Using landscape genomics to help create climate-resilient eggplant varieties – results of new research

Eggplants are important vegetables, including the common global ‘brinjal’ (Solanum melongena) and African eggplants (S. aethiopicum, S. anguivi and S. macrocarpon). But despite their significance, eggplant has trailed in the use of genomic tools compared to other solanaceae crops such as potato and tomato. Crop wild relatives possess traits of interest for breeding climate resilient varieties of any crop, because many are adapted to marginal environments. However, it is not often clear what specific adaptive traits they possess and to what stresses they are adapted to.

Landscape genomics of eggplant wild relatives offers a much larger basket of options for plant breeders to use

African eggplant is a very popular and important crop on the continent, as here in Eswatini and Tanzania

Now we have ‘landscape genomics’, an emerging tool that can support breeding programs by speeding up the detection of valuable traits. It does this by integrating spatial statistics, population genomics, and landscape ecology to rapidly identify markers associated with specific environmental factors. Crop wild relatives are especially interesting to screen because they possess large untapped genetic diversity and traits of environmental adaptation that disappeared from eggplant varieties during domestication and breeding. And sub-Saharan Africa is a hotspot for wild relatives of all domesticated eggplants including both the global brinjal and African eggplant.

Findings from this research indicated that environmental factors shape genomic variation over time, but are not the main driver of selection in eggplant wild relatives. Groups patterns were revealed, associating certain genes with environmental variables. Four genotype–environment association methods then detected 396 candidate genes (2.5% of the initial sample) associated with eight factors that would help to adapt to environmental stresses such as drought, heat, cold, salinity, pests and diseases. These candidate genes – or to give them their proper scientific description – ‘single nucleotide polymorphisms’ (or SNPs), can now be used in marker-assisted selection and developing new climate-resilient eggplant varieties. This study also provides a model for applying landscape genomics to the screening of crop wild relatives in any other plant.

See: Omondi EO, Lin C-Y, Huang S-M, Liao C-A, Lin Y-P, Oliva R, van Zonneveld M. 2024. Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplants. Ecology and Evolution. 2024;14:e11662. doi:10.1002/ece3.11662

Funding for WorldVeg’s general research activities is provided by core donors: Taiwan, UK aid from the UK government, the United States Agency for International Development (USAID), the Australian Centre for International Agricultural Research (ACIAR), the Federal Ministry for Economic Cooperation and Development of Germany, Thailand, Philippines, Korea, and Japan. Additional financial support was also received from the Taiwan Africa Vegetable Initiative supported by the Taiwan Ministry of Foreign Affairs and Ministry of Agriculture, and from BMZ and Deutsche Gesellschaft für Internationale Zusamme through the Fund International Agricultural Research.