Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Insights into deployment of DNA markers in plant variety protection and registration

Abstract

Key message

The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed models in the era of next-generation breeding.

Abstract

The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can be costly, time-consuming and often restricted to a relatively small number of traits that can be influenced by environmental conditions. This calls for the adoption of a DNA-based system which is endorsed by the International Union for the Protection of New Varieties of Plants (UPOV). This could enable examiners to deploy trait-specific DNA markers in DUS testing as well as using such genetic markers to manage reference collections. Within UPOV’s system, breeders can freely use protected varieties in breeding programs. However, breeders of protected varieties may seek sharing in ownership of essentially derived varieties once it is proven that they, with the exception of a few distinctive DUS trait(s), conform to parental varieties in essential characteristics. As well as their complementary role in DUS testing, DNA markers have been known as a good replacement of morphological traits in defining boundaries between independently and essentially derived varieties. With the advent of new breeding technologies that allow minor modification in varieties with outcomes of specific merit or utility, detecting distinctness between varieties may become increasingly challenging. This, together with the ever-increasing number of varieties with which to compare new candidate varieties, supports the potential utility of using DNA-based approaches in variety description.

This is a preview of subscription content, log in to check access.

Abbreviations

CKV:

Common knowledge varieties

DUS:

Distinctness, uniformity, and stability

EDV:

Essentially derived variety

IPR:

Intellectual property rights

PBR:

Plant breeder’s rights

PVP:

Plant variety protection

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

UPOV:

International Union for the Protection of New Varieties of Plants

References

  1. Annicchiarico P, Nazzicari N, Ananta A, Carelli M, Wei Y, Brummer EC (2016) Assessment of cultivar distinctness in alfalfa: a comparison of genotyping-by-sequencing, simple-sequence repeat marker, and morphophysiological observations. Plant Genome 9(2):1–12

  2. Arens P, Mansilla C, Deinum D, Cavellini L, Moretti A, Rolland S, van der Schoot H, Calvache D, Ponz F, Collonnier C, Mathis R, Smilde D, Caranta C, Vosman B (2010) Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor Appl Genet 120:655–664

  3. Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94:773–781

  4. Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L (2016) Next generation breeding. Plant Sci 242:3–13

  5. Bernet GP, Bramardi S, Calvache D, Carbonell EA, Asins MJ (2003) Applicability of molecular markers in the context of protection of new varieties of cucumber. Plant Breed 122:146–152

  6. Bonow S, Von Pinho EVR, Vieira MGC, Vosman B (2009) Microsatellite markers in and around rice genes: applications in variety identification and DUS testing. Crop Sci 49:880–886

  7. Borchert T, Krueger J, Hohe A (2008) Implementation of a model for identifying essentially derived varieties in vegetatively propagated Calluna vulgaris varieties. BMC Genet 9:1

  8. Bradbury LMT, Henry RJ, Jin Q, Reinke RF, Waters DLE (2005) A perfect marker for fragrance genotyping in rice. Mol Breed 16:279–283

  9. Bredemeijer G, Cooke R, Ganal M, Peeters R, Isaac P, Noordijk Y, Rendell S, Jackson J, Röder M, Wendehake K (2002) Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor Appl Genet 105:1019–1026

  10. Chen Y, Dai X, Hou J, Guan H, Wang Y, Li Y, Yin T (2016) DNA fingerprinting of oil camellia cultivars with SSR markers. Tree Genet Genomes 12:7

  11. Choi S, Sim S, Hong J, Choi K, Jin M, Park B, Kim D, Kwon Y (2016) Genetic characterisation of commercial Chinese cabbage varieties using SSR markers. Seed Sci Technol 44:595–608

  12. Cockram J, Mackay I (2018) Genetic mapping populations for conducting high-resolution trait mapping in plants. In: Blakebrough N, Ghose TK, Fiechter A (eds) Advances in biochemical engineering/biotechnology. Springer, Berlin

  13. Cockram J, Norris C, O’Sullivan DM (2009) PCR-based markers diagnostic for spring and winter seasonal growth habit in barley. Crop Sci 49:403–410

  14. Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D et al (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Nat Acad Sci USA 107:21611–21616

  15. Cockram J, Jones H, Norris C, O’Sullivan DM (2012) Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet 125:1735–1749

  16. Cockram J, Horsnell R, E-h Soh, Norris C, O’Sullivan DM (2015) Molecular and phenotypic characterization of the alternative seasonal growth habit and flowering time in barley (Hordeum vulgare ssp. vulgare L.). Mol Breed 35:1–11

  17. Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

  18. Cooke RJ, Reeves JC (2003) Plant genetic resources and molecular markers: variety registration in a new era. Plant Genet Resour 1:81–87

  19. Cooke RJ, Bredemeijer GMM, Ganal MW, Peeters R, Isaac P, Rendell S, Jackson J, Roder MS, Korzun V, Wendehake K, Areshchenkova T, Dijcks M, Laborie D, Bertrand L, Vosman B (2003) Assessment of the uniformity of wheat and tomato varieties at DNA microsatellite loci. Euphytica 132:331–341

  20. Cristo-Araújo M, Molles DB, Rodrigues DP, Clement CR (2017) Genetic analysis identifies the region of origin of smuggled peach palm seeds. Forensic Sci Int 273:e15–e17

  21. Curtis F, Nilsson M (2012) Collection systems for royalties in wheat: an international study. Bio-Sci Law Rev 12:215

  22. De la Fuente G, Frei UK, Lübberstedt T (2013) Accelerating plant breeding. Trends Plant Sci 18:667–672

  23. De Riek J, Calsyn E, Everaert I, Van Bockstaele E, De Loose M (2001) AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theor Appl Genet 103:1254–1265

  24. Delfini J, Moda-Cirino V, de Fátima Ruas C, dos Santos Neto J, Ruas PM, Buratto JS, Ruas EA, Gonçalves LSA (2017) Distinctness of Brazilian common bean cultivars with carioca and black grain by means of morphoagronomic and molecular descriptors. PLoS ONE 12:e0188798

  25. Fan C, Yu S, Wang C, Xing Y (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118:465–472

  26. Ferrante A, Nocito FF, Morgutti S, Sacchi GA (2017) Plant breeding for improving nutrient uptake and utilization efficiency. In: Tei F, Nicola S, Benincasa P (eds) Advances in research on fertilization management of vegetable crops. Springer, Berlin, pp 221–246

  27. Fossati T, Zapelli I, Bisoffi S, Micheletti A, Vietto L, Sala F, Castiglione S (2005) Genetic relationships and clonal identity in a collection of commercially relevant poplar cultivars assessed by AFLP and SSR. Tree Genet Genomes 1:11–20

  28. Gao L, Jia J, Kong X (2016) A SNP-based molecular barcode for characterization of common wheat. PLoS ONE 11(3):e0150947

  29. Giancola S, Poltri SM, Lacaze P, Hopp HE (2002) Feasibility of integration of molecular markers and morphological descriptors in a real case study of a plant variety protection system for soybean. Euphytica 127:95–113

  30. Gilliland TJ, Gensollen V (2010) Review of the protocols used for assessment of DUS and VCU in Europe—perspectives. In: Huyghe C (ed) Sustainable use of genetic diversity in forage and turf breeding. Springer, Berlin, pp 261–275

  31. Gilliland T, Coll R, Calsyn E, De Loose M, Van Eijk M, Roldán-Ruiz I (2000) Estimating genetic conformity between related ryegrass (Lolium) varieties. 1. Morphology and biochemical characterisation. Mol Breed 6:569–580

  32. Gunjaca J, Buhinicek I, Jukic M, Sarcevic H, Vragolovic A, Kozic Z, Jambrovic A, Pejic I (2008) Discriminating maize inbred lines using molecular and DUS data. Euphytica 161:165–172

  33. Hall BD, Fox R, Zhang Q, Baumgarten A, Nelson B, Cummings J, Drake B, Phillips D, Hayes K, Beatty M (2016) Comparison of genotypic and expression data to determine distinctness among inbred lines of maize for granting of plant variety protection. Crop Sci 56:1443–1459

  34. Heckenberger M (2004) Identification of essentially derived varieties in maize (Zea mays L.) using molecular markers, morphological traits, and heterosis. Ph.D. thesis, University of Hohenheim

  35. Heckenberger M, Bohn M, Ziegle JS, Joe LK, Hauser JD, Hutton M, Melchinger AE (2002) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. Mol Breed 10:181–191

  36. Heckenberger M, van der Voort JR, Peleman J, Bohn M (2003) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties: II. Genetic and technical sources of variation in AFLP data and comparison with SSR data. Mol Breed 12:97–106

  37. Heckenberger M, Bohn M, Melchinger A (2005a) Identification of essentially derived varieties obtained from biparental crosses of homozygous lines. Crop Sci 45:1120–1131

  38. Heckenberger M, Bohn M, Frisch M, Maurer H, Melchinger A (2005b) Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations. Theor Appl Genet 111:598–608

  39. Heckenberger M, Muminović J, van der Voort JR, Peleman J, Bohn M, Melchinger A (2006) Identification of essentially derived varieties obtained from biparental crosses of homozygous lines. III. AFLP data from maize inbreds and comparison with SSR data. Mol Breed 17:111–125

  40. Hong J-H, Kwon Y-S, Mishra RK, Kim DH (2015) Construction of EST-SSR databases for effective cultivar identification and their applicability to complement for lettuce (Lactuca sativa L.) distinctness test. Am J Plant Sci 6:113

  41. Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK, Gaur P, Leung H, Varshney RK, Cavanagh CR (2015) MAGIC populations in crops: current status and future prospects. Theor Appl Genet 128:999–1017

  42. Ibàñez J, Vélez MD, de Andrés MT, Borrego J (2009) Molecular markers for establishing distinctness in vegetatively propagated crops: a case study in grapevine. Theor Appl Genet 119:1213–1222

  43. Iquebal MA, Arora V, Verma N, Rai A, Kumar D (2013) First whole genome based microsatellite DNA marker database of tomato for mapping and variety identification. BMC Plant Biol 13:197

  44. ISF, International Seed Federation (2004) Guidelines for the handling of a dispute on essential derivation in lettuce. https://www.worldseed.org/wp-content/uploads/2015/10/Guidelines_EDV_Lettuce_2004.pdf. Accessed 26 Apr 2019

  45. ISF, International Seed Federation (2012) ISF view on intellectual property. https://www.worldseed.org/wp-content/uploads/2015/10/View_on_Intellectual_Property_2012.pdf. Accessed 26 Apr 2019

  46. ISF, International Seed Federation (2014) Guidelines for the handling of a dispute on essential derivation in maize lines. https://www.worldseed.org/wp-content/uploads/2015/10/ISF_Guidelines_Disputes_EDV_Maize_2014.pdf. Accessed 26 Apr 2019

  47. IWGSC, International Wheat Genome Sequencing Consortium (2018) Shifting the limits of wheat research and breeding using a fully annotated reference genome. Science 361:eear7191

  48. Jaiswal S, Sheoran S, Arora V, Angadi UB, Iquebal MA, Raghav N, Aneja B, Kumar D, Singh R, Sharma P (2017) Putative microsatellite DNA marker-based wheat genomic resource for varietal improvement and management. Front Plant Sci 8:2009

  49. Jamali S, Sadeghi L, Sadeghin-Motahhar S (2011) Identification and distinction of soybean commercial cultivars using morphological and microsatellite markers. Iran J Crop Sci 13:131–145

  50. Jamali SH, Mohammadi SA, Sadeghzadeh B (2017) Association mapping for morphological traits relevant to registration of barley varieties. Span J Agric Res 15:0704

  51. Janis MD, Smith S (2007) Technological change and the design of plant variety protection regimes. Chicago-Kent Law Rev 82(3):1557–1615

  52. Jones H, Mackay I (2015) Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley. Theor Appl Genet 128:2461–2470

  53. Jones H, Jarman R, Austin L, White J, Cooke R (2003) The management of variety reference collections in distinctness, uniformity and stability testing of wheat. Euphytica 132:175–184

  54. Jones H, Norris C, Smith D, Cockram J, Lee D, O’Sullivan DM, Mackay I (2013) Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley. Theor Appl Genet 126:901–911

  55. Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC (2015) Functional molecular markers for crop improvement. Crit Rev Biotechnol 16:1–14

  56. Kahler AL, Kahler JL, Thompson SA, Ferriss RS, Jones ES, Nelson BK, Mikel MA, Smith S (2010) North American study on essential derivation in maize: II. Selection and evaluation of a panel of simple sequence repeat loci. Crop Sci 50:486–503

  57. Karsai I, Szűcs P, Mészáros K, Filichkina T, Hayes P, Skinner J, Láng L, Bedő Z (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative × winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet 110:1458–1466

  58. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4(2):403–410

  59. Kumar V, Rani A, Jha P, Rawal R, Husain S (2017) Molecular identification of dominant cultivars of soybean using simple sequence repeat markers. Proc Natl Acad Sci India Sect B Biol Sci 87:647–653

  60. Kwon YS (2016) DNA fingerprinting analysis for soybean (Glycine max) varieties in Korea using a core set of microsatellite marker. J Plant Biotechnol 43:457–465

  61. Kwon YS, Lee JM, Yi GB, Yi SI, Kim KM, Soh EH, Bae KM, Park EK, Song IH, Kim BD (2005) Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol Cells 19:428–435

  62. Law JR, Donini P, Koebner RMD, James CR, Cooke RJ (1998) DNA profiling and plant variety registration. III: the statistical assessment of distinctness in wheat using amplified fragment length polymorphisms. Euphytica 102:335–342

  63. Leigh F, Law JR, Lea VJ, Donini P, Reeves JC (2003) A comparison of molecular markers and statistical tools for diversity and EDV assessments. In: The wake of the double helix: from the green revolution to the gene revolution: proceedings of an international congress held in Bologna, May 27–31, pp 349–363

  64. Lesser W, Mutschler M (2004) Balancing investment incentives and social benefits when protecting plant varieties. Crop Sci 44:1113–1120

  65. Li H, Rasheed A, Hickey LT, He Z (2018) Fast-forwarding genetic gain. Trends Plant Sci 23:184–186

  66. Lin Z, Hayes B, Daetwyler H (2014) Genomic selection in crops, trees and forages: a review. Crop Pasture Sci 65:1177–1191

  67. Liu C, Moschou PN (2018) Phenotypic novelty by CRISPR in plants. Dev Biol 425:170–175

  68. Liu Y, He Z, Appels R, Xia X (2012) Functional markers in wheat: current status and future prospects. Theor Appl Genet 125:1–10

  69. Lombard V, Baril CP, Dubreuil P, Blouet F, Zhang D (2000) Genetic relationships and fingerprinting of rapeseed cultivars by AFLP: consequences for varietal registration. Crop Sci 40:1417–1425

  70. Lombard V, Tireau B, Blouet F, Zhang D, Baril CP (2002) Usefulness of AFLP markers to estimate varietal homogeneity of rapeseed inbred line varieties in the context of plant registration and protection. Euphytica 125:121–127

  71. Lombardo L (2014) Genetic use restriction technologies: a review. Plant Biotechnol J 12:995–1005

  72. Lu Y, Xiao P, Shao Y, Zhang G, Thanyasiriwat T, Bao J (2010) Development of new markers to genotype the functional SNPs of SSIIa, a gene responsible for gelatinization temperature of rice starch. J Cereal Sci 52:438–443

  73. Maccaferri M, Stefanelli S, Rotondo F, Tuberosa R, Sanguineti MC (2007a) Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome 50:373–384

  74. Maccaferri M, Sanguineti MC, Xie C, Smith JSC, Tuberosa R (2007b) Relationships among durum wheat accessions. II. A comparison of molecular and pedigree information. Genome 50:385–399

  75. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X, Cruickshank A (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:2320

  76. Mall N, Chawla H (2014) Suitability of SSR marker for establishing distinctiveness in French bean varieties (Phaseolus vulgaris L.). Legume Res Int J 37:353–358

  77. Myint KM, Arikit S, Wanchana S, Yoshihashi T, Choowongkomon K, Vanavichit A (2012) A PCR-based marker for a locus conferring the aroma in Myanmar rice (Oryza sativa L.). Theor Appl Genet 125(5):887–896

  78. Nogué F, Mara K, Collonnier C, Casacuberta JM (2016) Genome engineering and plant breeding: impact on trait discovery and development. Plant Cell Rep 35(7):1475–1486

  79. Noleppa S (2016) The economic, social and environmental value of plant breeding in the European Union, an ex post evaluation and ex ante assessment. HFFA Research paper 03/2016. https://www.agrarzeitung.de/news/media/3/EU-Studie_zum_Nutzen_der_Pflanzenzu__chtung.pdf-22944.pdf. Accessed 26 Apr 2019

  80. Noli E, Teriaca MS, Sanguineti MC, Conti S (2008) Utilization of SSR and AFLP markers for the assessment of distinctness in durum wheat. Mol Breed 22:301–313

  81. Noli E, Teriaca MS, Conti S (2012) Identification of a threshold level to assess essential derivation in durum wheat. Mol Breed 29:687–698

  82. Noli E, Teriaca MS, Conti S (2013) Criteria for the definition of similarity thresholds for identifying essentially derived varieties. Plant Breed 132:525–531

  83. Nováková A, Šimáčková K, Bárta J, Čurn V (2009) Potato variety identification by molecular markers based on retrotransposon analyses. Czech J Genet Plant Breed 45:1–10

  84. Nuel G, Baril C, Robin S (2001) Varietal distinctness assisted by molecular markers: a methodological approach. In: International symposium on molecular markers for characterizing genotypes and identifying cultivars in horticulture, vol 546, pp 65–71

  85. Oliveira MB, Vieira ESN, Schuster I (2010) Construction of a molecular database for soybean cultivar identification in Brazil. Genet Mol Res 9:705–720

  86. Park YJ, Dixit A, Ma KH, Lee JK, Lee MH, Chung CS, Nitta M, Okuno K, Kim TS, Cho EG, Rao VR (2008) Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers. Genet Resour Crop Evol 55(4):523–535

  87. Patra N, Chawla HS (2010) Biochemical and RAPD molecular markers for establishing distinctiveness of basmati rice (Oryza sativa L.) varieties as additional descriptors for plant variety protection. Indian J Biotechnol 9:371–377

  88. Phan NT, Kim M-K, Sim S-C (2016) Genetic variations of F1 tomato cultivars revealed by a core set of SSR and InDel markers. Sci Hortic 212:155–161

  89. PBRA, Plant Breeder’s Rights Act (1994) Australian Government, No. 110. https://www.legislation.gov.au/Details/C2018C00361. Accessed 26 Apr 2019

  90. Pourabed E, Jazayeri Noushabadi MR, Jamali SH, Moheb Alipour N, Zareyan A, Sadeghi L (2015) Identification and DUS testing of rice varieties through microsatellite markers. Int J Plant Genom. Article ID 965073

  91. Ramkumar G, Sivaranjani AKP, Pandey MK, Sakthivel K, Shobha Rani N, Sudarshan I, Prasad GSV, Neeraja CN, Sundaram RM, Viraktamath BC (2010) Development of a PCR-based SNP marker system for effective selection of kernel length and kernel elongation in rice. Mol Breed 26(4):735–740

  92. Rani A, Kumar V, Shukla S, Jha P, Rawal R (2016) DNA barcoding of Indian soybean varieties as constructed through SSR markers. Seed Sci Technol 44:357–369

  93. Reid A, Kerr EM (2007) A rapid simple sequence repeat (SSR)-based identification method for potato cultivars. Plant Genet Resour 5:7–13

  94. Reid A, Hof L, Felix G, Rücker B, Tams S, Milczynska E, Esselink D, Uenk G, Vosman B, Weitz A (2011) Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue. Euphytica 182:239–249

  95. Röder M, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke R (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73

  96. Roldán-Ruiz I, Calsyn E, Gilliland T, Coll R, Van Eijk M, De Loose M (2000) Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Mol Breed 6:593–602

  97. Rotondi A, Magli M, Ricciolini C, Baldoni L (2003) Morphological and molecular analyses for the characterization of a group of Italian olive cultivars. Euphytica 132:129–137

  98. Sakthivel K, Rani NS, Pandey MK, Sivaranjani A, Neeraja C, Balachandran S, Madhav MS, Viraktamath B, Prasad G, Sundaram R (2009) Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties. Mol Breed 24:185–190

  99. Sarao NK, Vikal Y, Singh K, Joshi MA, Sharma RC (2009) SSR marker-based DNA fingerprinting and cultivar identification of rice (Oryza sativa L.) in Punjab state of India. Plant Genet Resour Char Util 1:3

  100. Shao G, Tang A, Tang S, Luo J, Jiao G, Wu J, Hu P (2011) A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice. Plant Breed 130:172–176

  101. Shi W, Yang Y, Chen S, Xu M (2008) Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed 22:185–192

  102. Shukla S, Joshi D, Srivastava R, Qureshi M, Singh U (2011) Suitability of RAPD and ISSR to complement agro-morphological DUS descriptors for establishing distinctiveness in indigenous local strains of Kalanamak rice (Oryza sativa). Indian J Agric Sci 81:994

  103. Singh RK, Sharma RK, Singh AK, Singh VP, Singh NK, Tiwari SP, Mohapatra T (2004) Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135:135–143

  104. Smulders MJM, Esselink D, Voorrips RE, Vosman B (2009) Analysis of a database of DNA profiles of 734 Hybrid Tea Rose varieties. In: 23rd International Eucarpia symposium, section ornamentals: colourful breeding and genetics, vol 836, pp 169–175

  105. Smỳkal P, Horacek J, Dostalova R, Hybl M (2008) Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers. J Appl Genet 49:155–166

  106. Sonnante G, Pignone D (2007) The major Italian landraces of lentil (Lens culinaris Medik.): their molecular diversity and possible origin. Genet Res Crop Evol 54(5):1023–1031

  107. Sousa TV, Caixeta ET, Alkimim ER, de Oliveira ACB, Pereira AA, Zambolim L, Sakiyama NS (2017) Molecular markers useful to discriminate Coffea arabica cultivars with high genetic similarity. Euphytica 213:75

  108. Staub J, Chung SM, Fazio G (2005) Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus L.). Plant Breed 124:44–53

  109. Tian H-L, Wang F-G, Zhao J-R, Yi H-M, Wang L, Wang R, Yang Y, Song W (2015) Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. Mol Breeding 35:136

  110. Tiwari JK, Ali N, Devi S, Kumar V, Zinta R, Chakrabarti SK (2018) Development of microsatellite markers set for identification of Indian potato varieties. Sci Hortic 231:22–30

  111. Tommasini L, Batley J, Arnold GM, Cooke RJ, Donini P, Lee D, Law JR, Lowe C, Moule C, Trick M, Edwards KJ (2003) The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor Appl Genet 106:1091–1101

  112. UPOV, International Union for the Protection of New Varieties of Plants (1991) International convention for the protection of new varieties of plants, Publication No. 221 (E), March 19, Geneva

  113. UPOV, International Union for the Protection of New Varieties of Plants (2004) Guidelines for the conduct of tests for distinctness, uniformity and stability, rice (Oryza sativa L.). TG/16/8. https://www.upov.int/edocs/tgdocs/en/tg016.pdf. Accessed 26 Apr 2019

  114. UPOV, International Union for the Protection of New Varieties of Plants (2011) Combining morphological and molecular distance in the management of the reference collection of potato. BMT/13/10. https://www.upov.int/edocs/mdocs/upov/en/bmt_13/bmt_13_10.pdf. Accessed 26 Apr 2019

  115. UPOV, International Union for the Protection of New Varieties of Plants (2013a) Guidance on the use of biochemical and molecular markers in the examination of distinctness, uniformity and stability (DUS), TGP/15. https://www.upov.int/edocs/tgpdocs/en/tgp_15.pdf. Accessed 26 Apr 2019

  116. UPOV, International Union for the Protection of New Varieties of Plants (2013b) Guidelines for the conduct of tests for distinctness, uniformity and stability, tomato (Solanum lycopersicum L.). TG/44/11 Rev. https://www.upov.int/edocs/tgdocs/en/tg044.pdf. Accessed 26 Apr 2019

  117. UPOV, International Union for the Protection of New Varieties of Plants (2014a) The use of molecular markers (SNP) for maize DUS testing. BMT/14/10. https://www.upov.int/edocs/mdocs/upov/en/bmt_14/bmt_14_10.pdf. Accessed 26 Apr 2019

  118. UPOV, International Union for the Protection of New Varieties of Plants (2014b) Identification of SNP markers to aid assessment of essential derivation in maize. BMT/14/7 Rev. https://www.upov.int/edocs/mdocs/upov/en/bmt_14/bmt_14_7_rev.pdf. Accessed 26 Apr 2019

  119. UPOV, International Union for the Protection of New Varieties of Plants (2018) Guidelines for the conduct of tests for distinctness, uniformity and stability, barley (Hordeum vulgare L. sensu lato). TG/19/10. https://www.upov.int/edocs/tgdocs/en/tg019.pdf. Accessed 26 Apr 2019

  120. Van Eeuwijk F, Law J (2004) Statistical aspects of essential derivation, with illustrations based on lettuce and barley. Euphytica 137:129–137

  121. Van Wijk A, Louwaars N (2014) Framework for the introduction of Plant Breeder’s Rights: guidance for practical implementation. Naktuinbouw, Roelofarendsveen, p 207

  122. Vélez MD, Ibánez J (2012) Assessment of the uniformity and stability of grapevine cultivars using a set of microsatellite markers. Euphytica 186(2):419–432

  123. Vosman B, Visser D, van der Voort JR, Smulders MJ, van Eeuwijk F (2004) The establishment of ‘essential derivation’ among rose varieties, using AFLP. Theor Appl Genet 109:1718–1725

  124. Voss-Fels KP, Herzog E, Dreisigacker S, Sukumaran S, Watson A, Frisch M, Hayes B, Hickey LT (2019) “SpeedGS” to accelerate genetic gain in spring wheat. In: Miedaner T, Korzun V (eds) Application of genetic and genomic research in cereals. Woodhead Publishing, Elsevier, ‎Sawston. https://doi.org/10.1016/B978-0-08-102163-7.00014-4

  125. Wang LX, Li HB, Gu TC, Liu LH, Pang BS, Qiu J, Zhao CP (2013) Assessment of wheat variety stability using SSR markers. Euphytica 195:435–452

  126. Wang L-X, Jun Q, Chang L-F, Liu L-H, Li H-B, Pang B-S, Zhao C-P (2015) Assessment of wheat variety distinctness using SSR markers. J Integr Agric 14:1923–1935

  127. Wang J, Cogan NO, Forster JW (2016) Prospects for applications of genomic tools in registration testing and seed certification of ryegrass varieties. Plant Breed 135:405–412

  128. Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey M-D, Asyraf Md Hatta M, Hinchliffe A, Steed A, Reynolds D et al (2018) Speed breeding is a powerful tool to accelerate crop research and breeding. Nat Plants 4:23–29

  129. Yadav VK, Singh IS (2010) Comparative evaluation of maize inbred lines (Zea mays L.) according to DUS testing using morphological, physiological and molecular markers. Agric Sci 1:131–142

  130. Yamanaka S, Nakamura I, Watanabe KN, Sato Y-I (2004) Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theor Appl Genet 108:1200–1204

  131. Yim GR, Ding DR, Wang CP, Leong WH, Hong Y (2009) Microsatellite markers to complement distinctness, uniformity, stability testing of Brassica chinensis (Xiao baicai) varieties. Open Horticulture Journal 2:54–61

Download references

Acknowledgements

SHJ acknowledged a grant support No. 8229/253 from Seed and Plant Certification and Registration Institute. JC’s time was supported by Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/L011700/1. LTH was supported by an Australian Research Council Early Career Discovery Research Award (Project Code DE170101296). The authors also thank Mr. Deon Goosen, Director of Commercial Engagement-Agricultural and Food Sciences, Uniquest, Australia, for his comments to improve this article.

Author information

Correspondence to Seyed Hossein Jamali.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Communicated by Rajeev K. Varshney.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jamali, S.H., Cockram, J. & Hickey, L.T. Insights into deployment of DNA markers in plant variety protection and registration. Theor Appl Genet 132, 1911–1929 (2019). https://doi.org/10.1007/s00122-019-03348-7

Download citation