of indicators based on temporal phenotypic and genotypic data and applied them on an early maize grain program implying two breeding pools (Dent and Flint) selected in a reciprocal manner. Both breeding populations showed a significant positive genetic gain summing up to 1.43 qx/ha/year but contrasted evolutions of genetic variance. Advances in high-throughput genotyping permitted the identification of regions of low diversity, mainly localized in pericentromeric regions. Observed changes in genetic diversity were multiple, reflecting a complex breeding system. We estimated the impact of linkage disequilibrium (LD) and of allelic diversity on the additive genetic variance at a genome-wide and chromosome-wide scale. Consistently with theoretical expectation under directional selection, we found a negative contribution of LD to genetic variance, which was unevenly distributed between chromosomes. This suggests different chromosome selection histories and underlines the interest to recombine specific chromosome regions. All three sets of indicators valorize in house data and are easy to implement in the era of genomic selection in every breeding program.

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Data availability

The datasets analyzed in this study are not publicly available.


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The authors thank the experimental staff at RAGT2n for managing field experiments and data extractions. This research was funded by RAGT2n and the ANRT CIFRE Grant No. 2016/1281 for AA.

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Correspondence to Alain Charcosset.

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The authors declare that they have no conflict of interest. The experiments reported in this study comply with the current laws in Europe.

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Allier, A., Teyssèdre, S., Lehermeier, C. et al. Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program. Theor Appl Genet 132, 1321–1334 (2019). https://doi.org/10.1007/s00122-019-03280-w

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