The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History

Area of Science:

• Evolutionary biology
• Genomics
• Plant breeding

Background:

• Domestication can impact deleterious mutations, with some studies suggesting a 'cost of domestication' via accumulated gene disruptions.
• Recent findings indicate a more nuanced view of this phenomenon across different domesticated species.
• Understanding these genetic changes is crucial for crop improvement and evolutionary insights.

Purpose of the Study:

• To investigate the evolution of deleterious mutations and genomic structural variants (SVs) during tomato domestication.
• To identify and characterize potentially harmful genetic variations in wild, semi-wild, and domesticated tomato accessions.
• To create a resource for breeders to guide experiments involving deleterious alleles.

Main Methods:

• Analysis of genomic sequences from 253 tomato accessions.
• Application of phylogeny-based methods to identify deleterious mutations.
• Comparison of genetic variant loads across wild, semi-wild, and domesticated tomato populations.

Main Results:

• A general downward trend in the number of genetic variants, including deleterious mutations and SVs, throughout tomato domestication, likely driven by demographic factors reducing genetic diversity.
• An initial increase in the proportion of nonsynonymous and deleterious alleles during early domestication in Ecuador.
• Identification of frequent deleterious alleles in genes associated with stress response, fruit development, and flavor, with a higher-than-expected frequency under neutral evolution.

Conclusions:

• Tomato domestication involved a reduction in overall genetic diversity and deleterious alleles, alongside the loss of some beneficial alleles.
• Early domestication stages presented unique patterns of deleterious allele accumulation.
• The study provides a valuable database (TomDel) of 21,162 potentially deleterious alleles for future breeding strategies.