Copy number variation and disease resistance in plants

Abstract

Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.

Extreme copy number variation at a tRNA ligase affecting phenology and fitness in yellow monkeyflowers

“…Along with the increasing evidence that CNV contributes to fitness-relevant variation in crops and humans (Girirajan et al 2011; Maron et al 2013; Mickelbart et al 2015; Dolatabadian et al 2017), our results suggest that explicit CNV surveys should be routine part of genome-wide scans for adaptive loci. A number of new pipelines combine coverage, read-pair information, and other data to infer structural variants from short-read data (Layer et al 2014; Mohiyuddin et al 2015), and could fruitfully be used to catalog CNV in (for example) the Iron Mountain inbred line set.…”

Surviving in a Hostile World: Plant Strategies to Resist Pests and Diseases

“…R genes are often assembled in gene clusters (158), and some R genes, like Rp1 genes in grasses, show unusually high variation in copy numbers within the same species (42,125). This enhanced duplication rate can in part be attributed to the high incidence of retrotransposons within R-gene clusters (65,122), as retrotransposons can increase gene duplication through nonallelic homologous recombination (116).…”

Re-registration Challenges of Glyphosate in the European Union

“…As for emerging plant resistance against glyphosate, glyphosate itself and glyphosate-based herbicides have been shown to affect the disease resistance and health of plants by undermining their innate physiological defenses in mechanisms related to the mode of action of glyphosate, even in crops engineered for glyphosate-tolerance, and by interferences with the local microbial ecology in the rhizosphere (Martinez et al, 2018). The evolution of resistance was shown to occur due to gene amplification (Chen et al, 2017;Dolatabadian et al, 2017;Fernandez-Escalada et al, 2017;Han et al, 2017;Jugulam and Gill, 2018). Epigenetic alterations through increased levels of DNA and histone methylation were identified in response to exposure to glyphosate (Nardemir et al, 2015;Kim et al, 2017;Margaritopoulou et al, 2018;Markus et al, 2018).…”