Crops Hold Onto Harmful Mutations That Reduce Productivity

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Limits on improving yield and other critical traits in maize likely are due to rare harmful mutations genetically linked to a beneficial gene combination that were selected for during domestication and breeding, according to a study published today in the journal Nature.

These so-called deleterious genetic mutations result from errors in the DNA that occur randomly every generation and accumulate from ancient mutations right up through the breeding of today’s best varieties. The same problem is likely to be true not only in maize but in all crops.

“The next generation of enhanced varieties is likely to come by fixing these kinds of rare mutations, which could lead to improved crop yields, more efficient high-performing plants and being able to grow crops on less acreage,” says Karl Kremling, lead author of the paper.

Kremling is a graduate student of geneticist Edward Buckler with the Agricultural Research Service’s (ARS) Plant, Soil and Nutrition Research Laboratory in Ithaca, New York. Buckler is the paper’s senior author and an adjunct professor of plant breeding and genetics at Cornell University.

To evaluate the impact of deleterious mutations, the researchers created one of the largest public datasets of gene expression in plants. Deleterious mutations can lead to gene expression that is too high or too low, causing subpar performance. In humans, like plants, deleterious mutations, including those that dysregulate expression (suboptimal gene expression), can lead to subpar performance and diseases.

The dataset includes nearly 300 lines of maize varieties and nearly 80 million observations of gene expression. With it, breeders will be able to link a phenotype—an observable or physically expressed trait—to differences in gene expression. Even subtle correlations between a phenotype and gene expression can be teased out for many physiological, disease or nutritional trait with this database.

In this study, the data set allowed the researchers to link deleterious mutations in maize to certain abnormal phenotypes. They also showed that some of these rare mutations were made more abundant during the process of domestication and adaptation to U.S. environments.

“We were able to show that a substantial portion of the variation in productivity in maize is coming from dysregulation,” says Buckler. “The data set is a community resource that will allow maize and other crop researchers to address numerous questions.”

The study was funded by the ARS, the National Science Foundation, Cornell University’s Plant Breeding and Genetics Section, and the Taiwanese Ministry of Science and Technology.

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