Mining and Survey of Simple Sequence Repeats in Expressed Sequence Tags of Tomato Species

Expressed Sequence Tags (ESTs) of three tomato species were computationally mined for simple sequence repeats (SSRs). A total of 4,490, 291 and 1,270 simple sequence repeats identified in analyzed non-redundant ESTs of Solanum lycoperisicum, Solanum pennellii and Solanum habrochaites, respectively. In S. lycopersucum, 416 sequences contained more than one SSR and 264 motifs were present in compound formation. 24 and 137 EST sequences contained more than one SSR, and 16 and 93 motifs were found in compound formation in S. pennellii and S. habrochaites, respectively. The frequency of repeats within all retrieved S. lycopersicum EST sequences were 7.6%, whereas this number was corresponded to 6.5% in S. pennellii and 9% in S. habrochaites. An average density was one SSR per 9 kb in S. lycopersicum, per 7.9 kb in S. pennellii and per 9.4 kb in S. habrochaites. AT/AT, AG/CT and AAG/CTT motifs, considering sequence complementary, detected more frequently among all types of identified repeats

Assessment Of Genetic Diversity In Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest simi-larity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘El-nur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diver-sity calculated from RAPD data was 0.665

Genetic diversity among melon (Cucumis melo L.) accessions revealed by morphological traits and ISSR markers

The genetic relationships among 48 melon (Cucumis melo L.) genotypes collected from various parts of Azerbaijan were determined by comparing their phenotypic and molecular traits. Eleven agromorphological traits and 10 polymorphic inter-simple sequence repeat (ISSR) primers were used to define the genetic diversity. Principal component analysis grouped the agromorphological traits into the first four axes, describing 78% of the total variations. The highest genetic variation coefficient was found for yield per hectare (20.32%) and for fruit length (17.35%). Calculated heritability for yield was 0.96. The analysis of morphological traits grouped the accessions into four clusters. The 10 ISSR primers yielded 35 polymorphic alleles, representing 85.4% of all the amplified loci. The average genetic diversity index determined was 0.70. The highest and the lowest similarity indexes were equal to 0.97 and 0.36, respectively. The 48 accessions were grouped into 10 clusters based on ISSR markers. Correlation between distance matrices based on agromorphological traits and ISSR markers was not statistically significant (r = 0.012)

Verification of taxonomic relationships within the genus Secale (Poaceae: Pooideae: Triticeae) based on multiple molecular methods

This study aimed to verify the taxonomic relationships within the genus Secale. The plant material included 16 wild rye accessions from four species. Two approaches were applied: 1) whole genome scanning using three molecular marker systems: diversity arrays technology sequencing, simple sequence repeats and sequence-specific amplification polymorphism; and 2) characterisation based on polymorphisms within the sequences of two genes involved in benzoxazinoid biosynthesis: ScBx1 and ScBx5. Bayesian and neighbour-joining clustering and principal coordinate analysis were applied to illustrate relationships among species and accessions of Secale based on genetic distance (GD) matrices. Pearson’s correlation analysis between GD matrices was conducted. Clustering of Secale accessions revealed that S. sylvestre samples were the most divergent. The remaining accessions formed two clusters. One of them comprised S. strictum accessions while the second cluster consisted of subspecies of S. cereale, the species S. vavilovii and S. strictum subsp. ciliatoglume

DArT Markers Effectively Target Gene Space in the Rye Genome

Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes

Biodiversity of Vegetable Genetic Resources in Azerbaijan

Azerbaijan is considered one of the origin and cultivated center for many agricultural plants. Nowadays, more than 30 species of vegetables are widely cultivated with their 84 registered varieties and hybrids. The main collections of vegetable plants are protected at the National Genebank of the Genetic Resources Institute, at the Scientific Research Institute of Vegetable-Growing and at the Azerbaijan State Agricultural Academy