A review and viewpoint research paper by Sangam L. Dwivedi, Pat Heslop-Harrison, Charles Spillane, Peter C. McKeown, David Edwards, Irwin Goldman and Rodomiro Ortiz
Trends in Plant Science, on-line first https://doi.org/10.1016/j.tplants.2023.01.006 and 2023

Deleterious mutations are genetic changes that negatively impact the function and fitness of an organism. Our new review paper highlights how some deleterious mutations in crop gene pools can actually be beneficial for domesticated crops. The paper, titled “Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools,” by Sangam L. Dwivedi, Rodomiro Ortiz and others, explores the complex role of deleterious mutations in crop breeding and how emerging genomic tools can aid in their identification, removal, or exploitation.

We begin by explaining how deleterious mutations can be conditionally deleterious in crop plants. While these mutations may reduce fitness under natural conditions and be subject to purifying selection, they can be under positive selection in domesticates. In other words, some deleterious alleles may actually be adaptive in an agricultural context. We highlight how breeding may hasten the accumulation of deleterious variants in crop gene pools, and how current efforts focus on predicting the functional consequences of these mutations on a genome-wide scale and comparing the effects across species. It is notable that crop species vary in their pattern and distribution of deleterious mutations, and there are differences between mating systems, ploidy levels, and propagation systems.

Our thoughts, building on our review of published work, include how some deleterious mutations are associated with breeding-relevant phenomena, such as heterosis, genetic variation, and key loss-of-function domestication traits that underpin crop production. We explain that the difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles.

Finally, we think forward and explore the potential of emerging genomic tools, including HapMaps and pangenome analysis, to aid in the identification, removal, or exploitation of deleterious mutations. Strategies for removal of deleterious variants with techniques such as gene editing may facilitate breeding and accelerate the redomestication of crops from wild species.

Overall, I hope we provide a comprehensive overview of the complex role of deleterious mutations in crop breeding and production. While some deleterious mutations may negatively impact crop performance, others may be associated with important breeding-relevant phenomena. We highlight the potential of emerging genomic tools to aid in the identification and exploitation of these mutations, ultimately leading to improved crop production and food security.

https://doi.org/10.1016/j.tplants.2023.01.006

Deleterious mutations are common in plant genomes and present both challenges and opportunities for domesticated crops.
While many deleterious mutations can negatively impact crop performance, some deleterious mutations are associated with breeding-relevant phenomena, such as heterosis, genetic variation, and key loss-of-function domestication traits that underpin crop production. Breeding may hasten the accumulation of deleterious variants.
Crop species vary in their pattern and distribution of deleterious mutations, and differences are noted among mating systems, ploidy levels, and propagation systems. Current efforts focus on predicting functional consequences of deleterious mutations on a genome-wide scale and comparing the effects across species.
Strategies for removal of deleterious variants with techniques such as gene editing may facilitate breeding and accelerate the redomestication of crops from wild species.
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.

• crop improvement
• mutations
• genes
• genetics
• genomics
• review
• viewpoint
• deleterious variants
• genome editing
• genomic prediction
• HapMaps
• mating system
• propagation
• selective sweeps
• wild relatives