Comparison of in vitro and in silico SNP detection approach using validated SNPs from two lignin genes. (A) The SNPs detected in vitro and in silico approach in C4H (top) and CAD (bottom) gene were compared to SNPs validated using Illumina GoldenGate assay. The tick and cross indicates polymorphic and monomorphic SNP, respectively, while a dash indicates a failed assay; (B) The nucleotide and protein sequence of two SNP haplotypes found in CAD gene observed in individual AA3. The haplotypes consist of 12 SNPs within 452 bp. Six non-synonymous SNPs from haplotype 2 which caused a change in amino acid sequences are indicated in bold font. The SNP that is detected only by Bowtie/Samtools approach are circled in red.