Abstract
Improving agronomic traits is a key objective in crop improvement programmes, with many of these traits governed by complex quantitative inheritance. The identification of quantitative trait loci (QTLs), followed by their fine mapping and cloning, plays a critical role in trait mapping. Pre-next-generation sequencing (pre-NGS) methods had limited scope and precision in trait discovery. In contrast, the advent of NGS has revolutionised trait discovery, improved our understanding of complex trait genetics and facilitated the efficient use of genomic regions in molecular breeding, QTL/gene cloning, and functional validation studies. This chapter provides an overview of the transformative impact of post-NGS tools and approaches on trait mapping in crops. We explore the role of widely used NGS platforms and advanced genotyping methods in improving genetic resolution. The shift from single-reference genomes to de novo genome assemblies and pan-genomics is also explored, highlighting their role in capturing genetic diversity across species. Advancements in QTL mapping, meta-QTL analysis, association mapping, fine mapping, and cloning are highlighted, focusing on their role in understanding the genetic control of complex traits in the post-NGS era. Further, how the integration of genomics and phenomics can accelerate trait discovery is discussed. Finally, we outline future research areas, specifically the potential of emerging tools such as single-cell genomics, synthetic biology, systems biology, and AI-driven approaches, in trait mapping for crop improvement.