Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses

Abstract

Abstract Oilseed rape faces many challenges, especially at the beginning of its developmental cycle. Achieving rapid and uniform seed germination could help to ensure a successful establishment, and therefore enabling the crop to compete with weeds and tolerate stresses during the earliest developmental stages. The polygenic nature of seed germination was highlighted in several studies, and more knowledge is needed about low- to moderate-effect underlying loci in order to enhance seed germination effectively by improving the genetic background and incorporating favorable alleles. A total of 17 QTL were detected for seed germination-related traits, for which the favorable alleles often corresponded to the most frequent alleles in the panel. Genomic and phenomic predictions methods provided moderate to high predictive abilities, demonstrating the ability to capture small additive and non-additive effects for seed germination. This study also showed that phenomic prediction better estimated breeding values than genomic prediction. Finally, as the predictive ability of phenomic prediction was less influenced by the genetic structure of the panel, it is worth using this prediction method to characterize genetic resources, particularly with a view to design prebreeding populations.

Plant phenotyping relevance

種子発芽形質を対象に、フェノミック予測の予測性能とゲノミック予測との比較を主要課題として扱っており、形質推定手法が中心である。

Code and data availability

The paper's germination phenotyping (RGB imaging), NIRS spectra, and SNP datasets are deposited on recherche.data.gouv.fr, but only via a private review-token link; the authors state the data will be made freely available with a DOI only upon article acceptance. No author analysis code/scripts or trained models are公开ly

No evidence-backed public reproduction asset is currently recorded.