Genotyping by RAD-seq in jute for linkage map construction, comparative genomics and QTL analyses

Restriction-site-associated DNA sequencing (RAD-seq) has become an attractive approach for relatively economical screening of a large number of genetic markers and individuals with very high coverage. For non-model organisms without reference genome sequences, RAD-seq allows genome-wide detection of SNPs and construction of dense linkage maps that can be used for comparative genomics and detection of QTL for economically important traits. Jute (Corchorus olitorius L.) is an important bast fibre crop belonging to the family Malvaceae, with least genomic information and resources. It has a narrow genetic base and is characterized by low polymorphism information content of anonymous DNA markers like AFLP, SSR, etc. The lack of an abundance of informative molecular markers has impeded the construction of a dense linkage map of jute. In this project, we employed RAD-seq to detect genome-wide SNPs and construct a RAD-based linkage map for comparative genomics and QTL analyses of bast fibre yield and yield-related traits.