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SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India

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Abstract

A set of 24 of SSR markers were used to estimate the genetic diversity in 16 rice genotypes found in Western Himalayas of Kashmir and Himachal Pradesh, India. The level of polymorphism among the genotypes of rice was evaluated from the number of alleles and PIC value for each of the 24 SSR loci. A total of 68 alleles were detected across the 16 genotypes through the use of these 24 SSR markers The number of alleles per locus generated varied from 2 (RM 338, RM 452, RM 171) to 6 (RM 585, RM 249, RM 481, RM 162). The PIC values varied from 0.36 (RM 1) to 0.86 (RM 249) with an average of 0.62 per locus. Based on information generated, the genotypes got separated in six different clusters. Cluster 1 comprised of 4 genotypes viz; Zag 1, Zag 13, Pusa sugandh 3, and Zag 14, separated from each other at a similarity value of 0.40. Cluster second comprised of 3 landraces viz; Zag 2. Zag 4 and Zag10 separated from each other at a similarity value of 0.45. Cluster third comprised of 3 genotypes viz; Grey rice, Mushk budji and Kamad separated from each other at a similarity value of 0.46. Cluster fourth had 2 landraces viz; Kawa kreed and Loual anzul, and was not sub clustered. Fifth cluster had 3 genotypes viz; Zag 12, Purple rice and Jhelum separated from each other at a similarity value of 0.28. Cluster 6 comprised of a single popular variety i.e. Shalimar rice 1 with independent lineage.

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Acknowledgments

The authors are grateful to Professor Farooq A. Zaki for the helpful suggestions during the course of research and his administrative support. We are also thankful to the staff of the Mountain Research Centre for Field Crops, Khudwani for their help in the field experiments.

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Authors and Affiliations

  1. Centre for Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, India

    Humaira Ashraf, Amjad M. Husaini, M. Ashraf Bhat & Nazir A. Ganai

  2. Mountain Research Centre for Field Crops, Khudwani, Anantnag, Jammu and Kashmir, India

    GA Parray

  3. Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia

    Salim Khan

Authors
  1. Humaira Ashraf
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  2. Amjad M. Husaini
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  3. M. Ashraf Bhat
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  4. GA Parray
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  5. Salim Khan
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  6. Nazir A. Ganai
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Correspondence to Amjad M. Husaini.

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Ashraf, H., Husaini, A.M., Ashraf Bhat, M. et al. SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India. Physiol Mol Biol Plants 22, 547–555 (2016). https://doi.org/10.1007/s12298-016-0377-8

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  • DOI: https://doi.org/10.1007/s12298-016-0377-8

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