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<p>As a result of growing industrial demand for the medicinal and economic benefits of phytoconstituents, the illicit trade of <i>Saussurea costus</i> (Falc.) Lipsch in the North-Western Himalayas is causing severe habitat destruction and fragmentation. Therefore, the present study employed a conservation genetic approach to examine the genetic diversity and population structure of <i>S</i>. <i>costus</i> across the North-Western Himalayas on the basis of genic markers (EST-SSRs) implicated in the biosynthesis of secondary metabolites. There is very limited genetic information available due to the unavailability of genomic as well as EST-SSR-based genic markers in this herb. By utilizing root tissue-specific transcriptome data, a total of 109,820 unigenes yielded 16,866 SSR loci, of which tri-nucleotide repeats (13,641/80.88%) were found to be predominant, followed by di-nucleotide (2434/14.43%), tetra-nucleotide (412/2.44%), hexa-nucleotides (206/1.22%), and penta-nucleotide repeats (173/1.03%). Among 37 selected EST-SSRs related to bioactive compound biosynthesis, 26 primer pairs displayed an average 0.88% polymorphism with an observed number of alleles (Na = 2.83), expected number of alleles (Ne = 2.00), expected heterozygosity (He = 0.47), observed heterozygosity (Ho = 0.51), marker index (MI = 0.76), polymorphic information content (PIC = 0.50), resolving power (Rp = 3.15), effective multiplex ratio (EMR = 1.39), and Shannon’s information index (<i>I</i> = 0.76). Furthermore, neighbor-joining-based hierarchical clustering and Bayesian clustering analysis classified <i>S</i>. <i>costus</i> genotypes into two major groups according to their respective elevations. Thus, novel EST-SSR markers linked to the various secondary metabolic pathways indicate their importance and potential use for analyzing desirable traits in <i>S</i>. <i>costus</i> and its closely related <i>Saussurea</i> species.</p>

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De Novo Transcriptome Assembly, Novel EST-SSR Development, and Preliminary Genetic Analysis in Saussurea costus (Falc.) Lipsch, an Industrially Important Endangered Medicinal Herb of the North-Western Himalayas

  • 期刊论文

  • 发表日期：

    2025年2月4日

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  • Kamal Thakur,
  • Rajnish Sharma,
  • Parul Sharma,
  • Anamika Thakur,
  • Ashwini Zadokar,
  • Vinay Kumar,
  • Bhupender Dutt

摘要

As a result of growing industrial demand for the medicinal and economic benefits of phytoconstituents, the illicit trade of Saussurea costus (Falc.) Lipsch in the North-Western Himalayas is causing severe habitat destruction and fragmentation. Therefore, the present study employed a conservation genetic approach to examine the genetic diversity and population structure of S. costus across the North-Western Himalayas on the basis of genic markers (EST-SSRs) implicated in the biosynthesis of secondary metabolites. There is very limited genetic information available due to the unavailability of genomic as well as EST-SSR-based genic markers in this herb. By utilizing root tissue-specific transcriptome data, a total of 109,820 unigenes yielded 16,866 SSR loci, of which tri-nucleotide repeats (13,641/80.88%) were found to be predominant, followed by di-nucleotide (2434/14.43%), tetra-nucleotide (412/2.44%), hexa-nucleotides (206/1.22%), and penta-nucleotide repeats (173/1.03%). Among 37 selected EST-SSRs related to bioactive compound biosynthesis, 26 primer pairs displayed an average 0.88% polymorphism with an observed number of alleles (Na = 2.83), expected number of alleles (Ne = 2.00), expected heterozygosity (He = 0.47), observed heterozygosity (Ho = 0.51), marker index (MI = 0.76), polymorphic information content (PIC = 0.50), resolving power (Rp = 3.15), effective multiplex ratio (EMR = 1.39), and Shannon’s information index (I = 0.76). Furthermore, neighbor-joining-based hierarchical clustering and Bayesian clustering analysis classified S. costus genotypes into two major groups according to their respective elevations. Thus, novel EST-SSR markers linked to the various secondary metabolic pathways indicate their importance and potential use for analyzing desirable traits in S. costus and its closely related Saussurea species.