Integrating genomic prediction into crop DUS testing: new approaches in support of reference collection management and distinctness assessment.

Abstract

Key message A new approach is proposed for the use of the genetic markers to manage DUS trials, targeted at individual phenotypic characteristics using genomic prediction, as well for supporting Distinctness decisions. High-performing crop varieties underpin food security. Due to the cost of developing varieties, systems have been established to provide breeders with legal protection for their varieties. In many countries, such protection is afforded by the International Union for the Protection of New Varieties of Plants (UPOV) system. New varieties must be phenotypically Distinct from existing varieties using a set of crop-specific characteristics, as well as Uniform and Stable (DUS). For many crops, DUS assessment is costly as candidates must be compared to many existing varieties in field trials, based on numerous DUS characteristics. The use of genetic markers has long been considered as a potential tool for managing costs of such trials, for example, by identifying existing varieties that need not be compared to candidate varieties. Under UPOV guidance, the use of genetic markers must be reflective of phenotypic differences in DUS characteristics. Within this framework, we propose a new approach for using markers based on the application of genomic prediction, which is used to predict variety differences in individual characteristics. The approach is evaluated with perennial ryegrass and wheat, yielding promising results. Additionally, we propose a novel approach in which genomic prediction is used to refine Distinctness decisions after DUS trials have been run by integrating genetic and trial information. Using perennial ryegrass as an example, we demonstrate that this approach, which respects the primacy of phenotype in DUS testing, could be used to support distinctness decisions, especially for cross-pollinated agricultural crops where Distinctness may be harder to achieve.

Plant phenotyping relevance

ゲノム予測を用いてDUS特性の品種差を予測し、DUS試験後のDistinctness判定を支援する手法を提案・評価しており、植物表現型の推定と判定支援が研究の中心である。

Code and data availability

The paper's perennial ryegrass phenotypic DUS data is stated to be in the Supplementary Information, but no public URL for the supplement is present in the supplied blocks or allowed_urls; the only deposited data mentioned is genome resequencing reads (NCBI SRA BioProject PRJNA1255563), which is a molecular omics asset

No evidence-backed public reproduction asset is currently recorded.