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<p>Teak (<i>Tectona grandis</i> Linn f.) is an economically important hardwood forest tree species from the tropics. We studied the genome features of Indian teak population represented in the national teak germplasm bank (NTGB) using single nucleotide polymorphism (SNP) obtained from whole genome resequencing (WGRS). This is the first genomic characterization study on NTGB clones using high-density SNPs spread across the whole genome. The short-range linkage disequilibrium (LD) spanned over the physical distance of 1.25&#xa0;kb at <i>r</i><sup>2</sup> threshold of 0.2 obtained with fine-scale linkage decay analysis using 50,39,635 SNPs is much higher than that obtained in previous studies of teak. We used these genome features to identify the population structure and loci associated with wood traits such as heartwood: sapwood ratio and density. Three distinct subpopulations aligning with the theory of South and Central centers of origin and transfer of accessions from Myanmar were obtained using 4,93,591 SNPs (LD pruning at <i>r</i><sup>2</sup> = 0.2) from 132 accessions. A 39.4% variation among these subpopulations from the analysis of molecular variance (AMOVA) reassured this population structure demarcation. The heterozygosity was higher in South and Central subpopulations while the subpopulation from Uttar Pradesh and Odisha was assumed to be transferred from Myanmar containing a large number of rare alleles. Totally 71 significant SNPs related to the wood traits were identified. Some of these SNPs in genic regions were known for stress response and wood formation. Discoveries from this study laid a strong foundation for molecular breeding techniques as well as management and conservation efforts. Additionally, genetic variant hotspots found in different pseudomolecules will facilitate targeted functional genomics and marker-trait association on wood trait studies.</p>

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Whole genome resequencing unveils population structure and wood trait associations for Indian teak germplasm

  • 期刊论文

  • 发表日期：

    2025年2月24日

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  • Maheswari Patturaj,
  • Adwaith Manikantan,
  • Sivakumar Veerasamy,
  • Ani A. Elias,
  • Yasodha Ramasamy

摘要

Teak (Tectona grandis Linn f.) is an economically important hardwood forest tree species from the tropics. We studied the genome features of Indian teak population represented in the national teak germplasm bank (NTGB) using single nucleotide polymorphism (SNP) obtained from whole genome resequencing (WGRS). This is the first genomic characterization study on NTGB clones using high-density SNPs spread across the whole genome. The short-range linkage disequilibrium (LD) spanned over the physical distance of 1.25 kb at r2 threshold of 0.2 obtained with fine-scale linkage decay analysis using 50,39,635 SNPs is much higher than that obtained in previous studies of teak. We used these genome features to identify the population structure and loci associated with wood traits such as heartwood: sapwood ratio and density. Three distinct subpopulations aligning with the theory of South and Central centers of origin and transfer of accessions from Myanmar were obtained using 4,93,591 SNPs (LD pruning at r2 = 0.2) from 132 accessions. A 39.4% variation among these subpopulations from the analysis of molecular variance (AMOVA) reassured this population structure demarcation. The heterozygosity was higher in South and Central subpopulations while the subpopulation from Uttar Pradesh and Odisha was assumed to be transferred from Myanmar containing a large number of rare alleles. Totally 71 significant SNPs related to the wood traits were identified. Some of these SNPs in genic regions were known for stress response and wood formation. Discoveries from this study laid a strong foundation for molecular breeding techniques as well as management and conservation efforts. Additionally, genetic variant hotspots found in different pseudomolecules will facilitate targeted functional genomics and marker-trait association on wood trait studies.