Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools

• Published in: Trends in plant science Vol. 28; no. 6; pp. 685 - 697
• Main Authors: Dwivedi, Sangam L., Heslop-Harrison, Pat, Spillane, Charles, McKeown, Peter C., Edwards, David, Goldman, Irwin, Ortiz, Rodomiro
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.06.2023
• Subjects: Biological Evolution; crop improvement; deleterious variants; Gene Pool; genes; genome editing; Genome, Plant - genetics; genomic prediction; Genomics; HapMaps; heterosis; mating system; Mutation - genetics; Phenotype; Plant Breeding; propagation; selective sweeps; wild relatives; genome editing; mating system; propagation; genomic prediction; wild relatives; deleterious variants; HapMaps; selective sweeps; crop improvement
• ISSN: 1360-1385; 1878-4372; 1878-4372
• DOI: 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. 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.