Exploring impact of recombination landscapes on breeding outcomes

Abstract

Plant breeding relies on crossing-over to create novel combinations of alleles needed to confer increased productivity and other desired traits in new varieties. However, crossover (CO) events are rare, as usually only one or two of them occur per chromosome in each generation. In addition, COs are not distributed evenly along chromosomes. In plants with large genomes, which includes most crops, COs are predominantly formed close to chromosome ends, and there are few COs in the large chromosome swaths around centromeres. This situation has created interest in engineering CO landscape to improve breeding efficiency. Methods have been developed to boost COs globally by altering expression of anti-recombination genes and increase CO rates in certain chromosome parts by changing DNA methylation patterns. In addition, progress is being made to devise methods to target COs to specific chromosome sites. We review these approaches and examine using simulations whether they indeed have the capacity to improve efficiency of breeding programs. We found that the current methods to alter CO landscape can produce enough benefits for breeding programs to be attractive. They can increase genetic gain in recurrent selection and significantly decrease linkage drag around donor loci in schemes to introgress a trait from unimproved germplasm to an elite line. Methods to target COs to specific genome sites were also found to provide advantage when introgressing a chromosome segment harboring a desirable quantitative trait loci. We recommend avenues for future research to facilitate implementation of these methods in breeding programs.

Plant reproduction research in Latin America: Toward sustainable agriculture in a changing environment

“…In these countries, past production gains were a result of an increase in area, not yield (Prasanna et al., 2022). Thus, novel breeding techniques based on manipulation of recombination in crops are top priority to boost yield (Epstein et al., 2023; Prasanna et al., 2022).…”

Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future

“…These advances have provided a much-needed foundation to understand the individual, environmental, and genomic factors associated with variation in recombination rates and distribution, often through a combination of multiple approaches. Furthermore, the ability to quantify recombination has also been crucial for advancing many evolutionary analyses, such as identifying and interpreting selective sweeps ( Josephs and Wright 2016 ), inferring phylogenies and demographic histories ( Li et al 2019 ; Feng et al 2023 ; Soni et al 2024 ), and predicting population responses to selection ( Battagin et al 2016 ; Epstein et al 2023 ).…”

“…In contrast, some plant species have shown evidence of evolution on recombination under domestication, including rye, tomato and barley as described above ( Dreissig et al 2019 ; Fuentes et al 2022 ; Schreiber et al 2022 ). This may be a consequence of crop plants having large nonrecombining regions, meaning that modifying the distribution of recombination will be particularly beneficial for generating novel linked genetic variation ( Epstein et al 2023 ).…”

Genome of Raphanus sativus L. Bakdal, an elite line of large cultivated Korean radish

“…There are numerous varieties and traits of R. sativus and various breeding schemes worldwide aim to develop new traits for this species. The major obstacle in breeding schemes is retaining the crossbreed for multiple generations (i.e., the elite line for each trait/variety) (Kang et al, 2016;Epstein et al, 2023). There are hundreds of economic elite lines available globally; in South Korea, the term "Korean food" specifies that all raw materials used to prepare the food item originate in South Korea (Song et al, 2021).…”