Abstract
Drought stress is a major abiotic factor causing yield loss in safflower and limited studies have been carried out to dissect the molecular mechanism at EST-SSR level. In this study, a possible relationship between simple sequence repeats (SSRs) distribution and drought stress was studied using three EST libraries of safflower, Ct-D-EST, Ct-NEST and Co-EST. The Ct-D-EST was generated from drought tolerant safflower cultivar A-1; Ct-N-EST and Co-EST were the EST datasets of safflower and its wild progenitor C. oxycanthus, respectively. In total, 156 (45%), 1194 (5%) and 1550 (9%) EST-SSRs were mined from Ct-D-EST, Ct-N-EST and Co-EST libraries, respectively. Comparison of EST-SSRs from Ct-D-EST with that of SSRs from other two libraries showed reasonable differences for each class of repeats. Large variations were observed for dinucleotide repeats in all the libraries. In drought EST-SSRs, only one kind of amino acid was produced by repeat (ATG)14 which encodes met indicating the loci and repeat observed to be 100%. Since three ESTs with SSRs from Ct-D-EST, annotated to putative candidate genes, S-adenosylmethionine synthetase, one-helix protein and myo-inositol 1-phosphate synthetase, did not express with SSRs in the Ct-N-EST, these can be considered as potential candidate genes for drought tolerance. A trinuceotinde SSR, encoding met, was also found in the EST annotated to putative s-adenosylmethionine synthetase, hence, both can be considered as indices for drought tolerance. The genomic resources and the information generated in this study may be useful for the safflower breeders particularly for the development of drought tolerant cultivar.
Highlights
In India, safflower (Carthamus tinctorious L.) is cultivated mainly for the high-quality edible oil extracted from the seeds. valued
52145 ESTs were analyzed by simple sequence repeats (SSRs) Locator; 591 ESTs belonged to Ct-D-EST, and 24,299 ESTs belonged to Ct-N-EST and 27,255 Co-EST (Table 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
Summary
In India, safflower (Carthamus tinctorious L.) is cultivated mainly for the high-quality edible oil extracted from the seeds. valued. Wild safflower (Carthamus oxyacanthus) show high drought tolerance making it is as a suitable source for transferring drought tolerant genes to cultivated species [3,4]. ESTs are short piece of cDNA sequences generated by large-scale single pass sequencing of cDNA clones They serve as low-cost alternative to whole genome sequencing; they are efficient in gene discovery and development of DNA markers. SSRs (single sequence repeats) are sequences in which one or few bases are tandemly repeated, ranging from 1-6 base pair (bp) long units. They are ubiquitous in eukaryotic and prokaryotic genomes, found in both coding and non-coding regions [8,9]. By comparing and analyzing drought SSRs with normal ones, we tried to find a possible relationship between SSRs distribution and drought stress
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