Genomic diversity, population structure, and genome-wide association reveal genetic differentiation and trait improvements in mango

Abstract

Mango ( Mangifera indica L.) has been widely cultivated as a culturally and economically significant fruit tree for roughly 4000 years. Despite its rich history, little is known about the crop’s domestication, genomic variation, and the genetic loci underlying agronomic traits. This study employs the whole-genome re-sequencing of 224 mango accessions sourced from 22 countries, with an average sequencing depth of 16.37 ×, to explore their genomic variation and diversity. Through phylogenomic analysis, M. himalis J.Y. Liang, a species grown in China, was reclassified into the cultivated mango group known as M. indica. Moreover, our investigation of mango population structure and differentiation revealed that Chinese accessions could be divided into two distinct gene pools, indicating the presence of independent genetic diversity ecotypes. By coupling genome-wide association studies with analyses of genotype variation patterns and expression patterns, we identified several candidate loci and dominant genotypes associated with mango flowering capability, fruit weight, and volatile compound production. In conclusion, our study offers valuable insights into the genetic differentiation of mango populations, paving the way for future agronomic improvements through genomic-assisted breeding.

Acknowledgements

This work was financially supported by the Natural Science Foundation of Guangdong Province (2021A1515010966), Hainan Provincial Natural Science Foundation of China (322CXTD524), Hainan Province Key Research and Development Plan (ZDYF2022XDNY255), National Natural Science Foundation of China (32360727), Guangdong Province Seed Industry Revitalization Project (2022-NPY-00-030), and China Agriculture Research System of MOF and MARA (CARS-31).

Author contributions

X.M. and X.L. performed the data analysis, prepared the figures, and drafted the manuscript. H.W., W. X., and S. W. provided support for data analysis. H.A, B.L., Y. Z., and B.Z. provide help for verification of the manuscript. M. S., P.H., and J.W. were in charge of field management and collected the samples. B.D., H. P., and Q. C. collected the phenotype data.

Data availability

The re-sequencing data of 224 accessions have been uploaded to the National Genomics Data Center (NGDC) with the BioProject accession PRJCA025449.

Conflict of interest statement:

The authors declare no conflict of interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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