loading page

The evolutionary dynamics of genetic mutational load throughout tomato domestication history
  • +4
  • Hamid Razifard,
  • Sofia Visa,
  • Naama Menda,
  • Lukas Mueller,
  • Denise Tieman,
  • Esther van der Knaap,
  • Ana Caicedo
Hamid Razifard
Cornell University

Corresponding Author:[email protected]

Author Profile
Sofia Visa
Author Profile
Naama Menda
Author Profile
Lukas Mueller
Author Profile
Denise Tieman
Author Profile
Esther van der Knaap
University of Georgia
Author Profile
Ana Caicedo
University of Massachusetts
Author Profile

Abstract

Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A “cost of domestication” has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the cultivated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in fully cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavor regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).
01 May 2024Submitted to Molecular Ecology
22 Jul 2024Review(s) Completed, Editorial Evaluation Pending
05 Aug 2024Editorial Decision: Revise Minor
04 Oct 20241st Revision Received
10 Oct 2024Submission Checks Completed
10 Oct 2024Assigned to Editor
10 Oct 2024Review(s) Completed, Editorial Evaluation Pending
11 Oct 2024Reviewer(s) Assigned