Integrative genomics for mango genetics and breeding

Abstract

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 Breeding efforts are hindered by the long juvenile period, outdated breeding system, and high heterozygosity, resulting in a slow pace of mango improvement programs.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, multiomics 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 multiomics approaches with quantitative genetics for crop improvement. Furthermore, we highlight the key research gaps that limit breeding efficiency and propose integrative strategies combining pangenomics, multiomics, and machine learning with improved transformation protocols and multienvironment testing to accelerate the development of climate-resilient, high-quality mango cultivars.

Acknowledgments

This work was supported by the National Key Research and Development Program of China (no. 2024YFE0214700), the Central Government Guides Local Science and Technology Development Projects of China (no. 2023ZYZX1224), the National Natural Science Foundation of China (no. 32372662), and the Hainan Mango Agriculture Research System (grant no. HNARS-07). Additional support was provided by the Project of National Key Laboratory for Tropical Crop Breeding (no. NKLTCB-RC202501) and the State Key Laboratory of Tropical Crop Breeding (no. SKLTCBYWF202507; no. NKLTCBCXTD40 ).

Author contributions

Y.Z. and X.T. conceived the project. B.A. wrote the initial draft of the manuscript, and B.A., Y.S., R.A., C.C., P. W., M.J.W., Y.C., Y.B., Z.D., J.H., X.T., and Y.Z. thoroughly edited the paper. B.A., T.R., Y.Z., T.H., Y.Z., C.L., and Z.J. performed the figure and table drawings. All authors contributed to the proofreading of the manuscript.

Conflicts of interest statement

The authors declare that they have no conflicts of interest.

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