Jute genomics: emerging resources and tools for molecular breeding

Abstract

Perhaps no other natural fibre crop is as versatile as jute ( Corchorus capsularis L. and C. olitorius L.; Malvaceae s. l.) in the industrial and engineering uses of textiles. Yet, genomics research was rather delayed in this typical lignocellulosic bast fibre crop, which has been characterized by slow responses to classical genetic selection due to several limitations, the most important being narrow genetic base, strong sexual incompatibility and dearth of compatible genetic and/or genomic resources. Recent depreciation of the genome sizes of Corchorus spp. concomitant with a drastic fall in the cost of next-generation sequencing has now made it possible to explore and characterize jute genomes at affordable prices. This has resulted in the development and validation of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers from transcriptomic unigenes, genome-wide discovery of single nucleotide polymorphisms (SNPs) using reduced-representation restriction-site-associated DNA (RAD) sequencing de novo, construction of a dense RAD-SNP-based genetic linkage map, detection of QTL and candidate gene analysis for bast fibre yield and its components, and generation and characterization of reference bast transcriptomes using next-generation RNA-seq. A structured association mapping panel has been developed for C. olitorius , and a large number of RAD-SNP markers are being used for genome-wide association mapping of complex bast fibre quality traits. Current results have further addressed some of the basic issues of jute genome biology, ranging from chromosomal evolution to comparative genomics to cellulose and lignin biosynthesis in bast fibres. Here, we have discussed the present status of jute genomics, with a historical perspective on DNA markers development and utilization. The potentials of genomic selection to accelerate the rate of genetic gain in selection for bast fibre quality traits and mutagenesis-based reverse genetic approach for developing low-lignin jute are also discussed.