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  • The use of DNA markers for ...
    Pipan, Barbara; Sinkovic, Lovro; Rutar, Romana; Meglic, Vladimir

    Journal of Central European agriculture, 06/2021, Letnik: 22, Številka: 2
    Journal Article

    The usefulness of genetic identification of varieties for seed quality analyses becomes important, when we suspect the presence of another variety, species or even genus, based on morphological seed traits in the purity analysis and germination test, With genetic analyses, the doubt about the authenticity of the naked oats (Avena nuda L.) variety 'Kamil' was successfully solved. There were atypical seeds with chaff among the samples of this variety, so it was not possible to confirm with certainty, whether these were seeds of the same species/variety or impurities of common oats (Avena sativa L.). Based on the seed phenotype of the 'Kamil' variety (two independent samples 284 and 285), four sub-samples were prepared (284AN, 284AS, 285AN, 285AS); AN label was the sub-sample with naked seeds and AS label was the sub-sample with chaffed seeds. In addition, another variety ('Noni') and four accessions of common oats (ACC378, ACC379, ACC380, ACC381) from the Slovene Plant Gene Bank were included as common oat standards. A total of 36 plant samples of Avena sp. were included in the genetic differentiation. Using a set of six highly informative SSR markers and the results of diversity parameters at individual loci and paired genetic comparisons, we were able to confirm that the analysed sub-samples belonged to the same variety, i.e. 'Kamil'. In addition, despite the morphological similarity, the chaffed seeds of naked oats variety 'Kamil' were sufficiently (genetically) different from the analysed variety and/or accessions of common oats. Keywords: genetic identification, SSR markers, oat, varietal authenticity Uporabnost genetske identifikacije sort se kaže pri analizah kakovosti semena, ko se na osnovi morfoloških znakov semena pri analizi cistote in/ali klic v postopku kalivosti pojavi sum na drugo sorto, vrsto ali celo rod. Z aplikativno uporabo genetskih analiz smo uspešno rešili dvom o pristnosti sorte 'Kamil' vrste golega ovsa (Avena nuda L.). Med semenom omenjene sorte je bilo namrec prisotno tudi seme s plevo, a se ni dalo z gotovostjo potrditi ali gre za seme iste vrste s plevo ali za primes semen navadnega ovsa (Avena sativa L.). Na podlagi fenotipa semena sorte 'Kamil' (dva neodvisna vzorca 284 in 285) so bili pripravljeni štirje pod-vzorci (284AN, 284AS, 285AN, 285AS), kjer AN pomeni golce, AS pa plevence. Kot standardi navadnega ovsa so bili v genetsko identifikacijo vkljucene še sorta navadnega ovsa 'Noni' in štiri akcesije navadnega ovsa (ACC378, ACC379, ACC380, ACC381) iz Slovenske rastlinske genske banke. Skupno je bilo v genotipizacijo vkljucenih 36 vzorcev rastlin rodu Avena sp. Z uporabo seta šestih visoko informativnih SSR markerjev in rezultatov analize parametrov raznolikosti na posameznih lokusih ter parnih genetskih primerjav smo lahko potrdili, da so analizirani pod-vzorci pripadali isti vrsti in sorti, t.j. golemu ovsu 'Kamil'. Poleg tega so bili kljub morfološki podobnosti plevenci sorte Kamil' genetsko dovolj razlicni od analizirane sorte in/ali akcesij navadnega ovsa. Kljucne besede: genetska identifikacija, SSR markerji, oves, vrstna pristnost DETAILED ABSTRACT Varietal authenticity and seed quality of varieties that are adapted to Slovenian production conditions are of key importance for successful agricultural production and consequently for ensuring food security and reducing the risk in agricultural production. In practice, when confirming seed crops during growing season, the problem of identifying varieties of atypical plants, especially within plant species of cereals and crosses, arises. The usefulness of genetic identification of varieties is shown in seed quality analyses, when on the basis of morphological traits of seeds in the purity analysis and germination test there is a suspicion of another variety, species or even genus. With the application of genetic analyses the doubt regarding the authenticity of the variety 'Kamil' of naked oats (Avena nuda L.) was successfully solved. Among the seeds of variety 'Kamil' there was a presence of seeds with chaff, so it was not possible to confirm with certainty whether these were seeds of the same species with chaff or impurities of seeds of common oats. Based on the verification of varietal purity and morphology of oat seeds, four sub-samples (284AS, 284AN, 285AS, 285AN) of the A. nuda variety 'Kamil' were prepared. In addition variety of the A. sativa ('Noni') and four accessions of common oats (ACC378, ACC379, ACC380, ACC381) from Slovene Plant Gene Bank were included. Each sample was represented by four individual plants (a, b, c, d) to ensure diversity within each variety/accession. A total of 36 genotypes/individual plants of Avena sp. were included in the genetic identification. DNA isolation from young plant leaves was performed on a nucleic acid isolation robot using isolation kit. The original DNA was used for genetic analysis for PCR using six specific SSR markers presented in Table 1. The results were read by GeneMapper4.0 and prepared for codominant matrices for further processing. Based on the obtained results, a detailed computer analysis was required at both, the 2n and 6n levels. Several statistical programs and software packages were used to visualize the quantitative results presented in Tables 2&3 and Figs 1-4. The overall polymorphic information content of six SSR markers was 0.710. There was also small deviation (0.126) between total expected (0.752) and observed heterozygosity (0.878). According to the principal coordinate analysis and analysis of the genetic structure, two groups of genotypes were formulated. Pairwise comparisons of Nei's genetic distance showed that genetic relatedness of AN and AS sub-samples within variety 'Kamil' was higher (>0.8) compared to the common oat variety/accessions (>0.7). Despite the high degree of genetic similarity among the studied 36 Avena sp. genotypes, based on statistical analysis and relevant genetic diversity parameters at the codominant 6n level, we were able to confirm that the analysed sub-samples belonged to the same species and variety, i.e. 'Kamil'.