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

• Published in: Journal of forestry research Vol. 30; no. 6; pp. 2247 - 2258
• Main Authors: Vaishnav, Vivek, Ansari, Shamim Akhtar
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.12.2019; Springer; Springer Nature B.V; Institute of Forest Productivity,Lalgutwa,NH-23,Ranchi 835303,India
• Subjects: Analysis; Banks (Finance); Biomedical and Life Sciences; Biosynthesis; Breeding; breeding programs; clones; Coefficient of variation; Density; enzymes; Expressed sequence tags; Forestry; gene frequency; Gene mapping; Gene polymorphism; Genes; Genetic aspects; Genetic improvement; genetic polymorphism; Genetic polymorphisms; Genetic structure; genetic variation; genotype; Genotypes; Germplasm; India; Life Sciences; Lignin; Linkage disequilibrium; loci; Markers; Original Paper; phenotype; Physiological aspects; plus trees; Polymorphism; Quantitative genetics; Quantitative trait loci; Recombinase; Tectona grandis; Wood; wood density; India; Mixed linear model (MLM); Association mapping; General linear model (GLM); Lignin; Expressed sequence tags (EST); Linkage disequilibrium (LD); Principal co-ordinate analysis (PCoA)
• ISSN: 1007-662X; 1993-0607
• DOI: 10.1007/s11676-018-0751-1

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.