Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations
Simko, I. ; Eujayl, I. ; Hintum, T.J.L. van - \ 2012
Plant Science 184 (2012). - ISSN 0168-9452 - p. 54 - 62.
simple sequence repeat - beta-vulgaris l. - genetic diversity - linkage disequilibrium - microsatellite markers - technology dart - genome - inference - map - polymorphisms
Dominant and co-dominant molecular markers are routinely used in plant genetic research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A set of 54 diploid sugar beet (Beta vulgaris L. ssp. vulgaris) hybrid varieties from five seed companies was genotyped with 702 Diversity Array-Technology (DArT), 34 Single Nucleotide Polymorphisms (SNP), and 30 Simple Sequence Repeats (SSR) markers. Analysis of the population structure revealed three well-defined populations and clustering of varieties that generally correlates with their seed company origin. Two populations each contained varieties from two different seed companies indicating genetic similarity of this material. The third population was comprised only of varieties from a single seed company. Analysis of the SSR and SNP datasets indicates that some of the hybrid varieties likely have a common (or very closely related) parent. Comparison of the three marker-systems revealed substantial differences in the number of loci needed for analyses. Varietal clustering required approximately 1.8–2 × more SSR, 3–4.5 × more SNP, and 4.8 × more DArT markers than were required for detection of genotypic diversity. When marker-systems were compared across different types of analyses per locus success-rate was the highest for the SSR and the lowest for the DArT markers. Generally, about 1.4–3 × more SNPs, and 4.9–13.3 × more DArTs then SSRs were needed to achieve the 100% success-rate. However, using only DArT markers with a high level of polymorphism decreased the number of DArT loci needed for analyses by 38–61%. Results from the present work provide a premise to selecting the type(s) and number of markers that are needed for genetic diversity analysis of sugar beet hybrid varieties
Diversity between and within farmers’ varieties of tomato from Eritrea
Asgedom, S. ; Vosman, B. ; Esselink, D. ; Struik, P.C. - \ 2011
African journal of biotechnology 10 (2011)12. - ISSN 1684-5315 - p. 2193 - 2200.
simple sequence repeat - ssr-markers - lycopersicon-esculentum - genetic-variation - polymorphic dna - identification - regions - plants - aflp - l.
Tomato yields in Eritrea are low (15 Mg/ha) compared with 19 Mg/ha in Africa and 27 Mg/ha worldwide. This is partly caused by poor quality of varieties used. This study analysed the diversity among and heterogeneity within farmers’ varieties of tomato from Eritrea and compared these varieties with other African and Italian varieties. Fifteen simple sequence repeat (SSR) markers were used for the genetic analysis. Genetic similarities among the varieties were calculated and an Unweighted Pair Group Method with Arithmetic Mean analysis was performed. Furthermore, individual plants of varieties were genotyped to evaluate uniformity within varieties. A high degree of diversity was observed among the Eritrean varieties. Thirteen out of the 15 SSRs were polymorphic, with 2 to 5 alleles per marker. The dendrogram showed two major types of varieties: San-Marzano and Marglob. Eritrean varieties were closely related to old Italian varieties in both types. Analysis of the within-variety variation showed that the Eritrean tomato genotypes were less uniform than the other varieties, probably because of deliberate mixing. A survey among farmers showed that some of them purposely mixed seeds to prolong the harvesting period, for yield stability and stress tolerance. Farmers value ‘new material’ as a source of influx