Enhancing Pathogen Tolerance

Problem

How can we ensure the adaptability of plant populations facing increasing disease pressures?

• Molecular geneticists have known for about a decade that genomic structural variants, involving large deletions or translocations in chromosomes, can play important roles in the adaptation and speciation of both plants and animals, but their overall influence on the fitness, or ability of plant populations to survive, is poorly understood.

Findings

Researchers analyzed and compared chromosome-scale genome assemblies of 31 naturally occurring individuals from four divergent populations of Theobroma cacao, the long-lived tree species that is the source of chocolate.

• They observed more than 160,000 structural variants, most of which were detrimental to the fitness of the plant and therefore constrained adaptation. They also detected several variations in the genomes that may contribute to local adaptation mainly through traits involved in pathogen resistance.

Impact

This study provided critical data and analyses needed to understand the evolutionary significance of structural variation in all plants.

• The findings from this research will be a valuable resource for molecular geneticists and plant breeders in developing varieties that are resistant to emerging and persistent diseases that threaten valuable crops like cacao.

Research Credit

Team

• Tuomas Hämälä, Eric Wafula, Mark Guiltinan, Paula Ralph, Claude dePamphilis, Peter Tiffin

Participating Department

• Plant Science

Partners

• Centro Agronómico Tropical de Investigación y Enseñanza (CATIE)
• Penn State Institute for Computational and Data Sciences
• Minnesota Supercomputing Institute, University of Minnesota

Competitive Funding

• NSF (Plant Genome Research Project)

Federal and State Appropriations

• USDA NIFA Hatch project PEN04569, Accession #1003147.

Emerging Discoveries

Study of structural variants in cacao genomes yields clues about plant diversity

August 16, 2021

An exhaustive and painstaking comparison of the genomes of multiple strains of the cacao tree by a team of researchers has provided insights into the role genomic structural variants play in the regulation of gene expression and chromosome evolution, giving rise to the differences within populations of the plant.

Published Research

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

• Hämälä, T., Wafula, E. K., Guiltinan, M. J., Ralph, P. E., dePamphilis, C. W., & Tiffin, P. (2021). Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. Proceedings of the National Academy of Sciences of the United States of America, 118(35), [e2102914118]. https://doi.org/10.1073/pnas.2102914118