Explore the vast range of titles available.

Background Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However, strictly speaking, scientists did not use most existing variety identification techniques for “identification” but for “distinction of a limited number of cultivars,” of which generalization ability always not be well estimated. Because many varieties have similar genetic backgrounds, even some essentially derived varieties (EDVs) are involved, which brings difficulties for identification and breeding progress. A fast, accurate variety identification method, which also has good performance on EDV determination, needs to be developed. Results In this study, with the strategy of “Divide and Conquer,” a variety identification method Conditional Random Selection (CRS) method based on SNP of the whole genome of 3024 rice varieties was developed and be applied in essentially derived variety (EDV) identification of rice. CRS is a fast, efficient, and automated variety identification method. Meanwhile, in practical, with the optimal threshold of identity score searched in this study, the set of SNP (including 390 SNPs) showed optimal performance on EDV and non-EDV identification in two independent testing datasets. Conclusion This approach first selected a minimal set of SNPs to discriminate non-EDVs in the 3000 Rice Genome Project, then united several simplified SNP sets to improve its generalization ability for EDV and non-EDV identification in testing datasets. The results suggested that the CRS method outperformed traditional feature selection methods. Furthermore, it provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties and be useful for crop breeding.

True breeding of button mushrooms has hardly been done in the last decades, despite this species being one of the most cultivated mushrooms worldwide. Research done in the last 20 years has identified and characterised new germplasm and improved our understanding of the genetic base for some traits. A substantial collection of wild-collected strains is now available and partly characterised for a number of important traits such as disease resistance and yield. Most of the variations found in a number of important agronomic traits have a considerable heritability and are thus useful for breeding. Genetic marker technology has also developed considerably for this mushrooms in the last decade and used to identify quantitative trait loci (QTL) for important agronomic traits. This progress has, except for one example, not resulted so far into new commercially varieties. One of the reasons lies in the typical life cycle of the button mushroom Agaricus bisporus var. bisporus which hampers breeding. Joint investment is needed to solve technical problems in breeding. Special attention is needed for the protection of new varieties. Due to its typical life cycle, it is very easy to generate so called “look-a-likes” from protected cultivars by screening fertile single spore cultures. A consensus has been reached within the mushroom (breeding) industry to consider this method as the generation of essentially derived varieties as defined in plant breeding.

Breeders persistently supply farmers with the best varieties in order to exceed consumer demand through plant-breeding processes that are resource-intensive. In order to motivate continuous innovation in variety development, a system needs to provide incentives for plant breeders to develop superior varieties, for example, exclusive ownership to produce and market those varieties. The most common system is the acquisition of intellectual property protection through plant variety protection, also known as the breeder’s right. Most countries have adopted the system established by the International Union for the Protection of New Varieties of Plants (UPOV). To be granted plant variety protection, the variety should prove to be unique by meeting three requirements: distinctness, uniformity, and stability. This review summarizes (1) the plant variety protection via UPOV convention, (2) technical methods for distinctness, uniformity, and stability testing via phenotype, molecular markers, and sequencing as well as their challenges and potentiality, and (3) additional discussions in essentially derived variety, value for cultivation and use testing, and open source seed initiative.

The continuous emergence of Essentially Derived Varieties (EDVs) in the process of tea tree breeding will endanger and affect the innovation ability and development potential of tea tree breeding. In this study, genotyping by sequencing (GBS) technology was used to screen high-quality genomic SNPs for the first time to investigate the derived relationships of 349 tea trees from 12 provinces in China. A total of 973 SNPs uniformly covering 15 tea tree chromosomes with high discrimination capacity were screened as the core SNP set. A genetic similarity analysis showed that 136 pairs of tea trees had a genetic similarity coefficient (GS) > 90%, among which 60 varieties/strains were identified as EDVs, including 22 registered varieties (19 were indisputably EDVs). Furthermore, 21 SNPs with 100% identification of 349 tea trees were selected as rapid identification markers, of which 14 SNP markers could be used for 100% identification of non-EDV. These results provide the basis for the analysis of the genetic background of tea trees in molecular-assisted breeding.

This review examines the categorization of Essentially Derived Varieties (EDV) introduced in the 1991 revision of the Convention of the Union internationale pour la protection des obtentions végétales (UPOV). Other non-UPOV member countries (India, Malaysia, and Thailand) have also introduced the concept of essential derivation. China, a UPOV member operating under the 1978 Convention, is introducing EDVs via seed laws. Challenges in the implementation of the concept and progress made to provide greater clarity and more efficient implementation are reviewed, including in Australia and India. The current approach to EDV remains valid provided (i) clarity on thresholds can be achieved including through resource intensive research on an individual crop species basis and (ii) that threshold clarity does not lead to perverse incentives to avoid detection of essential derivation. However, technological advances that facilitate the simultaneous introduction or change in expression of more than “a few” genes may well fundamentally challenge the concept of essential derivation and require a revision of the Convention. Revision could include deletion of the concept of essential derivation coupled with changes to the breeder exception on a crop-by-crop basis. Stakeholders might also benefit from greater flexibility within a revised Convention. Consideration should be given to allowing members to choose if and when to introduce changes according to a revised Convention on a crop specific basis.

Well-developed maize reference genomes and genotyping technology along with fast decreasing detection costs have enabled the chance of shifting essentially derived varieties (EDV) identification to high-throughput SNP genotyping technology. However, attempts of using high-throughput technologies such as SNP array on EDV identification and the essential baseline parameters such as genetic homozygosity and/or stability in EDV practices have not been characterized. Here, we selected 28 accessions of 21 classical maize inbreds, which definitely form a pedigree network from initial founders to derivatives that had made huge contribution to corn production, to demonstrate these fundamental analyses. Our data showed that average residual heterozygosity (RH) rate of these 28 accessions across genome was about 1.03%. However, the RH rate of some accessions was higher than 3%. In addition, some inbreds were found to have an overall RH rate lower than 2% but over 8% level at certain chromosomes. Genetic drift (GD) between two accessions from different years or breeding programs varied from 0.13% to 13.16%. Accessions with low GD level showed cluster distribution pattern and compared with RH distributions indicated that RH was not the only resource of GD. Both RH and GD data suggested that genetic purity analysis is an essential procedure before determining EDV. Eleven derivative lines were characterized with regard to their genome compositions and were inferred as their breeding histories. The backcross, bi-parental recycling, and mutation breeding records could be identified. The data provide insights of underlining fundamental parameters for defining EDV threshold and the results demonstrate the EDV identification process.

Do new breeding techniques (NBT) lead to essentially derived varieties (EDV)? It depends! It depends on the definition of EDV in the plant variety right (PVR) laws and their interpretation by the courts. This paper aims at providing an overview of the EDV concept and an analysis of the question whether NBT lead to EDV on the basis of the UPOV 1991 Act, the most recent UPOV Explanatory Notes on EDV of 2017 as well as some selected PVR laws. Almost 30 years ago, the concept of EDV has been incorporated into the UPOV 1991 Act. In order to strengthen the rights of breeders, in particular to provide breeders of original genotypes an additional source of remuneration, a system of \"Plant Variety Right specific dependency,\" based on \"essential derivation,\" was developed. Only a very limited number of court cases have been concerned with EDV. However, an escalation in EDV-related conflicts can be expected in the future due to increased competition in the ornamental and fruit breeding business as well as to the application of more sophisticated NBT.

Plant breeders’ rights (PBRs) are an important IP right, and as plant breeding has a crucial role to play in sustainability, it is vital that innovations in plant breeding receive the appropriate innovation incentives. The full breeders’ exemption ensures that there is always free access to the plant variety protected by a PBR for developing new varieties. The price to pay for this exemption is that PBR holders cannot prevent third parties from taking advantage of their efforts and investments in developing a new variety. This invites free-riding, at the detriment of the PBR holder. The concept of “essentially derived varieties” (EDV), introduced in 1991, provided a “fix” for this problem. It allows PBR holders to extend, at least to some extent, the scope of protection of their PBR to those varieties which use all or most essential characteristics of the initial protection variety. Decades have passed, but no adequate interpretation of the complex EDV concept has been found. The advent of new breeding techniques (NBTs) has made the discussion about a fair scope of protection of PBRs all the more relevant. This necessitates a modernization of the EDV concept, if the PBR system is to remain relevant and continue to be an innovation-incentivizing mechanism. I argue that a broader scope for the EDV concept is essential and fair. Determining what essential derivation is will remain a difficult task also in the future. This is why I have additionally proposed a collaborative reward model, which will facilitate the functioning of the EDV system and is capable of providing more legal certainty in this area.

Plant variety protection laws based on the 1991 revision of the Union Internationale pour la Protection des Obtentions Vegetales (UPOV) include the concept of an essentially derived variety (EDV). It is widely accepted that molecular markers can provide data to help determine EDV status. We screened publicly available simple sequence repeat (SSR) loci using a set of inbred lines, including those that have been widely used or are of historic importance to maize (Zea mays L.) breeding in the United States. As a result of that screening process we hereby publish a set of 285 SSRs that have been validated by the American Seed Trade Association (ASTA) for use in variety identification and for assistance in determining EDV status in U.S. maize. One hundred and fifty SSRs constitute the ASTA Core Set 1; additional data, if required, can be obtained by using the additional 135 SSRs. We also report on comparisons of abilities of the ASTA-designated SSRs to discriminate among and show associations among inbred lines compared with results obtained from another (partially overlapping) set of SSRs selected by the French Association of Maize Breeders (SEPROMA). There was a high correlation (R2 = 0.79) for pairwise distances among a subset of 30 U.S. inbreds for SSR data obtained using the ASTA protocols compared with those obtained using the SEPROMA protocols. Consequently, there are now two published sets of protocols and procedures that can be used to assist in variety identification and in the determination of essential derivation in maize depending on circumstances and available resources.

Genetic distances (GDs) based on molecular markers are important parameters for identifying essentially derived varieties (EDVs). In this context information about the variability of molecular markers within maize inbred lines is essential. Our objectives were to (1) determine the variation in the size of simple sequence repeat (SSR) fragments among different accessions of maize inbreds and doubled haploid (DH) lines, (2) attribute the observed variation to genetic and marker system-specific sources, and (3) investigate the effect of SSR fragment size differences within maize lines on the GD between maize lines and their consequences for the identification of essentially derived varieties. Two to five accessions from nine inbred lines and five DH lines were taken from different sources or drawn as independent samples from the same seed lot. Each accession was genotyped with 100 SSR markers that evenly covered the whole maize genome. In total, 437 SSR fragments were identified, with a mean of 4.4 alleles per locus. The average polymorphic information content (PIC) was 0.58. GD estimates between two accessions of the same genotype ranged from 0.00 to 0.12 with an average of 0.029 for inbred lines and 0.001 for DH lines. An average of 11.1 SSRs was polymorphic between accessions of the same inbred line due to non-amplification (8.1 SSRs), heterogeneity (4.0 SSRs) or unknown alleles (2.6 SSRs). In contrast to lab errors, heterogeneity contributed considerably to the observed variation for GD. In order to decrease the probability to be suited for infringing an EDV threshold by chance, we recommend to increase the level of homogeneity of inbred lines before applying for plant variety protection.