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Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.)

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Abstract

With the aim of developing additional genomic resources in safflower, a set of 41,011 ESTs of safflower were mined for the presence of SSRs. 18,773 SSR containing ESTs (SSR-ESTs) were identified and were analyzed to remove redundant sequences leading to identification of 8,810 non-redundant SSR-ESTs (categorized into 6104 singletons and 2,706 contigs) having 13,085 non-redundant SSRs. The average number of non-redundant SSRs per EST was 0.32 and they predominantly consisted of dinucleotide (57.7 %), and trinucleotide (37.7 %) repeat motifs. 500 primer pairs were designed for the non-redundant EST-SSRs of which, 151 were tested. 60 markers which gave robust amplicons, were validated in a set of 19 Carthamus lines. A subset of EST-SSR markers, having average polymorphism information content (PIC) ≥0.4 could precisely elucidate the pedigree relatedness among these lines. Further, these markers exhibited high cross-species transferability to five other wild species of Carthamus. The markers reported here would be a valuable addition to existing safflower marker resources aiding in hastening its improvement.

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Abbreviations

DSC:

Dice Standard Coefficiient

ISSR:

Inter-simple Sequence Repeats

MAS:

Marker-assisted Selection

NTSYS:

Numerical Taxonomy System

PAGE:

Polyacrylamide gel electrophoresis

UPGMA:

Unweighted Pair-Group Method Arithmetic Average

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Authors and Affiliations

  1. Directorate of Oilseeds Research, Rajendranagar, Hyderabad, 500 030, Andhra Pradesh, India

    Kamtam Ramesh, Vasupalli Naresh, Kammili Anjani & Viswanathaswamy Dinesh Kumar

  2. A.N.G.R. Agricultural University, Regional Agricultural Research Station, Warangal, 506 007, Andhra Pradesh, India

    Kalinati Narasimhan Yamini

  3. Directorate of Sorghum Research, Rajendranagar, Hyderabad, 500 030, Andhra Pradesh, India

    Passoupathy Rajendrakumar

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  1. Kalinati Narasimhan Yamini
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  2. Kamtam Ramesh
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Correspondence to Viswanathaswamy Dinesh Kumar.

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K. N Yamini and K. Ramesh have contributed equally for the work.

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Yamini, K.N., Ramesh, K., Naresh, V. et al. Development of EST-SSR markers and their utility in revealing cryptic diversity in safflower (Carthamus tinctorius L.). J. Plant Biochem. Biotechnol. 22, 90–102 (2013). https://doi.org/10.1007/s13562-012-0115-4

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