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<p><i>Dalbergia sissoo</i> is a premier timber species of the rosewood genus experiencing severe population decline throughout the distribution range in Indian subcontinent but lacking critical knowledge of population genetics required for its conservation and management. The present study was aimed to develop de novo simple sequence repeat (SSR) markers using genome survey sequencing (GSS) approach in <i>D. sissoo</i> and characterizing germplasm set from northern and central India. Approximately 74 million raw reads were generated through a next-generation sequencing (NGS) platform, leading to a partial de novo assembly of 359,272 contigs and an N50 length of 3,781&#xa0;bp. By scanning of genome assembly, 25,596 microsatellite repeats were identified wherein di-nucleotide repeats were most abundant, and AT-rich motifs were more frequent in all the repeat classes. Subsequently, primer pairs were developed for 15,614 SSR loci, and 121 of these were confirmed by polymerase chain reaction (PCR) amplification. Of these, 82 SSR loci were successfully amplified, and 14 demonstrated polymorphism. Present study recorded a moderate genetic diversity (He = 0.418; Ar = 2.75) and moderate genetic differentiation (F<sub>ST</sub> = 0.118) for the studied germplasm set of <i>D. sissoo</i>. All the clustering methods based on Neighbour-Joining, principal coordinate analysis (PCoA), discriminant analysis of principal components (DAPC) and Bayesian analysis revealed a strong genetic structure where the germplasm of arid part of central India (Bundelkhand region) formed a distinct genetic cluster. These genomic resources and population-level insights lay a foundational platform for future genetic improvement, adaptive trait discovery, and long-term conservation planning, thereby enhancing the species’ resilience and ensuring the sustainable utilization of <i>D. sissoo</i> across its native range.</p>

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Genome survey sequencing-based SSR marker development and population genetic structure of Dalbergia sissoo: a premier hardwood timber species

  • 期刊论文

  • 发表日期：

    2026年2月28日

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  • Rajendra K. Meena,
  • Payal Dhyani,
  • Priyanka Kashyap,
  • Ajay Sojitra,
  • Maneesh S. Bhandari,
  • Shailesh Pandey,
  • Rama Kant,
  • Ajay Thakur,
  • Ashok Kumar,
  • Santan Barthwal

摘要

Dalbergia sissoo is a premier timber species of the rosewood genus experiencing severe population decline throughout the distribution range in Indian subcontinent but lacking critical knowledge of population genetics required for its conservation and management. The present study was aimed to develop de novo simple sequence repeat (SSR) markers using genome survey sequencing (GSS) approach in D. sissoo and characterizing germplasm set from northern and central India. Approximately 74 million raw reads were generated through a next-generation sequencing (NGS) platform, leading to a partial de novo assembly of 359,272 contigs and an N50 length of 3,781 bp. By scanning of genome assembly, 25,596 microsatellite repeats were identified wherein di-nucleotide repeats were most abundant, and AT-rich motifs were more frequent in all the repeat classes. Subsequently, primer pairs were developed for 15,614 SSR loci, and 121 of these were confirmed by polymerase chain reaction (PCR) amplification. Of these, 82 SSR loci were successfully amplified, and 14 demonstrated polymorphism. Present study recorded a moderate genetic diversity (He = 0.418; Ar = 2.75) and moderate genetic differentiation (FST = 0.118) for the studied germplasm set of D. sissoo. All the clustering methods based on Neighbour-Joining, principal coordinate analysis (PCoA), discriminant analysis of principal components (DAPC) and Bayesian analysis revealed a strong genetic structure where the germplasm of arid part of central India (Bundelkhand region) formed a distinct genetic cluster. These genomic resources and population-level insights lay a foundational platform for future genetic improvement, adaptive trait discovery, and long-term conservation planning, thereby enhancing the species’ resilience and ensuring the sustainable utilization of D. sissoo across its native range.