Study of structural variants in cocoa genomes gives clues to plant diversity

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UNIVERSITY PARK, Pa .– An exhaustive and careful comparison of the genomes of several strains of cocoa by a team of researchers has provided insight into the role that genomic structural variants play in regulating gene expression and the evolution of chromosomes, giving rise to the differences within populations of the plant.

The research, which has implications for plant genetics in general, would not have been possible until powerful computers made affordable and relatively fast high-resolution genome sequencing possible, according to Mark Guiltinan, J. Franklin Styer. and professor of plant molecular biology at the College of Agricultural Sciences at Penn State.

“The genomes of different populations of cocoa trees are 99.9% identical, but it is the structural variants in that tenth of 1% of their genomes that explain the plant’s diversity in different regions and its adaptation to climate and various diseases. “, did he declare. noted. “This study establishes an association between structural variation and a plant’s ability to adapt to a local environment.”

In this study, researchers analyzed and compared chromosome-wide genomic assemblies from 31 naturally occurring populations of Theobroma cacao, the long-lived tree species that originated chocolate. This map shows their origins in the Amazon Basin in South America.

Molecular geneticists have known for about a decade that genomic structural variants can play an important role in adaptation and speciation in plants and animals, but their overall influence on the fitness of plant populations is poorly understood. This is in part because the precise population-level identification of structural variants requires the analysis of several high-quality genome assemblies, which are not widely available.

In this study, researchers investigated the fitness consequences of genomic structural variants in natural populations by analyzing and comparing genomic assemblies at the chromosome scale of 31 natural populations of Theobroma cacao, the tree species. long shelf life which is the source of chocolate. Among these 31 strains of cocoa, they found more than 160,000 structural variants.

In results published today (August 16) in the Proceedings of the National Academy of Sciences, researchers reported that most structural variants are deleterious and thus limit the adaptation of the cocoa tree. These adverse effects are likely the result of impaired gene function and an indirect result of suppressing recombination of genes over long periods of time, they noted.

However, despite the overall adverse effects, the study also identified individual structural variants carrying signatures of local adaptation, many of which are associated with genes expressed differently between populations. Genes involved in resistance to pathogens are among these candidates, highlighting the contribution of structural variants to this important local adaptation trait.

chocolate pods

Genomic structural variants are associated with genes expressed differently between populations, such as genes involved in resistance to pathogens like the one that causes black rot rot, shown here.

IMAGE: Andrew Fister / Penn State

Overall, their findings provide important information about the processes underlying the fitness effects of structural variants in natural populations, the researchers pointed out. They suggest that structural variants influence gene expression, which likely alters gene function and contributes to their detrimental effects. They also provided empirical support for a theoretical prediction that structural variants lead to the suppression of genetic recombination, making it less likely that plants can adapt to stressors.

Beyond revealing new empirical evidence for the evolutionary importance of structural variants in all plants, the documentation of genomic differences and structural variants among the 31 strains of cocoa provides a valuable resource for genetic and selection studies in course for this precious plant, Guiltinan noted.

“All the cocoa comes from the Amazon Basin – the plants were collected from the wild a long time ago by collectors and they have been cloned, so we have a permanent collection,” he said. “Their genomes have been sequenced, which is a huge amount of work and data. Thanks to this study, we know that the structural variation is important for the survival of the plant, for the evolution of the plant and especially for the adaptation of the plant to local conditions.

Claude dePamphilis, director of the Center for Parasitic and Carnivorous Plants, Dorothy Foehr Huck and J. Lloyd Huck Distinguished Chair in Plant Biology and Evolutionary Genomics, and professor of biology also participated in the research at Penn State; Eric Wafula, bioinformatics programmer, Eberly College of Science; and Paula Ralph, Senior Research Technologist, Eberly College of Science. The other members of the team were Tuomas Hamala and Peter Tiffin, Department of Plant and Microbial Biology, University of Minnesota.

The National Science Foundation and the United States Department of Agriculture’s National Institute of Food and Agriculture supported this work.

chocolate tree

Beyond revealing new empirical evidence for the evolutionary importance of structural variants in all plants, the documentation of genomic differences and structural variants among the 31 strains of cocoa provides a valuable resource for genetic and selection studies in course for this precious plant.

IMAGE: superoke GettyImages


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