Genome-wide identification and expression profile analysis of the

Abstract

Context Soybean cyst nematode is the most important pest of soybean (Glycine max (L.) Merr.) worldwide, causing serious yield losses. Lignin is a vital component of the cell wall that can provide resistance to cyst nematode. O-Methyltransferase (OMT) is a key enzyme involved in lignin metabolism in the phenylalanine pathway. Aims In this study, the soybean OMT gene family was systematically identified, and the expression response of GmOMT to abiotic and cyst nematode stresses was investigated. Methods In total, 67 OMT genes were obtained from the soybean genome through conserved structural domain alignment. GmOMT expression under abiotic stress of soybean was examined based on next-generation RNA sequencing (RNA-Seq). Comprehensive analysis of the genes was conducted, including gene structure, conserved structure, affinity, chromosomal localisation, functional prediction, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, promoter analysis, and expression pattern analysis. Key results The 67 GmOMT genes were identified and distributed among the 19 chromosomes. The GmOMT genes were classified into two categories: CCOMT subfamily and COMT subfamily. GmOMT genes from the same family shared similar gene structures and conserved structural domains, which have undergone strong purifying selection during evolution. The presence of multiple cis-responsive elements in the promoters of GmOMT genes suggested that members of the soybean OMT family may be involved in growth and developmental activities and resistance to stress in soybean. Conclusions GmOMT expression under abiotic stress showed that some of the genes may play a role in abiotic stress. Of them, GmCCOMT3 and GmCCOMT7 were closely associated with lignin synthesis based on both RNA-Seq and quantitative real-time PCR analysis. Implications These findings are valuable for elucidating the function of GmOMT in lignin metabolism and the relationship with SCN resistance.