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\begin{document}

\title{Landscape genomics reveals genetic signals of environmental adaptation
of African wild eggplant}



\author[1]{Emmanuel Omondi}%
\author[1]{Chen-yu Lin}%
\author[1]{Shu-mei Huang}%
\author[2]{Cheng-An  Liao}%
\author[1]{Ya-ping Lin}%
\author[1]{Oliva Ricardo}%
\author[1]{Maarten van Zonneveld}%
\affil[1]{AVRDC World Vegetable Center}%
\affil[2]{National Taiwan University}%


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  \date{May 20, 2024}


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\begin{abstract}
Crop wild relatives provide a valuable resource for improving crops.
They possess desirable traits that confer resilience to various
environmental stresses. To fully utilize crop wild relatives in breeding
and conservation programs, it is important to understand the genetic
basis of their adaptation. Landscape genomics associates environments
with genomic variation and allows for examining the genetic basis of
adaptation. In this study, we applied landscape genomics to examine the
differences in allele frequency of 15,416 Single Nucleotide
Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives
from Africa, the principal hot spot of these wild relatives. Further, we
explored the correlation between these variations and the bio-climatic
and soil conditions at their collection sites. Our results showed that
the environment has a greater impact on the genetic variation in the
eggplant wild relative populations compared to the geographical
distances between collection sites while controlling for population
structure. These findings indicate the relevance of the environment in
shaping genetic variation in eggplant relatives over time. We detected
396 candidate SNPs associated with ten environmental factors by applying
four genotype-environment association methods. Some of these SNPs signal
genes involved in pathways that help with adaptation to environmental
stresses such as drought, heat, cold, salinity, pests, and diseases.
These candidate SNPs will be useful for marker-assisted improvement and
characterizing the germplasm of this crop for developing
climate-resilient eggplant varieties. The study provides a model for how
we can apply landscape genomics to the wild relatives of other crops.%
\end{abstract}%



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