Genetic analysis of the genus Diospyros ssp. using RAPD and i-PBS methods

Abstract

Molecular techniques (RAPD and i-PBS) were used to study genetic diversity within persimmon collection at Horticulture Faculty of Mendel University in Lednice. The aim of the work was to distinguish 14 known and 6 of unknown origin persimmon cultivars. The basic screening of 20 OPT primers was applied to 4 cultivars differring in the place of origin. Within the group of screened primers there were chosen those, which gave polymorphic repeatable strong and middle strong bands. Selected primers were used for the RAPD reactions within the whole persimmon collection. Three OPA primers previously described in the literature were also used for the RAPD reactions within the whole persimmon collection. Additional 16 i-PBS primers previously described in the literature were also used for i-PBS analysis of the whole group of cultivars. Amplification was successful with 12 i-PBS primers. The FreeTree software package was used to gen­erate a similarity matrix and then to produce a dendrogram using UPGMA analyses. The similarity dendrograms of all persimmon cultivars were created based on both approaches and also on combination of both analyses by program Tree View. All the dendrograms clearly separated the assessed cultivars into 4 clusters. There are cluster of American persimmons – Meader’ (1), ’Garretson’ (2) and ’Early Golden’ (3). They are representatives ofD. virginiana. Further part of dendrogram includes singleD. lotus(5), which is also clearly separated from other cultivars of the genusDiospyros. The third cluster includes interspecific hybrids ’Rossiyanka’ (10) and ’Nikitskaiya Bordovaiya’ (13), which arised from crosses ofD. virginianaandD. kaki. The last cluster is formed by cultivars of Japanese persimmon – ’Mikatani Gosho’, ’Zenjimaru’, ’Tone Wase’, ’Hiratanenashi’, ’Fuyu’, Chinese cultivar – ’Sansi’ and two Italian cultivars ’Vaniglia’ and ’Tipo’. They are clustered without significant distinction. The similarities and the differences revealed among incorporation of cultivars into groups were compared with the literature findings.

Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system

“…Although iPBS primers are universal markers for plant and animal kingdoms, they have been used to investigate genetic diversity in only a few plant species such as Saussurea esthonica (Gailīte et al ., 2011), Diospyros ssp. (Raddová et al ., 2012), Cicer species (Andeden et al ., 2013), Myrica rubra (Fang-Yong and Ji-Hong, 2014), grape (Guo et al ., 2014), Lens species (Baloch et al ., 2015a) and pea (Baloch et al ., 2015b). All of the earlier studies clearly demonstrated that iPBS retrotransposons were very efficient for genetic diversity and molecular studies in plants.…”

“…The advantages of iPBS marker system are: (1) ability to screen large regions of plant genomes; (2) primers can be used for any organism; (3) easy to perform; and (4) comparatively cheap due to requirement of basic laboratory facilities. Besides, iPBS primers have previously been shown to be a powerful marker system for fingerprinting and genetic similarity studies in plants (Gailīte et al , 2011; Raddová et al , 2012; Andeden et al , 2013; Fang-Yong and Ji-Hong, 2014; Guo et al , 2014; Baloch et al , 2015a, b). Because of these advantages, in the present study, iPBS marker system was used for fingerprinting potato genotypes and identification of genetic similarity within potato genotypes located in Turkey.…”

Genetic Diversity and Breeding of Persimmon

“…The authors suggested that more cultivars were needed as plant materials in terms of determining the degree of relationships of RAPD and FAME data which could help delimiting taxonomic classes within persimmon. Raddová et al [58] indicated that RAPD and inter-primer binding site (i-PBS) were reliable enough to detect differences between the genetically close cultivars of persimmon. In addition, Badenes et al [45] studied the genetic diversity of introduced and local Spanish persimmon cultivars as revealed by RAPD markers.…”

Genetic Diversity in Diospyros Germplasm in the Western Caucasus Based on SSR and ISSR Polymorphism

“…Nowadays, three species are grown in these regions: D. lotus (2n = 2x = 30), D. virginiana (2n = 6x = 90) and D. kaki (2n = 6x = 90; 2n = 9x = 135). D. lotus and D. virginiana are the most cold-tolerant species in the genus Diospyros and are important for the development of new drought or cold-tolerant varieties [ 11 ]. The standard assortment for this region included famous cultivars such as “Hachiya”, “Hiyakume”, and “Zenjimaru”.…”

“…In Diospyros , molecular markers have been developed in recent years for the efficient characterization and further utilization of germplasm resources. Phylogenetic relationships of Diospyros species are mainly studied based on random amplification of polymorphic DNA (RAPD) [ 11 ], simple sequence repeats (SSRs) [ 12 , 13 , 14 , 15 , 16 ], internal transcribed spacer (ITS) [ 17 ], sequence-related amplified polymorphism (SRAP) [ 14 , 18 ], inter-retrotransposon-amplified polymorphism (IRAP) [ 19 ], start codon-targeted (SCoT) [ 19 , 20 , 21 ] or organelle sequences (orgDNA) [ 22 ].…”