Detection of QTL (quantitative trait loci) associated with wood density by evaluating genetic structure and linkage disequilibrium of teak

Abstract

To find the quantitative trait loci associated with wood density in teak (Tectona grandis L.f.), 21 co-dominant markers including 13 site specific recombinase and 8 EST-based co-dominant markers designed from lignin biosynthesis genes were applied to 174 teak plus tree clones at the National Germplasm Bank, Chandrapur, India. The germplasm bank exhibited 10.6% coefficient of variation for wood densities with 84.5 ± 31.3 genetic polymorphism (%). The highly panmictic set of genotypes (F_ST = 0.035 ± 0.004) harbored 96.47 ± 0.40 genetic variability (%). The average allelic frequency of the 21 co-dominant markers was 0.65 ± 0.11 with 12.9% pairs of loci in significant LD (p < 0.05, R ² values > 0.1), confirming their suitability for a strong marker-trait association study. The marker CCoAMT-1 was significantly (p < 0.01) associated with wood density showing stability by both GLM and MLM models and explained 4.3% of the phenotypic effect. The marker from the EST representing CCoAMT can be further developed for gene-assisted selection of elite genotypes of teak with greater wood density. Therefore, we believe that the report will help accelerate the genetic improvement and advance the breeding program of the species.

Keywords

Association mapping / Expressed sequence tags (EST) / General linear model (GLM) / Linkage disequilibrium (LD) / Lignin / Mixed linear model (MLM) / Principal co-ordinate analysis (PCoA)

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