Integrative Genomics for Mango Genetics and Breeding

Mango is the second most important tropical fruit crop. Due to ever-changing environmental conditions, world mango production is facing challenges such as diseases (anthracnose and mango malformation), physiological disorders (alternate bearing), low fruit setting, poor fruit quality, short shelf life, and climate change adaptation. Breeding efforts are hindered by the long juvenile period, outdated breeding system, and high heterozygosity, resulting in a slow pace of mango improvement programs. However, over the last decade, significant advances in high-quality genome assemblies, pangenomics, genetic mapping, multi-omics data, and phenomics of large populations have accelerated crop genetics and breeding. Here, we summarize recent progress on the origin and domestication of mango, advancements in genome assemblies, development of genetic maps, functional and comparative genomics, evolutionary insights, and assessments of global phenotypic and genotypic diversity, including species at risk. We also discuss the integration of multi-omics approaches with quantitative genetics for crop improvement. Further, we highlight the key research gaps that limit breeding efficiency and propose integrative strategies combining pangenomics, multi-omics, and machine learning with improved transformation protocols and multi-environment testing to accelerate the development of climate-resilient, high-quality mango cultivars.