Counting on Crossovers: Controlled Recombination for Plant Breeding

Abstract

Crossovers (COs), that drive genetic exchange between homologous chromosomes, are strongly biased toward subtelomeric regions in plant species. Manipulating the rate and positions of COs to increase the genetic variation accessible to breeders is a longstanding goal. Use of genome editing reagents that induce double-stranded breaks (DSBs) or modify the epigenome at desired sites of recombination, and manipulation of CO factors, are increasingly applicable approaches for achieving this goal. These strategies for 'controlled recombination' have potential to reduce the time and expense associated with traditional breeding, reveal currently inaccessible genetic diversity, and increase control over the inheritance of preferred haplotypes. Considerable challenges to address include translating knowledge from models to crop species and determining the best stages of the breeding cycle at which to control recombination.

Gene network simulations provide testable predictions for the molecular domestication syndrome

“…The limited genetic diversity available in modern cultivated species is often considered as a limitation to further response to artificial selection. Controlling recombination has been proposed as crucial for plant breeders to engineer novel allele combinations and reintroduce diversity from wild crop relatives (reviewed in Taagen et al 2020). Yet, if the domestication syndrome was also associated with changes in the pleiotropy of the genetic architecture, genetic progress might also be limited by undesirable genetic correlations among traits of interest (Yang et al 2019).…”

CRISPR targeting of MEIOTIC-TOPOISOMERASE VIB-dCas9 to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis

“…During prophase I of meiosis, homologous chromosomes undergo programmed recombination, which can result in reciprocal crossover (Mercier et al 2015; Villeneuve and Hillers 2001). Crossovers contribute to genetic variation in progeny and result in new haplotypes, which can allow combination of useful traits in crop species (Taagen et al 2020). However, recombination frequency and pattern can significantly limit breeding, as crossovers are relatively low per meiosis (typically 1-2 per chromosome) and show a highly uneven distribution (Taagen et al 2020; Mercier et al 2015).…”

“…Crossovers contribute to genetic variation in progeny and result in new haplotypes, which can allow combination of useful traits in crop species (Taagen et al 2020). However, recombination frequency and pattern can significantly limit breeding, as crossovers are relatively low per meiosis (typically 1-2 per chromosome) and show a highly uneven distribution (Taagen et al 2020; Mercier et al 2015). For example, crossovers in wheat, barley and maize occur predominantly in the sub-telomeric regions (Darrier et al 2017; Rodgers-Melnick et al 2015; Higgins et al 2012; Mascher et al 2017), which can cause linkage drag in low-recombination regions that are under selection.…”

The Role of Structural Maintenance of Chromosomes Complexes in Meiosis and Genome Maintenance: Translating Biomedical and Model Plant Research Into Crop Breeding Opportunities

“…The overall aim is to guarantee food security. Of particular interest in modern agriculture is the control of crossover (CO) formation during meiosis, because the low frequency and uneven patterning of COs has traditionally required breeders to work with large populations over many generations to produce desirable haplotypes (Taagen et al, 2020). Fortunately, genome sequencing and advanced genome editing by CRISPR-Cas9 in rice (Li et al, 2020) and maize (Zhang et al, 2020) may enable the translation of knowledge obtained in humans, yeast and Arabidopsis thaliana.…”