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Assessment of genetic diversity and DNA profiling of linseed (Linum usitatissimum subsp. usitatissimum L.) germplasm using SSR markers

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Abstract

Access to genetic diversity is essential for any progress in adapting linseed (Linum usitatissimum subsp. usitatissimum L.) cultivation to changing environmental conditions or to the changing market needs. An attempt has been made in the present study to assess genetic diversity in 96 genotypes of linseed including varieties, landraces and exotic material. A total of 38 SSR primers amplified 153 alleles with 4.0 alleles per marker locus. The number of alleles ranged from 2 to 15 and the observed polymorphism ranged from 50 to 100%. Average genetic dissimilarity ranged from 2 to 50%. In order to analyze the efficiency for unambiguous identification of linseed germplasm, various statistical measures, viz., number of genotyping patterns, polymorphism information content, resolving power, discrimination power, probability of identity and probability of random identity, identified a set comprising of primers LU7, LU27, LU25, LU20 and LU31 (or LU637) for DNA fingerprinting of linseed germplasm. UPGMA cluster analysis showed that all genotypes could be grouped into four main clusters. Cluster 2 was the largest consisting of mainly landraces, whereas, Cluster 4 was the smallest. Cluster 1 consisted of mainly the released cultivars. Cluster 3 and Cluster 4 were smaller clusters and consisted of exotic genotypes. Principal co-ordinate analysis further substantiated the UPGMA clustering patterns of the observed genetic relationship. To explain 70–80% variability, 17–23 PCOs were needed, whereas 70 components were needed to explain the whole variability in the linseed material under study. Analysis of molecular variance indicated that most of the genetic variation is owing to the individuals within single population, whereas grouping of linseed material into varieties, landraces and exotics accounted for nearly 10% of the total genetic variation. The utility of SSR markers in diversity assessment and cultivar identification is discussed.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

CTAB:

Cetyltrymethylammonium bromide

ISSR:

Inter-simple sequence repeats

RAPD:

Random amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

SRAP:

Sequence related amplified polymorphism

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Acknowledgements

We greatly acknowledge financial support from the Indian Council of Agricultural Research (ICAR). Director, NBPGR and Officer-In-Charge, Division of Genomic Resources, NBPGR are also acknowledged for providing laboratory facilities for carrying out this work. Thanks are also due to the Council of Scientific and Industrial Research (CSIR) for awarding Senior Research Associateship to Ms. Sonika Singh.

Funding

This study was partly funded by Council of Scientific and Industrial Research (CSIR) to Sonika Singh in terms of Senior Research Associateship vide CSIR Letter No. 13(8547-A)/2012/pool dated 17/04/2012.

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  1. Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012, India

    M. K. Rana & Sonika Singh

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  1. M. K. Rana
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  2. Sonika Singh
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Correspondence to M. K. Rana.

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Rana, M.K., Singh, S. Assessment of genetic diversity and DNA profiling of linseed (Linum usitatissimum subsp. usitatissimum L.) germplasm using SSR markers. J. Plant Biochem. Biotechnol. 26, 293–301 (2017). https://doi.org/10.1007/s13562-016-0391-5

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