Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 28, Pages E2655-E2662Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1309606110
Keywords
domestication; biotic stress; abiotic stress
Categories
Funding
- National Science Foundation Grant [IOS-0820854]
- Human Frontier Science Program Fellowship [LT000783]
- Direct For Biological Sciences [1052395] Funding Source: National Science Foundation
- Division Of Integrative Organismal Systems [1052395] Funding Source: National Science Foundation
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [0820854] Funding Source: National Science Foundation
- Grants-in-Aid for Scientific Research [24770047] Funding Source: KAKEN
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Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
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