Application and Prospects of Modern Genomics to Deliver Climate-Smart Pigeonpea

Pigeonpea ( Cajanus cajan (L.) Millspaugh) is a cornerstone legume for semiarid smallholder farming systems. Pigeonpea productivity is constrained by drought, heat, salinity/flooding, insects, and diseases. This chapter covers recent advances in pigeonpea genomics and focuses on routes to delivering climate-smart cultivars. We review the recent progress on reference/pan-genomes, dense single nucleotide polymorphisms (SNP)/SSR/DArT resources, and trait discovery via quantitative trait loci (QTL)/GWAS/haplotype analyses for various traits of economic significance including Fusarium wilt, sterility mosaic disease, pod borer resistance, root architecture, phenology, and seed quality. Multi-omics (e.g., transcriptomics, metabolomics) could greatly help resolve the complexity underlying stress pathways. Recent progress in marker-assisted backcrossing, genomic selection coupled with high-throughput phenotyping, speed breeding, and CMS-based hybrid development has been presented in the chapter. We highlight the significance of accelerated prebreeding involving wild Cajanus and modern gene-editing platforms for creation of novel genetic variation. Public databases, bioinformatics pipelines, and the integration of enviromics and AI/ML for environment-aware prediction are discussed. Key challenges including narrow diversity, crossability barriers, G×E×M complexity, and limited transformation are highlighted with a discussion on mitigation strategies. The chapter provides a practical roadmap to deploy haplotype-led approaches, hybrid breeding, and targeted editing to deliver resilient and high-yielding pigeonpea.