Crop breeding is a significant investment, and Plant Variety Rights (PVR) protect breeders' investments. The DUS test, a key component of PVR, assesses distinctness, uniformity, and stability of new varieties, traditionally relying on morphological traits. However, this system faces increasing pressure due to several factors. The expansion of new varieties shrinks the available combinations of DUS traits. Many DUS traits have low heritability, leading to inconsistencies across environments and unreliable scoring. The system's implementation is challenging for minor or orphan crops where suitable DUS traits are hard to identify and for outbreeding species or hybrids. The definition of "essentially derived varieties" (EDVs) further complicates objective evaluation. Although molecular markers have been suggested for DUS testing since 1990, their adoption has been slow due to UPOV's requirement of perfect correlation with DUS traits. This study uses UK barley varieties to illustrate these challenges and proposes a solution using genomic DUS.

Previous research highlighted the need for improved DUS systems. Studies have explored using molecular markers, proposing various marker sets for different crops (minisatellites in soft fruits, SSR markers in maize and rice, SNP markers in barley). However, these marker sets were either too small or lacked sufficient throughput and were not officially adopted by UPOV. The UPOV guidelines require molecular markers to perfectly correlate with DUS traits, hindering the incorporation of advanced genotyping technologies. Cockram et al. (2010) conducted GWAS on barley DUS traits, identifying 16 loci. This work builds upon this foundation, expanding the analysis to a larger dataset and exploring the implications for a genomic DUS system.

The study analyzed a panel of 805 UK barley varieties, encompassing spring, winter, and alternative types, using 28 DUS traits. DUS trait data were sourced from NIAB and SASA, supplemented with data from Cockram et al. (2010). Marker data from the IMPROMALT collection (40,078 SNPs) were integrated. The researchers compared DUS trait scoring inconsistencies between NIAB and SASA, assessing consistency using the proportion of exact matches. Heritabilities were calculated using univariate mixed linear models, incorporating genetic relationships among varieties. Genetic and phenotypic correlations between DUS traits and yield were determined using bivariate mixed linear models, focusing on spring barley. Genome-wide association studies (GWAS) were conducted on each DUS trait using data from spring, winter, and combined datasets. The utility of a previously proposed small marker set for DUS was evaluated through simulations of F6 progeny from known parent pairs. The minimum number of markers needed for effective DUS was determined by comparing Manhattan distances from DUS traits and randomly sampled markers. Finally, a "genomic DUS" approach was illustrated using Manhattan distances based on genomic markers, simulating progeny to assess distinctness, uniformity, and stability. Cost and time comparisons were made between four DUS methods: morphological trait DUS, speed DUS, trait-specific marker DUS, and genomic DUS.

The analysis revealed significant inconsistencies in DUS trait scoring across different organizations (NIAB and SASA), with only two-thirds of scores matching exactly. Many DUS traits exhibited low heritabilities (h² < 0.50), indicating high environmental influence and poor reproducibility. The combinatorial space of DUS traits has shrunk over time, particularly in spring barley, suggesting reduced distinctiveness. Genetic correlations between DUS traits and yield were identified in spring barley, highlighting the potential for undesirable correlated responses during selection. GWAS identified 32 loci associated with DUS traits, more than previously reported, with some loci showing population-specific effects. The evaluation of a small marker set showed limited distinguishing power, especially for newer varieties. Simulations indicated that approximately 500-1000 markers are minimally required for effective variety separation. The genomic DUS approach demonstrated the feasibility of using genomic markers for accurate assessment of distinctness, uniformity, and stability. Genomic DUS offered a significant reduction in time and cost compared to the traditional morphological trait-based approach. Four varieties failed to meet the arbitrary minimum distance threshold in the genomic DUS approach, suggesting potential EDVs.

The findings demonstrate the limitations of the current DUS system relying on morphological traits. Low heritabilities, environmental inconsistencies, and shrinking trait space compromise the system's effectiveness. Genetic correlations with yield create challenges for breeders. The proposed genomic DUS approach overcomes these limitations, providing a more robust, reliable, and cost-effective method for variety registration. Genomic DUS also offers a clearer definition of EDVs, reducing ambiguity. The use of genomic markers allows for efficient identification of varieties and their uniformity across multiple generations.

This study strongly advocates for transitioning to a genomic DUS system. The current system, based on morphological traits, is inadequate due to low heritability, environmental inconsistencies, limited trait space, and genetic correlations with yield. Genomic DUS offers a robust alternative, improving accuracy, efficiency, and cost-effectiveness while clarifying EDV definitions and facilitating improved seed certification. Future research should focus on developing standardized genomic DUS protocols and expanding the approach to other crop species.

The analysis focused primarily on UK barley varieties, limiting the generalizability to other crops or regions. The arbitrary distance threshold used in genomic DUS requires further optimization and validation. The study's reliance on publicly available data may not represent the complete spectrum of UK barley varieties.