VARIETAL DISTINCTNESS ASSISTED BY MOLECULAR MARKERS: A METHODOLOGICAL APPROACH

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

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. 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.

Molecular characterization of intra-population variability of Jatropha curcas L. using DNA based molecular markers

Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference, number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers), 822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively. The Jaccard's similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively. Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection (MAS) and it can be useful for breeding programs and QTL mapping.

Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers

The distinctness, uniformity and stability (DUS) requirements involve expensive, space- and time-consuming measurements of morphological traits. Moreover, for a majority of traits, interactions between genotype and environment complicate the evaluation. Molecular markers have a potential to facilitate this procedure, increase the reliability of decisions, and substantially save the time and space needed for experiments. We chose 25 varieties of pea (Pisum sativum L.) from the list of recommended varieties for cultivation in the Czech Republic, and made both a standard classification by 12 morphological descriptors and a classification by biochemical-molecular markers. Two isozyme systems, 10 microsatellite loci, 2 retrotransposons for multilocus inter-retrotransposon amplified polymorphism (IRAP), and 12 retrotransposon-based insertion polymorphism (RBIP) DNA markers were analysed. The main objective of the study was to examine the potential of each method for discrimination between pea varieties. The results demonstrate a high potential and resolving power of DNA-based methods. Superior in terms of high information content and discrimination power were SSR markers, owing to high allelic variation, which was the only biochemical-molecular method allowing clear identification of all varieties. Retrotransposon markers in RBIP format proved to be the most robust and easy to score method, while multilocus IRAP produced informative fingerprint already in a single analysis. Isozyme analysis offered a fast and less expensive alternative. The results showed that molecular identification could be used to assess distinctness and complement morphological assessment, especially in cases where the time frame plays an important role. Currently developed pea marker systems might serve also for germplasm management and genetic diversity studies.

Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

The establishment of 'essential derivation' among rose varieties, using AFLP

In the International Union for the Protection of New Varieties of Plants Act of 1991, mutation is mentioned as one of the mechanisms to obtain an 'essentially derived' variety (EDV). For the implementation of the EDV concept in the case of mutation, it is important that the level of genetic relatedness between an initial variety and derived mutant varieties can clearly be distinguished from the level of relatedness between arbitrary pairs of varieties without a derivation relation. Conditions to be fulfilled for such a distinction include enough genetic differentiation in the germplasm pool of interest, sufficiently low levels of genomic sampling error and technical laboratory error and high reproducibility within and between laboratories. In rose, mutants or 'sports' are frequently observed during multiplication, making it a suitable crop for studying the possibilities for introduction of the EDV concept in ornamentals. We studied genetic similarities among 83 rose varieties, including 13 mutant groups. Twelve AFLP primer combinations generated 284 polymorphic markers and 114 monomorphic (fixed) bands. Pair-wise Jaccard similarities between original varieties and derived mutants were close to 1.0 (>0.96), whereas all similarities between original varieties were below 0.80, with 75% of the non-mutant similarities even being below 0.50. Values less than 1.0 for similarity among original varieties and their mutants were to a major extent due to scoring errors. Error rates in automated scoring proved to be lower than those in manually scored and transferred data. Experimental errors, even between laboratories, turned out to be very small. On the basis of a consistent and large difference between similarities, relations between an original variety and its mutants can easily be identified and distinguished from relations between original varieties. These results open the way for implementing the essential derivation concept in rose.