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The distribution and occurrence of mono, di, tri, tetra, penta, hexa, hepta, octa and deca nucleotide have been compared in Ct-D-EST, Ct-N-EST and Co-EST libraries.
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... assembly, unigenes were identified and the average lengths of the EST sequences in Ct-D-EST, Ct-N-EST and Co-EST were 494, 754 and 633 bp, respectively. The distribution and occurrence of type of SSR motif repeats in all the three ESTs libraries are presented in Figure 1. The EST-SSRs developed from Ct-D-EST, Ct-N-EST and Co-EST libraries were named as drought SSRs, normal SSRs and wild SSRs, respectively. ...
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... assembly, unigenes were identified and the average lengths of the EST sequences in Ct-D-EST, Ct-N-EST and Co-EST were 494, 754 and 633 bp, respectively. The distribution and occurrence of type of SSR motif repeats in all the three ESTs libraries are presented in Figure 1. The EST-SSRs developed from Ct-D-EST, Ct-N-EST and Co-EST libraries were named as drought SSRs, normal SSRs and wild SSRs, respectively. ...
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... Interestingly, it was reported that the trinucleotide repeats were more frequent in coding sequences of the human genes too (Krzyzosiak and Napierala, 2011). In contrast, monoand dinucleotide motifs were predominant in EST-SSRs obtained by RNA-seq analysis of safflower under drought stress (92.30% and 5.12%, respectively) (Sudhakar et al., 2019). This difference may be due to the use of all cDNA sequences for deriving SSR motifs in our research and the use of only drought responding transcripts for deriving SSR motifs in the mentioned work. ...
Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional features of the SSR-containing genes to elucidate their role in biological and cellular processes. We identified 1,841 SSR regions in 1,667 cDNA sequences. Among all types of repeats, trinucleotide repeats were the most abundant (35.7%), followed by hexanucleotide (29.6%) and dinucleotide repeats (22.0%). Thirty five SSR primer pairs were validated by PCR reaction, detected a high rate of polymorphism (>57%) among safflower accessions, physically mapped on safflower genome and could clearly discriminate the cultivated accessions from wild relatives. The cDNA-derived SSR markers are suitable for evaluation of genetic diversity, linkage and association mapping studies and genome-based breeding programmes. Occurrence of SSR repeats in biologically-important classes of proteins such as kinases, transferases and transcription factors was inferred from functional analyses, which along with variability of their repeat copies, can endow the cell and whole organism the flexibility of facing with continuously changing environment, and indicate a structure-based evolution mechanism of the genome which acts as an up-to-dating tool for the cell and whole origanism, which is realized in GO terms such as involvement of most SSR-containing genes in biological, cellular and metabolic processes, especially in response to stimulus, response to stress, interaction to other organisms and defense responses.
... Though there is low genetic conservation in Asteraceae (Whitton et al. 1997), previous studies in safflower have reported varied frequency of SSRs repeats for e.g., di-nucleotide repeats were reported as predominant SSRs by Yamini et al. (2013) and Ambreen et al. (2015), whereas Chapman et al. (2009) andSudhakar et al. (2019) reported tri-nucleotides to be the more abundant SSRs. In contrast to these studies, we observed almost a similar percentage of SSRs containing di, tri and hexa-nucleotide repeats. ...
Safflower, an important oil seed and medicinal crop has rich genetic diversity but limited genetic resources, which could be utilized for its improvement. In a bid to enrich safflower’s genetic resources polymorphic genic SSRs were identified by in silico comparisons of the de novo assembled transcriptome sequences from two safflower genotypes. Of the 145 exon-derived primer pairs, 125 produced reproducible amplifications and 44 primer pairs yielded products that showed polymorphism even between the two closely related safflower accessions. Out of the 44 primer pairs, 10 primers that were utilized for assessing the genetic diversity and cross-species transferability on a diverse panel consisting of 24 accessions, revealed high genetic diversity in the panel and cross-species transferability of the markers. The UPGMA dendrogram clustered the wild types and safflower genotypes in three major groups, of which wild types clustered in a subgroup of major group II, whereas the remaining genotypes were scattered in all three clusters with the majority (73.68%) being clustered in group I. The in silico identified polymorphic exon derived genic SSRs are an important addition to the available genetic resources and can be deployed for marker assisted breeding programs for improvement of safflower.
In silico approach was applied for the discovery and characterization of SSRs and SNP markers. RNA sequencing was applied
to generate large scale genome-wide transcripts associated with powdery mildew disease of sunfower (Helianthus annuus
L.). The sunfower materials from which the transcripts were generated comprised one susceptible (PS 2023B), two cultivated
resistant accessions (TX16R, ID 25) and three wild species (H. praecox [1823], H. niveus [1452], and H. debilis [DEB-689]).
For the susceptible and resistant accessions, control (no infection) and pooled (with infection) samples were created based on
which the transcripts were developed. A total of 123,058 SSRs were discovered from the assembled transcriptome of each
accession. Out of this total obtained SSRs, 112,326 were classifed as perfect and 10,732 as compound SSRs. The percent
contribution of compound SSRs in susceptible and in all the tolerant accessions ranged from 8.51 to 9.15%. There was no
prominent or signifcant diference in the number of SSR motifs, comparing the susceptible and resistant accessions tested.
A signifcantly higher CG motif was observed in the susceptible accessions than in the resistant accessions. We, therefore,
speculate that the CG motif might play a vital role in the susceptibility of sunfower to powdery mildew disease. Similarly,
the percentage of GC motif was found to be signifcantly higher in the resistant accessions. It is likely that the GC motifs
might be involved in the induction of resistance to powdery mildew in sunfower plants. Trinucleotide motif based predic�tions resulted in signifcantly higher levels of the following amino acids in the susceptible accession: Ile, Lys, Met, Phe, Pro,
Thr and Val. It is presumed that these amino acids might be involved in the vulnerability to the powdery mildew disease in
2023B. In total 35,390 Single Nucleotide Polymorphisms (SNPs) loci were identifed that were distributed on all 17 link�age groups with the average resolution of 443.2 Kb/SNP. Linkage group 10 had the highest localized SNPs (3631) with an
average of 576 Kb/ SNP and 7 had least (781) with average of 441 Kb/ SNP. Most of the SNPs identifed were observed to
be transition mutations with mainly A/G type substitutions. The discovered markers will prove useful after wet laboratory
studies for screening and marker assisted breeding for powdery mildew resistance in sunfower.
