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James Cockram - One of the best experts on this subject based on the ideXlab platform.
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Use of genetic markers for the detection of off-types for DUS phenotypic traits in the inbreeding crop, barley
Molecular Breeding, 2020Co-Authors: Benedetta Saccomanno, Margaret Wallace, Donal M. O’sullivan, James CockramAbstract:Detection of crop off-types is of interest for multiple uses, including the assessment of uniformity for new Plant variety applications during distinctness, uniformity and stability (DUS) testing for the awarding of Plant Breeders’ Rights (PBR). Here, we investigate whether genetic markers, in this case Kompetitive Allele-Specific PCR (KASP), can be used for the identification off-types for phenotypes assessed for DUS in the inbreeding cereal crop, barley ( Hordeum vulgare ). To demonstrate proof of principle, KASP markers diagnostic for phenotypic expression of nine DUS phenotypes, and DNA from two barley varieties (‘Pelican’ and ‘Felicie’) carrying contrasting alleles at each marker were used. We found that for the majority of markers, it was possible to robustly call alleles down to template DNA concentrations of 2 ng, but not ≤ 0.2 ng. When used in mixtures of DNA consisting of ‘Felicie’ DNA spiked with different concentrations of ‘Pelican’ DNA, robust allele calling was possible in DNA mixtures down to 18 ng:2 ng. Collectively, this demonstrates that where diagnostic markers are available, molecular identification of a single off-type for a given DUS trait within a bulk of ten individuals should be possible. We validated this assumption, with all of the diagnostic genetic markers investigated found to robustly detect DUS off-types at a frequency of 10% in DNA extracted from tissue collected from pools of 10 individuals. Ultimately, this work demonstrates that, where diagnostic polymorphisms are known for DUS traits, KASP markers should be able to robustly detect off-types or cross-contamination within DNA samples from a diploid inbred species down to 10%. While just two varieties that contrasted for the eight DUS targeted were investigated in this study, as the markers used are diagnostic for their relevant phenotype (or a proportion of the variation observed for that phenotype), in theory the approach should be valid for any variety studied—although the introduction of novel alleles via spontaneous mutation or more exotic germplasm pools may mean that marker sets would need to be periodically added to or updated. However, we nevertheless demonstrate the principle that, for a subset of DUS traits, molecular markers can now be robustly used as a tool towards determining all three components of the DUS testing process in barley. These results are relevant for the assessment of varietal uniformity by crop Breeders, crop testing authorities and germplasm maintenance, as well as highlighting the potential use of bulk samples rather than individual Plant samples for assessment of distinctness by molecular methods.
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variety protection and Plant Breeders Rights in the dna era
2013Co-Authors: Huw Jones, Carol Norris, James CockramAbstract:The development of new crop varieties offers potential benefits, in terms of yield to growers, and in quality improvements to end users. A new variety represents a considerable investment by Plant Breeders and this can be sustained by commercial returns. A robust system to protect a new variety, and thus the Plant Breeders’ intellectual property, is part of the infrastructure needed to promote the flow of new varieties. Here we describe current Plant variety protection systems and discuss how DNA based markers may be used within those legal and administrative provisions.
Johann F Kirsten - One of the best experts on this subject based on the ideXlab platform.
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the effects of Plant Breeders Rights on wheat productivity and varietal improvement in south african agriculture
Sustainability, 2019Co-Authors: Charity R Nhemachena, Johann F Kirsten, Binganidzo MucharaAbstract:The strengthening of the intellectual property Rights (IPRs) for Plant varieties provide incentives for breeding companies to invest more resources in Plant breeding. The main objective of this paper was to analyze the effects of strengthening the wheat variety intellectual protection on wheat productivity and the release of new varieties. The strength of IPR systems was measured using an intellectual property (IP) protection index, and Plant Breeders’ Rights (PBRs) granted for wheat varieties. The empirical analyses were based on correlation and multiple regression analyses. The results showed that strengthening IPR systems in South Africa contribute to improving wheat productivity and increasing the number of wheat varieties released. Furthermore, although the robust coefficients of the other IPR variables are positive, they are statistically insignificant for all scenarios. There is a need for more incentives beyond granting PBRs and strengthening of IPR systems to be provided in the whole wheat sector to stimulate increased investments and the release of new varieties.
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the effects of Plant Breeders Rights on wheat productivity and variety improvement in south africa
2018 Annual Conference September 25-27 Cape Town South Africa, 2018Co-Authors: Charity R Nhemachena, Johann F Kirsten, Binganidzo MucharaAbstract:The strengthening of the IPRs for Plant varieties provide incentives for breeding companies to invest more resources in Plant breeding. The main objective of this paper was to analyze the effects of strengthening wheat variety intellectual protection on wheat productivity and release of new varieties. The strength of IPR systems was measured using an IP protection index, and Plant Breeders' Rights granted for wheat varieties. The empirical analyses were based on correlation and multiple regression analyses. The results showed that strengthening IPR systems in South Africa contribute to improving wheat productivity and increasing the number of wheat varieties released. Furthermore, although the robust coefficients of the other IPR variables are positive, they are statistically insignificant for all scenarios. There is need for more incentives beyond granting PBRs and strengthening of IPR systems to be provided in the whole wheat sector to stimulate increased investments and release of new varieties.
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the evolving landscape of Plant Breeders Rights regarding wheat varieties in south africa
South African Journal of Science, 2016Co-Authors: Charity R Nhemachena, Frikkie Liebenberg, Johann F KirstenAbstract:Addressing the multiple challenges facing global agriculture requires integrated innovation in areas such as seeds, biotechnology, crop protection, grain storage and transport. Innovations related to Plant improvement and the development of new or improved Plant varieties will only happen at an optimal level if Plant Breeders’ Rights (PBR) are properly protected. The objective was to analyse the evolving landscape of wheat Plant Breeders’ Rights to address the dearth of empirical evidence of the patterns and trends of wheat varietal improvements in South Africa. We compiled a detailed and novel count and attribute database of wheat varietal innovations in South Africa from 1979 to 2013 using various sources. This data set was then analysed to ascertain the main trends in, and ownership of PBRs for wheat varietal improvements in South Africa over this period. A total of 134 PBR wheat varietal innovations were lodged from 1979 to 2013, an average of 6 applications per year. The administrative delays in granting PBR applications were substantially reduced by 77 days during the post-deregulation period (after 1996), indicating increased efficiency. The main PBR applicants were Sensako (39%), the Agricultural Research Council Small Grains Institute (ARC-SGI) (25%) and Pannar (15%). The ARC-SGI contributed to some of the PBRs owned by private companies through shared genetic resources before Plant Variety Protection (PVP) was implemented. Future innovations and dissemination of wheat innovations can be stimulated by Plant variety protection, together with broader variety sector legislation that encourages both public and private sector investment.
Charity R Nhemachena - One of the best experts on this subject based on the ideXlab platform.
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the effects of Plant Breeders Rights on wheat productivity and varietal improvement in south african agriculture
Sustainability, 2019Co-Authors: Charity R Nhemachena, Johann F Kirsten, Binganidzo MucharaAbstract:The strengthening of the intellectual property Rights (IPRs) for Plant varieties provide incentives for breeding companies to invest more resources in Plant breeding. The main objective of this paper was to analyze the effects of strengthening the wheat variety intellectual protection on wheat productivity and the release of new varieties. The strength of IPR systems was measured using an intellectual property (IP) protection index, and Plant Breeders’ Rights (PBRs) granted for wheat varieties. The empirical analyses were based on correlation and multiple regression analyses. The results showed that strengthening IPR systems in South Africa contribute to improving wheat productivity and increasing the number of wheat varieties released. Furthermore, although the robust coefficients of the other IPR variables are positive, they are statistically insignificant for all scenarios. There is a need for more incentives beyond granting PBRs and strengthening of IPR systems to be provided in the whole wheat sector to stimulate increased investments and the release of new varieties.
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the effects of Plant Breeders Rights on wheat productivity and variety improvement in south africa
2018 Annual Conference September 25-27 Cape Town South Africa, 2018Co-Authors: Charity R Nhemachena, Johann F Kirsten, Binganidzo MucharaAbstract:The strengthening of the IPRs for Plant varieties provide incentives for breeding companies to invest more resources in Plant breeding. The main objective of this paper was to analyze the effects of strengthening wheat variety intellectual protection on wheat productivity and release of new varieties. The strength of IPR systems was measured using an IP protection index, and Plant Breeders' Rights granted for wheat varieties. The empirical analyses were based on correlation and multiple regression analyses. The results showed that strengthening IPR systems in South Africa contribute to improving wheat productivity and increasing the number of wheat varieties released. Furthermore, although the robust coefficients of the other IPR variables are positive, they are statistically insignificant for all scenarios. There is need for more incentives beyond granting PBRs and strengthening of IPR systems to be provided in the whole wheat sector to stimulate increased investments and release of new varieties.
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the evolving landscape of Plant Breeders Rights regarding wheat varieties in south africa
South African Journal of Science, 2016Co-Authors: Charity R Nhemachena, Frikkie Liebenberg, Johann F KirstenAbstract:Addressing the multiple challenges facing global agriculture requires integrated innovation in areas such as seeds, biotechnology, crop protection, grain storage and transport. Innovations related to Plant improvement and the development of new or improved Plant varieties will only happen at an optimal level if Plant Breeders’ Rights (PBR) are properly protected. The objective was to analyse the evolving landscape of wheat Plant Breeders’ Rights to address the dearth of empirical evidence of the patterns and trends of wheat varietal improvements in South Africa. We compiled a detailed and novel count and attribute database of wheat varietal innovations in South Africa from 1979 to 2013 using various sources. This data set was then analysed to ascertain the main trends in, and ownership of PBRs for wheat varietal improvements in South Africa over this period. A total of 134 PBR wheat varietal innovations were lodged from 1979 to 2013, an average of 6 applications per year. The administrative delays in granting PBR applications were substantially reduced by 77 days during the post-deregulation period (after 1996), indicating increased efficiency. The main PBR applicants were Sensako (39%), the Agricultural Research Council Small Grains Institute (ARC-SGI) (25%) and Pannar (15%). The ARC-SGI contributed to some of the PBRs owned by private companies through shared genetic resources before Plant Variety Protection (PVP) was implemented. Future innovations and dissemination of wheat innovations can be stimulated by Plant variety protection, together with broader variety sector legislation that encourages both public and private sector investment.
I. Roldán-ruiz - One of the best experts on this subject based on the ideXlab platform.
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Comparison of image analysis and direct measurement of UPOV taxonomic characteristics for variety discrimination as determined over five growing seasons, using industrial chicory as a model crop
Euphytica, 2013Co-Authors: P. Lootens, B. Chaves, J. Baert, J. Pannecoucque, J. Waes, I. Roldán-ruizAbstract:Tests for distinctness, uniformity and stability (DUS) are an essential component of variety registration and granting Plant Breeders’ Rights. This study, performed on industrial chicory ( Cichorium intybus L. ), included (1) an evaluation of the discriminating power of the UPOV characteristics and (2) a comparison of the root shape between the UPOV-based characteristics and characteristics determined via image analysis. Five consecutive growing periods were studied to assess the long-term stability of the parameters. Lack of discriminating power of characteristics for examining distinctness may impede breeding progress by failing to discriminate novel candidate varieties. However, a balance needs to be set so that newly introduced characteristics or new evaluation methodologies are not too powerful as to damage the protection of registered varieties. The results showed great differences in the discriminating power of the UPOV characteristics. The elimination of some of these low-discriminating characteristics would probably result in savings, but would have no consequences on the decisions taken by DUS testing authorities. Image analysis-derived characteristics could either replace currently-used parameters or provide additional characteristics with good discriminating power, determined in an objective and standardized way. Here we discuss possible implications for variety registration.
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Estimating genetic conformity between related ryegrass (Lolium) varieties. 1. Morphology and biochemical characterisation
Molecular Breeding, 2000Co-Authors: T.j. Gilliland, R. Coll, E. Calsyn, M. De Loose, M.j.t. Van Eijk, I. Roldán-ruizAbstract:In this study the morphological and protein diversity of twelve diploid perennial ryegrass accessions ( Lolium perenne L.) was examined. These accessions comprised five closely related groups, each containing an `initial variety' (IV) and one or more declared `essentially derived varieties' (EDV), with differing degrees of relatedness. `Essential derivation' is a legal concept relating to intellectual property in Plant varieties and is additional to Plant Breeders Rights (PBR). An EDV is defined as clearly distinct from, but conforming in its expression of the essential characteristics of an IV, from which it is found to have been predominantly derived. Where an essential derivation has been confirmed, the breeder of the IV may be entitled to some royalty sharing of the EDV. Clearly, therefore, in any successful EDV claim, evidence of a high degree of conformity in either the phenotype or genotype would be required. Examination of Plant morphology indicated that all the EDVs were morphologically distinct from their corresponding IV in one or more morphological characteristic. using a principal co-ordinates analysis to give an overall measure of morphological difference, all twelve accessions were correctly clustered into their related groups and the magnitude of the differences within groups reflected their known breeding histories. Examining protein diversity by methods that targeted single- and multiple-locus genes also clustered the accessions into their correct groups, in most cases. However, only by examining diversity in seed storage proteins were within-group relationships accurately represented. The methods used provided no consistent representation of between-group relationships. It was concluded that the morphological method provided a creditable measure of genetic conformity, but to avoid incurring excessive time, work and cost, results from existing national PBR trials would need to be openly available. Within the limits of the genetic material examined, seed storage protein diversity appeared to provide a suitable combination of accuracy and efficiency on which to base a routine test. However, given more complex breeding relationships than those in this study, methods such as AFLP^1 markers that sample more genetic diversity, may be necessary to maintain this level of accuracy.
Borut Bohanec - One of the best experts on this subject based on the ideXlab platform.
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dna labelling of varieties covered by patent protection a new solution for managing intellectual property Rights in the seed industry
Transgenic Research, 2017Co-Authors: Karin Ljubic Fister, Iztok Fister, Jana Murovec, Borut BohanecAbstract:Plant Breeders’ Rights are undergoing dramatic changes due to changes in patent Rights in terms of Plant variety Rights protection. Although differences in the interpretation of »breeder’s exemption«, termed research exemption in the 1991 UPOV, did exist in the past in some countries, allowing Breeders to use protected varieties as parents in the creation of new varieties of Plants, current developments brought about by patenting conventionally bred varieties with the European Patent Office (such as EP2140023B1) have opened new challenges. Legal restrictions on germplasm availability are therefore imposed on Breeders while, at the same time, no practical information on how to distinguish protected from non-protected varieties is given. We propose here a novel approach that would solve this problem by the insertion of short DNA stretches (labels) into protected Plant varieties by genetic transformation. This information will then be available to Breeders by a simple and standardized procedure. We propose that such a procedure should consist of using a pair of universal primers that will generate a sequence in a PCR reaction, which can be read and translated into ordinary text by a computer application. To demonstrate the feasibility of such approach, we conducted a case study. Using the Agrobacterium tumefaciens transformation protocol, we inserted a stretch of DNA code into Nicotiana benthamiana. We also developed an on-line application that enables coding of any text message into DNA nucleotide code and, on sequencing, decoding it back into text. In the presented case study, a short command line coding the phrase »Hello world« was transformed into a DNA sequence that was inserted in the Plant genome. The encoded message was reconstructed from the resulting T1 seedlings with 100 % accuracy. The feasibility and possible other applications of this approach are discussed.