Discovery of SNPs in lignin biosynthesis genes (CAD1, MYB1 and MYB2) and their association with wood density in teak

Abstract

Abstract Forest trees like teak (Tectona grandis L.f.) with their prolonged growth period are well suited for association mapping (AM) or linkage disequilibrium (LD) mapping. The specifically designed primers successfully amplified the targeted lignin biosynthesis genes (CAD1, MYB1 and MYB2) in 150 unrelated genotypes assembled at National Teak Germplasm Bank, Chandrapur, Maharashtra, India. SNPs in the targeted amplified gene sequences were discovered and their associations with the wood density trait performed, following GLM and MLM statistical models and Bonferroni correction. CAD1 gene and MYB1 and MYB2 transcription factors brought out 112 SNPs/11 indels that were employed for association with the wood density trait with a mean value of 416.69kg/m3 (CV 4.97%). The teak genotypes comprised three admixed cryptic (K = 3) loosely structured sub-populations, harbouring 91.06% genetic variation within sub-populations and low sub-population differentiation (Fst = 0.03) with low intragenic LD (0–21% SNP pairs) at P < 0.05 and high LD decay (33bp-934bp) at R2 = 0.1 GLM and MLM models discounting systematic biases Q and K matrices to avoid false discovery revealed 5–7 loci at MAF < 0.003 and 3 loci at MAF > 0.05 to be significantly (P < 0.05) associated with wood density trait. However, Bonferonni correction (4.06–7.04×10− 4) yielded a single associated locus (B1485C/A) from exon of MYB1 transcription factor, contributing to about 12% phenotypic variation in wood density. The meticulously scored locus (B1485C/A) can be developed as a molecular probe for selection of improved planting stock with proven wood density trait for teak plantation.