Genome editing of polyploid crops: prospects, achievements and bottlenecks

Abstract

Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in polyploid crops, which helps e.g. for introgression breeding. However, methods such as random mutation breeding are difficult to apply in polyploid crops because there are multiple homoeologous copies (alleles) of each gene. Genome editing technology has revolutionized mutagenesis as it enables precisely selecting targets. The genome editing tool CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as all alleles and/or copies of a gene can be targeted at once. Even multiple genes, each with multiple alleles, may be targeted simultaneously. In addition to targeted mutagenesis, targeted replacement of undesirable alleles by desired ones may become a promising application of genome editing for the improvement of polyploid crops, in the near future. Several examples of the application of genome editing for targeted mutagenesis are described here for a range of polyploid crops, and achievements and bottlenecks are highlighted.

Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs

“…As mentioned, a complication is that transformation systems for tetraploid roses still have suboptimal efficiency. Genome editing may be used to modify elite rose cultivars, but also to increase the frequency of non-functional alleles in a breeding program, so that homozygosity at S gene loci may be achieved without affecting the genetic diversity of other genes (Schaart et al 2021 ).…”

Advances in Gene Editing of Haploid Tissues in Crops

“…Conventional introgression of these null mutations into the elite wheat backgrounds through MAS is a laborious and lengthy process. The rapid introduction of mutations through GE holds promise to speed up the development of hybrid wheat lines with better adaptation to the changing climate and higher yields [2].…”

“…Gene editing (GE), through the application of designed endonucleases, rapidly advances our understanding of gene function and regulatory elements involved in gene expression, as well as allows the engineering of DNA from base pair and to the chromosome level (reviewed in [1]). However, the complexity of polyploid genomes and recalcitrance of the major staple crops to transformation prevent the rapid introduction of desired traits into elite cultivars for the generation of field-ready varieties [2]. The genomic complexity can be reduced by directly editing the haploid plant tissues generated through various techniques of haploid induction (HI).…”

Grand Challenges in Microalgae Domestication

“…In the simplest example in maize, the crossing of homozygous parent lines can give rise to an heterozygous “hybrid” with superior robustness and productivity, a phenomenon called “heterosis” (Srivastava et al, 2020 ; Chen et al, 2021 ). Polyploidy can also “improve” patterns of gene expression (Schaart et al, 2021 ). On the one hand, it can be a high level of “autopolyploidy”, which can be induced by a variety of techniques (Chen et al, 2020 ).…”