Next-Generation Breeding Strategies for Climate-Ready Crops

Abstract

Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.

Keywords: CRISPR/Cas; abiotic stress; climate change; crop improvement; food security; genome editing; genomics; next-generation breeding.

Figure 1

Displaying the annual prevalence of undernourishment and food insecurity percentage during 2014–2019 in (A). Source: Food and Agriculture Organization (FAO) (http://www.fao.org/faostat/en/#data/FS/visualize). Illustration of changing trends in the world's temperature annually from 2000 to 2020 in (B). Source: FAO (http://www.fao.org/home/en/). (C) depicted the total number of climatic events that occurred from 2000 to 2020 around the world. The climatic events include drought, extreme temperature, flood, storm, wildfire, and insect attack. Source: Emergency Disaster Database.

Figure 2

Graphical representation of the total production of major crops in the world (2010–2017). Source: Data retrieved from FAOSTAT.

Figure 3

Representations of the key milestones achieved by conventional and modern plant breeding.

Figure 4

The crop wild relatives (CWRs), landraces, and cultivated varieties of crops can be used to assemble the crop pan-genomes via three approaches such as de novo assembly, de Bruijn graph, and iterative assembly. The core genome includes all the genes of individuals while the dispensable or assessor genome contains all remaining genes, which are not necessary to present in all individuals. Pan-genomes can be used to identify different structural variations (SVs) in any individual and detect novel genes that are lost in cultivated varieties during the breeding process. The elucidation of desired traits/genes can be used for crop improvement by providing biotic/abiotic stress tolerance through haplotype-based breeding and de novo domestication.

Figure 5

Diagrammatic illustration of the base editing, clustered regularly interspaced short palindromic repeat/CRISPR-associated 9 (CRISPR/Cas9) and Cpf1 mechanism, and de novo domestication. (A) In the CRISPR/Cas9 mechanism, Cas9 protein is guided and activated with the help of CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA), respectively, to produce double-standard breaks (DSBs) in DNA. The single-guide RNA (sgRNA) (blue) is developed with the grouping of tracrRNA and crRNA and identifies the 20-nucleotide (orange) target sequence. This makes a complex of Cas9-sgRNA, which moves along the target site and cuts double-standard DNA 3 bases upstream of protospacer adjacent motif (PAM) through HNH and RuvC domains. The DSBs are reconstructed via nonhomologous end-joining (NHEJ) or homology-directed repair (HDR) pathway. (B) Shows the Cpf1 mechanism that recognize the 24-nucleotide target sequence (blue) of crRNA and cleaves five nucleotides opposite to T-rich (TTTN) spacer at 5′ end. (C) Representing the base editing in which dead Cas9 (dCas9) is associated with cytidine deaminase (brown). It is directed by sgRNA (blue) for base substitute at target sequence (orange) distal to PAM site at 3' end. (D) depicted the de novo domestication process in wild plant using multiplex genome editing. Multiple guide RNA (gRNA) can be used to edit more than one gene simutanelously linked to some agronomic traits.

Figure 6

Limitations of the CRISPR/Cas system and a future way forward to develop ideal editing systems.

Figure 7

Integration of next-generation breeding pipelines for crop improvement.