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Development and validation of EST-derived SSR markers and diversity analysis in cluster bean (Cyamopsis tetragonoloba)

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Abstract

Cluster bean/guar (Cyamopsis tetragonoloba), has an important place in industry because of its seeds, which contain galactomannan (guar gum) rich endosperm. Guar gum, an important ingredient of many products, is purely an export oriented commodity. Development of molecular markers for this crop is essential to accelerate breeding for guar gum content in seeds. A total of 100 novel primers pairs were developed from 16,476 expressed sequence tags (ESTs) sequence of cluster bean. A total of 50 primers pairs with function annotation of gum synthesis were selected and validated on a panel of 32 genotypes. Among the 50 primers 39 primers were amplified with a total of 45 loci. The polymorphic information content (PIC) ranged from 0.00 to 0.42 with an average of 0.13. With low polymorphic simple sequence repeats (SSRs) and narrow genetic base, most of the genotypes scattered into three clusters regardless of their geographical origin. Present study showed the existence of very low genetic diversity in cluster bean. The results indicated that there is need to explore SSR markers from whole genome or alternative marker systems like SNP (single nucleotide polymorphism) markers, for effective implication of markers in cluster bean breeding.

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Abbreviations

EST:

Expressed sequence tag

SSR:

Simple sequence repeat

RAPD:

Random Amplified Polymorphic DNA

ISSR:

Inter simple sequence repeat

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India

    Sushil Kumar, Mithil J. Parekh, Chandni B. Patel, Harshvardhan N. Zala, Kalyani S. Kulkarni, Ranbir S. Fougat & Amar A. Sakure

  2. Division of Plant Improvement, Propagation and Pest Management, Central Arid Zone Research Institute (CAZRI), Jodhpur, 342003, India

    Ramavtar Sharma & Ram K. Bhatt

Authors
  1. Sushil Kumar
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  2. Mithil J. Parekh
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  3. Chandni B. Patel
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  4. Harshvardhan N. Zala
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  5. Ramavtar Sharma
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  6. Kalyani S. Kulkarni
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  7. Ranbir S. Fougat
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  8. Ram K. Bhatt
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  9. Amar A. Sakure
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Correspondence to Sushil Kumar.

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Kumar, S., Parekh, M.J., Patel, C.B. et al. Development and validation of EST-derived SSR markers and diversity analysis in cluster bean (Cyamopsis tetragonoloba). J. Plant Biochem. Biotechnol. 25, 263–269 (2016). https://doi.org/10.1007/s13562-015-0337-3

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  • DOI: https://doi.org/10.1007/s13562-015-0337-3

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