Molecular Cloning, Characterization, and Expression Analysis of Lignin Genes from Sugarcane Genotypes Varying in Lignin Content Lakshmi Kasirajan 1 & Kalaivaani Aruchamy 1,2 & Prathima P. Thirugnanasambandam 1 & Selvi Athiappan 1 Received: 6 September 2016 /Accepted: 6 October 2016 / Published online: 19 October 2016 # Springer Science+Business Media New York 2016 Abstract Sugarcane (Saccharum spp.) is one of the highest biomass-producing plant and the best lignocellulosic feedstock for ethanol production. To achieve more efficient conversion of biomass to ethanol, a better understanding of the main factors affecting biomass recalcitrance is needed. Therefore, with this objective, here, we report a systematic study on lignin content, deposition, identification, and cloning of genes involved in lignin biosynthesis and their differential expression in five sugarcane clones, EC11003, EC11010, IK 76-91, IK 76-99, and Co 86032. Lignin content among the clones varied from 26.87 to 23.19 % with the highest in the clone EC11010 and the lowest in high sugar Co86032. Lignin deposition studied through phloroglucinol staining of the cell walls implied that the sclerenchyma cells of the energy canes (EC11010 and EC11003) have more lignin deposition followed by the Erianthus (IK 76-91 and IK 76-99) clones whereas Co86032 has the minimum amount of lignin deposition. We cloned partial coding regions of important genes of lignification COMT (650 bp), CCR (332 bp), and PAL (650 bp) from Erianthus, wild relative of sugarcane Appl Biochem Biotechnol (2017) 181:1270–1282 DOI 10.1007/s12010-016-2283-5 * Lakshmi Kasirajan K.Lakshmi@icar.gov.in Kalaivaani Aruchamy kalaivaani.a@gmail.com Prathima P. Thirugnanasambandam Prathima.Pt@icar.gov.in Selvi Athiappan A.Selvi@icar.gov.in 1 Genomics Laboratory, Division of Crop Improvement, Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007, India 2 SRF, Centre for Plant Molecular Biology Department, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641007, India