ABSTRACT
The classical approach for molecular breeding is heavily dependent on marker-assisted selection (MAS) and the trait linked DNA markers as an alternative to support phenotypic screening. Literature has demonstrated its ability as powerful genomic tools to enhance the effectiveness and accuracy of breeding practices for crop improvement. The major worries, however, are the specificity, cost, and the sequence knowledge requirement for each species in their development. Recent technological advancement has shown that the next-generation sequencing (NGS) can decode a whole genome or transcriptome in a very short time and is the most powerful tool to identify and develop DNA/RNA molecular markers for MAS. The amalgamation of NGS technique with molecular breeding for crop improvement has been successfully exploited in many crops including Setaria italica Beauv, Lupinus angustifolius L., Mimulus, Cajanus cajan L., and Linum usitatissimum L., to name few, but many more are being experimented. Still more studies are required to make it routine. This chapter showcases some of the advanced NGS techniques and their utility in the large-scale development of molecular markers which is expected to enhance our understanding toward population genomics, mapping studies in crop improvement, and reference genome sequence assembly for non-model plant, specially.
